Mon Dec 16 04:55:29 UTC 2024 I: starting to build vg/unstable/arm64 on jenkins on '2024-12-16 04:55' Mon Dec 16 04:55:29 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_15/75276/console.log Mon Dec 16 04:55:29 UTC 2024 I: Downloading source for unstable/vg=1.59.0+ds-0.1 --2024-12-16 04:55:30-- http://deb.debian.org/debian/pool/main/v/vg/vg_1.59.0%2bds-0.1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2839 (2.8K) [text/prs.lines.tag] Saving to: ‘vg_1.59.0+ds-0.1.dsc’ 0K .. 100% 396M=0s 2024-12-16 04:55:30 (396 MB/s) - ‘vg_1.59.0+ds-0.1.dsc’ saved [2839/2839] Mon Dec 16 04:55:30 UTC 2024 I: vg_1.59.0+ds-0.1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: vg Binary: vg, vg-docs Architecture: amd64 arm64 ppc64el mips64el s390x riscv64 x32 all Version: 1.59.0+ds-0.1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://github.com/vgteam/vg#vg Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/vg Vcs-Git: https://salsa.debian.org/med-team/vg.git Testsuite: autopkgtest Testsuite-Triggers: libvcflib-tools Build-Depends: debhelper-compat (= 13), pv , bsdextrautils | bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa , protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libtinfo6, libncurses-dev, automake, libtool, jq, samtools , unzip, librdf0-dev, cmake, pkgconf, bc, gtk-doc-tools, raptor2-utils , rasqal-utils , bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-dev, libdeflate-dev, libboost-program-options-dev, libjemalloc-dev, libbackward-cpp-dev, elfutils, libdw-dev, libelf-dev, libraptor2-dev, libsparsehash-dev, rapidjson-dev, libfml-dev, libfastahack-dev, fastahack , tabix , xxd , libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools , libhts-dev, help2man , python3:any, libsimde-dev, libzstd-dev Build-Depends-Indep: doxygen , graphviz Package-List: vg deb science optional arch=amd64,arm64,ppc64el,mips64el,s390x,riscv64,x32 vg-docs deb doc optional arch=all Checksums-Sha1: 9cceebb48fb18c8618654723085c6aaa4321f386 69705744 vg_1.59.0+ds.orig.tar.xz ddd7d9f6b17fee1f35ac6d3a00de3d7b2e6e491c 117112 vg_1.59.0+ds-0.1.debian.tar.xz Checksums-Sha256: 17e43b91bce35905caf9af98e3b839eeff296af7105c1df818eb81004e6ab144 69705744 vg_1.59.0+ds.orig.tar.xz dfd2b9a5f833d45b9b5632b651de59668380352bc87fa2654b2c2c7acf6c423b 117112 vg_1.59.0+ds-0.1.debian.tar.xz Files: e8aff1b3feff38a4085bf4fbee107ac9 69705744 vg_1.59.0+ds.orig.tar.xz 66279467d1d25d09cdba16f34999a366 117112 vg_1.59.0+ds-0.1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQHEBAEBCgAuFiEEQGIgyLhVKAI3jM5BH1x6i0VWQxQFAmc/WKIQHGJhZ2VAZGVi aWFuLm9yZwAKCRAfXHqLRVZDFHNzDAChrlW8GHppGU1D++m3+LBMHm1tEC4x4pa4 85La0aNeKtBpMqH6R7GpLZJ2HkdjXCqWdKXv60UYX7ughXFl30EQoAT8OM6+gN1w XUfB4XXa/OAvF0grSmIE08PL4nnvGcJlnXd5vW+DF/R8Ll7bIJLtWIn2kHV28uTk 9Faz9DRF4xEtNkVhHBcmlwxott+Zhf2Prt6XyjhUHegCRAd3aAcVrZQl87cR+gIj JpVjf1H9jBG4HhgZ7yxjDQmaosSgAuKf41GAyAl8YbxeLTcIfg3KYQ+LOWMDiRWv bucCUzqPlanDR5OtNk1+ORER59FE83oXSq1tLUMAeP53sE9jhVLFafwjWc5YqsRz XHkA0FGcYdlbcYUkRaXBKPHyvcBXrE81cA4CO9Afa8C3kgDwArYfq5OY08CE++/u 3t9vc+kT+wE9w3x6W81ywxyPchFlTEhjnoAZJ2kUhlVgsGNTT+9wi5Cbq9HFW6Lt 17nlcUFy3vPmaFg8qzO9Kte7eCqp1Q0= =YEjD -----END PGP SIGNATURE----- Mon Dec 16 04:55:30 UTC 2024 I: Checking whether the package is not for us Mon Dec 16 04:55:30 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Mon Dec 16 04:55:30 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Mon Dec 16 05:14:35 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Jan 17 23:18:32 -12 2026 I: pbuilder-time-stamp: 1768735112 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 [vg_1.59.0+ds-0.1.dsc] I: copying [./vg_1.59.0+ds.orig.tar.xz] I: copying [./vg_1.59.0+ds-0.1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Nov 21 15:58:26 2024 gpgv: using RSA key 406220C8B8552802378CCE411F5C7A8B45564314 gpgv: issuer "bage@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./vg_1.59.0+ds-0.1.dsc: no acceptable signature found dpkg-source: info: extracting vg in vg-1.59.0+ds dpkg-source: info: unpacking vg_1.59.0+ds.orig.tar.xz dpkg-source: info: unpacking vg_1.59.0+ds-0.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying avoid_abs_confusion dpkg-source: info: applying gcc-12 dpkg-source: info: applying use_packaged_libdeflate dpkg-source: info: applying use_packaged_jemalloc dpkg-source: info: applying use_packaged_libbackward-cpp dpkg-source: info: applying use_packaged_elfutils dpkg-source: info: applying use_packaged_raptor2 dpkg-source: info: applying no_need_for_snappy dpkg-source: info: applying use_packaged_sparsehash dpkg-source: info: applying use_packaged_fermi-lite dpkg-source: info: applying no_rpath dpkg-source: info: applying no_pg dpkg-source: info: applying use_packaged_fastahack dpkg-source: info: applying hardening_flags dpkg-source: info: applying static dpkg-source: info: applying use_packaged_lz4 dpkg-source: info: applying parallize_better dpkg-source: info: applying use_packaged_libtsl-hopscotch-map-dev dpkg-source: info: applying libVCFH_unneeded dpkg-source: info: applying better_clean dpkg-source: info: applying use_packaged_vcflib dpkg-source: info: applying use_packaged_htslib dpkg-source: info: applying simde dpkg-source: info: applying crossbuild dpkg-source: info: applying python3 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2636781/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='51c40109a29749578de3aee026955615' 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='2636781' 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.13mrvSh8/pbuilderrc_R7h5 --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.13mrvSh8/b1 --logfile b1/build.log vg_1.59.0+ds-0.1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2636781/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: arm64 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), pv, bsdextrautils | bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa, protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libtinfo6, libncurses-dev, automake, libtool, jq, samtools, unzip, librdf0-dev, cmake, pkgconf, bc, gtk-doc-tools, raptor2-utils, rasqal-utils, bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-dev, libdeflate-dev, libboost-program-options-dev, libjemalloc-dev, libbackward-cpp-dev, elfutils, libdw-dev, libelf-dev, libraptor2-dev, libsparsehash-dev, rapidjson-dev, libfml-dev, libfastahack-dev, fastahack, tabix, xxd, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools, libhts-dev, help2man, python3:any, libsimde-dev, libzstd-dev, doxygen, graphviz dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20082 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 pv; however: Package pv is not installed. pbuilder-satisfydepends-dummy depends on bsdextrautils | bsdmainutils; however: Package bsdextrautils is not installed. Package bsdmainutils is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on rs; however: Package rs is not installed. pbuilder-satisfydepends-dummy depends on libffi-dev; however: Package libffi-dev is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa is not installed. pbuilder-satisfydepends-dummy depends on protobuf-compiler; however: Package protobuf-compiler is not installed. pbuilder-satisfydepends-dummy depends on libprotoc-dev; however: Package libprotoc-dev is not installed. pbuilder-satisfydepends-dummy depends on libprotobuf-dev; however: Package libprotobuf-dev is not installed. pbuilder-satisfydepends-dummy depends on libjansson-dev; however: Package libjansson-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses-dev; however: Package libncurses-dev is not installed. pbuilder-satisfydepends-dummy depends on automake; however: Package automake is not installed. pbuilder-satisfydepends-dummy depends on libtool; however: Package libtool is not installed. pbuilder-satisfydepends-dummy depends on jq; however: Package jq is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on unzip; however: Package unzip is not installed. pbuilder-satisfydepends-dummy depends on librdf0-dev; however: Package librdf0-dev is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on bc; however: Package bc is not installed. pbuilder-satisfydepends-dummy depends on gtk-doc-tools; however: Package gtk-doc-tools is not installed. pbuilder-satisfydepends-dummy depends on raptor2-utils; however: Package raptor2-utils is not installed. pbuilder-satisfydepends-dummy depends on rasqal-utils; however: Package rasqal-utils is not installed. pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on gawk; however: Package gawk is not installed. pbuilder-satisfydepends-dummy depends on liblz4-dev; however: Package liblz4-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libcairo2-dev; however: Package libcairo2-dev is not installed. pbuilder-satisfydepends-dummy depends on libpixman-1-dev; however: Package libpixman-1-dev is not installed. pbuilder-satisfydepends-dummy depends on libdeflate-dev; however: Package libdeflate-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libjemalloc-dev; however: Package libjemalloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libbackward-cpp-dev; however: Package libbackward-cpp-dev is not installed. pbuilder-satisfydepends-dummy depends on elfutils; however: Package elfutils is not installed. pbuilder-satisfydepends-dummy depends on libdw-dev; however: Package libdw-dev is not installed. pbuilder-satisfydepends-dummy depends on libelf-dev; however: Package libelf-dev is not installed. pbuilder-satisfydepends-dummy depends on libraptor2-dev; however: Package libraptor2-dev is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on rapidjson-dev; however: Package rapidjson-dev is not installed. pbuilder-satisfydepends-dummy depends on libfml-dev; however: Package libfml-dev is not installed. pbuilder-satisfydepends-dummy depends on libfastahack-dev; however: Package libfastahack-dev is not installed. pbuilder-satisfydepends-dummy depends on fastahack; however: Package fastahack is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on xxd; however: Package xxd is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libtsl-hopscotch-map-dev; however: Package libtsl-hopscotch-map-dev is not installed. pbuilder-satisfydepends-dummy depends on libvcflib-dev (>= 1.0.1); however: Package libvcflib-dev is not installed. pbuilder-satisfydepends-dummy depends on libvcflib-tools; however: Package libvcflib-tools is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3:any. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz 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} bc{a} bison{a} bsdextrautils{a} bwa{a} ca-certificates{a} cmake{a} cmake-data{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docbook{a} docbook-to-man{a} docbook-xml{a} docbook-xsl{a} doxygen{a} dwz{a} elfutils{a} fastahack{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gawk{a} gettext{a} gettext-base{a} girepository-tools{a} graphviz{a} groff-base{a} gtk-doc-tools{a} help2man{a} icu-devtools{a} intltool-debian{a} jq{a} krb5-multidev{a} libabsl20230802{a} libann0{a} libaom3{a} libarchive-zip-perl{a} libarchive13t64{a} libasm1t64{a} libavif16{a} libbackward-cpp-dev{a} libblas3{a} libblkid-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libcdt5{a} libcgraph6{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdebuginfod-common{a} libdebuginfod1t64{a} libdeflate-dev{a} libdeflate0{a} libdisorder-dev{a} libdisorder0{a} libdivsufsort-dev{a} libdivsufsort3{a} libdw-dev{a} libdw1t64{a} libedit2{a} libelf-dev{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfastahack-dev{a} libfastahack0{a} libffi-dev{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfmt10{a} libfontconfig-dev{a} libfontconfig1{a} libfreetype-dev{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libgfortran5{a} libgio-2.0-dev{a} libgio-2.0-dev-bin{a} libgirepository-2.0-0{a} libglib2.0-0t64{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libice-dev{a} libice6{a} libicu-dev{a} libicu72{a} libidn2-dev{a} libimagequant0{a} libjansson-dev{a} libjbig0{a} libjemalloc-dev{a} libjemalloc2{a} libjpeg62-turbo{a} libjq1{a} libjson-c5{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblab-gamut1{a} liblapack3{a} libldap-2.5-0{a} libldap-dev{a} liblerc4{a} libllvm19{a} liblocale-gettext-perl{a} libltdl7{a} liblz4-dev{a} liblzma-dev{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libmhash2{a} libmount-dev{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libnsl2{a} libonig5{a} libosp5{a} libp11-kit-dev{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpixman-1-dev{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-lite32t64{a} libprotobuf32t64{a} libprotoc-dev{a} libprotoc32t64{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraptor2-0{a} libraptor2-dev{a} libraqm0{a} librasqal3-dev{a} librasqal3t64{a} librav1e0.7{a} librdf0-dev{a} librdf0t64{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsepol-dev{a} libsharpyuv0{a} libsigsegv2{a} libsimde-dev{a} libsm-dev{a} libsm6{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libsparsehash-dev{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libssw-dev{a} libssw0{a} libsvtav1enc2{a} libsysprof-capture-4-dev{a} libtabixpp-dev{a} libtabixpp0t64{a} libtasn1-6-dev{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtsl-hopscotch-map-dev{a} libuchardet0{a} libunbound8{a} libuv1t64{a} libvcflib-dev{a} libvcflib-tools{a} libvcflib2{a} libwebp7{a} libwfa2-0{a} libwfa2-dev{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-render0-dev{a} libxcb-shm0{a} libxcb-shm0-dev{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxft2{a} libxml2{a} libxml2-dev{a} libxmu6{a} libxpm4{a} libxrender-dev{a} libxrender1{a} libxslt1-dev{a} libxslt1.1{a} libxss1{a} libxt6t64{a} libyajl-dev{a} libyajl2{a} libyuv0{a} libz3-4{a} libzstd-dev{a} littler{a} m4{a} man-db{a} media-types{a} native-architecture{a} netbase{a} nettle-dev{a} opensp{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} protobuf-compiler{a} pv{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-lxml{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-typeguard{a} python3-typing-extensions{a} python3.12{a} python3.12-minimal{a} r-base-core{a} r-cran-cli{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gridbase{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-plyr{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rlang{a} r-cran-scales{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} rapidjson-dev{a} raptor2-utils{a} rasqal-utils{a} readline-common{a} rs{a} samtools{a} sensible-utils{a} sgml-base{a} sgml-data{a} tabix{a} tzdata{a} ucf{a} unzip{a} uuid-dev{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} xdg-utils{a} xml-core{a} xorg-sgml-doctools{a} xsltproc{a} xtrans-dev{a} xxd{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-liberation krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libfl-dev libgpm2 libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libtasn1-doc libx11-protocol-perl linux-sysctl-defaults lynx psmisc publicsuffix python3-bs4 python3-cssselect python3-html5lib r-base-dev r-cran-abind r-cran-bit64 r-cran-callr r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-dichromat r-cran-digest r-cran-doparallel r-cran-dplyr r-cran-foreach r-cran-formattable r-cran-fs r-cran-generics r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-iterators r-cran-itertools r-cran-jpeg r-cran-kernlab r-cran-kernsmooth r-cran-knitr r-cran-lintr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-mockery r-cran-mockr r-cran-multcomp r-cran-mvtnorm r-cran-pkgdown r-cran-png r-cran-processx r-cran-profvis r-cran-ps r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-sf r-cran-shiny r-cran-shinyjs r-cran-stringi r-cran-svglite r-cran-testthat r-cran-tidyverse r-cran-unitizer r-cran-usethis r-cran-vcd r-cran-vdiffr r-cran-viridis r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html r-recommended redland-utils shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 382 newly installed, 0 to remove and 0 not upgraded. Need to get 251 MB of archives. After unpacking 1086 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 flex arm64 2.6.4-8.2+b3 [412 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libsigsegv2 arm64 2.14-1+b2 [34.3 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 gawk arm64 1:5.2.1-2+b2 [644 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0045 [45.2 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libdebuginfod-common all 0.192-4 [23.7 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.8-3 [810 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.8-3 [1941 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.7-1 [26.8 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-4 [256 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2~rc1-2 [23.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 24 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.8-3 [1906 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.8-3 [677 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B] Get: 32 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.7-1 [27.8 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-6 [1130 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-12 [91.4 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 bc arm64 1.07.1-4+b1 [101 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 bison arm64 2:3.8.2+dfsg-1+b2 [1149 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 bwa arm64 0.7.18-1 [198 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.2-1 [2267 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.1-1 [325 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.2-1 [9879 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2~rc1-2 [55.7 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 76 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 docbook all 4.5-11 [126 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libosp5 arm64 1.5.2-15+b1 [925 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 opensp arm64 1.5.2-15+b1 [444 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 docbook-to-man arm64 1:2.0.0-47+b1 [71.4 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 docbook-xml all 4.5-13 [77.4 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 docbook-xsl all 1.79.2+dfsg-7 [1221 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.5-1 [23.3 MB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libclang-cpp19 arm64 1:19.1.5-1 [12.0 MB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libclang1-19 arm64 1:19.1.5-1 [6850 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libfmt10 arm64 10.1.1+ds1-4 [121 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 doxygen arm64 1.9.8+ds-2+b3 [4515 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libdw1t64 arm64 0.192-4 [237 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libasm1t64 arm64 0.192-4 [28.2 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.11.1-1 [332 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libjson-c5 arm64 0.18+ds-1 [45.2 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libdebuginfod1t64 arm64 0.192-4 [31.3 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 elfutils arm64 0.192-4 [464 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-4+b2 [4920 B] Get: 107 http://deb.debian.org/debian unstable/main arm64 libfastahack0 arm64 1.0.0+dfsg-11+b2 [23.6 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 fastahack arm64 1.0.0+dfsg-11+b2 [12.2 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-3 [273 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-1.1+b1 [463 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 native-architecture all 0.2.3 [2108 B] Get: 117 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.4-1 [1411 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libgirepository-2.0-0 arm64 2.82.4-1 [130 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 girepository-tools arm64 2.82.4-1 [135 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libann0 arm64 1.1.2+doc-9+b2 [24.1 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libcdt5 arm64 2.42.4-2+b1 [39.4 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libcgraph6 arm64 2.42.4-2+b1 [61.3 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libaom3 arm64 3.11.0-1 [1690 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.5.0-1+b1 [248 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libabsl20230802 arm64 20230802.1-4 [432 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libgav1-1 arm64 0.19.0-2+b2 [493 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 librav1e0.7 arm64 0.7.1-7+b3 [655 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libyuv0 arm64 0.0.1898.20241125-1 [136 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libavif16 arm64 1.1.1-1 [109 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.19.3-1 [11.2 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b2 [153 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.19.3-1 [14.9 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.19.3-1 [419 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.1.0-1 [442 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b2 [53.2 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libgd3 arm64 2.3.3-12+b1 [115 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libgts-0.7-5t64 arm64 0.7.6+darcs121130-5.2+b1 [145 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.4.7-8 [392 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.55.0+ds-3 [212 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.55.0+ds-3 [52.1 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.55.0+ds-3 [33.4 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libpathplan4 arm64 2.42.4-2+b1 [41.4 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libgvc6 arm64 2.42.4-2+b1 [628 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libgvpr2 arm64 2.42.4-2+b1 [182 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 liblab-gamut1 arm64 2.42.4-2+b1 [198 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b1 [173 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b3 [55.6 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 graphviz arm64 2.42.4-2+b1 [574 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 libxslt1.1 arm64 1.1.35-1.1+b1 [222 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 python3-lxml arm64 5.3.0-1+b1 [1433 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 190 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 xsltproc arm64 1.1.35-1.1+b1 [115 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 gtk-doc-tools all 1.34.0-1 [328 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 icu-devtools arm64 72.1-5+b1 [195 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 libonig5 arm64 6.9.9-1+b1 [181 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 libjq1 arm64 1.7.1-3+b1 [148 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 jq arm64 1.7.1-3+b1 [77.3 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 libbackward-cpp-dev all 1.6-1 [34.3 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 uuid-dev arm64 2.40.2-12 [48.0 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 libblkid-dev arm64 2.40.2-12 [209 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-4 [10.6 MB] Get: 210 http://deb.debian.org/debian unstable/main arm64 libboost-program-options1.83.0 arm64 1.83.0-4 [331 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 libboost-program-options1.83-dev arm64 1.83.0-4 [371 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 213 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 libcairo-gobject2 arm64 1.18.2-2 [130 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-3+b1 [49.6 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 libcairo-script-interpreter2 arm64 1.18.2-2 [57.4 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 libpng-dev arm64 1.6.44-3 [360 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 libfreetype-dev arm64 2.13.3+dfsg-1 [600 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 libfontconfig-dev arm64 2.15.0-1.1+b1 [411 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 libffi-dev arm64 3.4.6-1 [57.0 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 libsepol-dev arm64 3.7-1 [354 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 libpcre2-16-0 arm64 10.44-5 [230 kB] Get: 226 http://deb.debian.org/debian unstable/main arm64 libpcre2-32-0 arm64 10.44-5 [220 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 libpcre2-posix3 arm64 10.44-5 [60.5 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libpcre2-dev arm64 10.44-5 [704 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 libselinux1-dev arm64 3.7-3+b1 [164 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 libmount-dev arm64 2.40.2-12 [29.1 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 libsysprof-capture-4-dev arm64 47.2-1 [49.1 kB] Get: 232 http://deb.debian.org/debian unstable/main arm64 libgio-2.0-dev arm64 2.82.4-1 [1698 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 libglib2.0-data all 2.82.4-1 [1276 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 libglib2.0-bin arm64 2.82.4-1 [123 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 236 http://deb.debian.org/debian unstable/main arm64 libgio-2.0-dev-bin arm64 2.82.4-1 [162 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 libglib2.0-dev-bin arm64 2.82.4-1 [52.0 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 libglib2.0-dev arm64 2.82.4-1 [52.7 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 libpixman-1-dev arm64 0.44.0-3 [11.4 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 241 http://deb.debian.org/debian unstable/main arm64 x11proto-dev all 2024.1-1 [603 kB] Get: 242 http://deb.debian.org/debian unstable/main arm64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 243 http://deb.debian.org/debian unstable/main arm64 libice-dev arm64 2:1.1.1-1 [73.0 kB] Get: 244 http://deb.debian.org/debian unstable/main arm64 libsm-dev arm64 2:1.2.4-1 [38.0 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 libxau-dev arm64 1:1.0.11-1 [23.9 kB] Get: 246 http://deb.debian.org/debian unstable/main arm64 libxdmcp-dev arm64 1:1.1.5-1 [44.2 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 libxcb1-dev arm64 1.17.0-2+b1 [182 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 libx11-dev arm64 2:1.8.10-2 [877 kB] Get: 250 http://deb.debian.org/debian unstable/main arm64 libxcb-render0-dev arm64 1.17.0-2+b1 [119 kB] Get: 251 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0-dev arm64 1.17.0-2+b1 [108 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 libxext-dev arm64 2:1.3.4-1+b2 [105 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libxrender-dev arm64 1:0.9.10-1.1+b2 [35.7 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 libcairo2-dev arm64 1.18.2-2 [43.0 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1 [553 kB] Get: 257 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Get: 258 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 260 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-2+b1 [208 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.5.18+dfsg-3+b1 [300 kB] Get: 268 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.6.0-2 [86.5 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.9.1-1 [23.0 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 libngtcp2-dev arm64 1.9.1-1 [162 kB] Get: 272 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.11.1-1 [461 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.22-1 [51.2 kB] Get: 279 http://deb.debian.org/debian unstable/main arm64 libdisorder-dev arm64 0.0.2+git20130809.8062ee1-4+b2 [4888 B] Get: 280 http://deb.debian.org/debian unstable/main arm64 libdivsufsort3 arm64 2.0.1-6+b1 [39.9 kB] Get: 281 http://deb.debian.org/debian unstable/main arm64 libdivsufsort-dev arm64 2.0.1-6+b1 [19.1 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 libelf-dev arm64 0.192-4 [94.9 kB] Get: 283 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 libdw-dev arm64 0.192-4 [320 kB] Get: 285 http://deb.debian.org/debian unstable/main arm64 libfastahack-dev arm64 1.0.0+dfsg-11+b2 [26.1 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 libfml0 arm64 0.1+git20221215.85f159e-1 [65.6 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 libfml-dev arm64 0.1+git20221215.85f159e-1 [79.9 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-9 [361 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 291 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB] Get: 292 http://deb.debian.org/debian unstable/main arm64 libicu-dev arm64 72.1-5+b1 [10.3 MB] Get: 293 http://deb.debian.org/debian unstable/main arm64 libjansson-dev arm64 2.14-2+b3 [43.6 kB] Get: 294 http://deb.debian.org/debian unstable/main arm64 libjemalloc2 arm64 5.3.0-2+b2 [217 kB] Get: 295 http://deb.debian.org/debian unstable/main arm64 libjemalloc-dev arm64 5.3.0-2+b2 [357 kB] Get: 296 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 297 http://deb.debian.org/debian unstable/main arm64 liblz4-dev arm64 1.9.4-3+b1 [79.1 kB] Get: 298 http://deb.debian.org/debian unstable/main arm64 libmhash2 arm64 0.9.9.9-10 [94.5 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 libncurses-dev arm64 6.5-2+b1 [338 kB] Get: 301 http://deb.debian.org/debian unstable/main arm64 libpaper1 arm64 1.1.29+b2 [13.0 kB] Get: 302 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 1.1.29+b2 [9128 B] Get: 303 http://deb.debian.org/debian unstable/main arm64 libprotobuf32t64 arm64 3.21.12-10+b1 [859 kB] Get: 304 http://deb.debian.org/debian unstable/main arm64 libprotobuf-lite32t64 arm64 3.21.12-10+b1 [250 kB] Get: 305 http://deb.debian.org/debian unstable/main arm64 libprotobuf-dev arm64 3.21.12-10+b1 [1261 kB] Get: 306 http://deb.debian.org/debian unstable/main arm64 libprotoc32t64 arm64 3.21.12-10+b1 [789 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 libprotoc-dev arm64 3.21.12-10+b1 [937 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 libyajl2 arm64 2.1.0-5+b2 [22.5 kB] Get: 309 http://deb.debian.org/debian unstable/main arm64 libraptor2-0 arm64 2.0.16-4+b1 [164 kB] Get: 310 http://deb.debian.org/debian unstable/main arm64 libxml2-dev arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [751 kB] Get: 311 http://deb.debian.org/debian unstable/main arm64 libxslt1-dev arm64 1.1.35-1.1+b1 [345 kB] Get: 312 http://deb.debian.org/debian unstable/main arm64 libyajl-dev arm64 2.1.0-5+b2 [31.0 kB] Get: 313 http://deb.debian.org/debian unstable/main arm64 libraptor2-dev arm64 2.0.16-4+b1 [205 kB] Get: 314 http://deb.debian.org/debian unstable/main arm64 librasqal3t64 arm64 0.9.33-2.1+b2 [178 kB] Get: 315 http://deb.debian.org/debian unstable/main arm64 librasqal3-dev arm64 0.9.33-2.1+b2 [224 kB] Get: 316 http://deb.debian.org/debian unstable/main arm64 librdf0t64 arm64 1.0.17-4+b1 [100 kB] Get: 317 http://deb.debian.org/debian unstable/main arm64 librdf0-dev arm64 1.0.17-4+b1 [239 kB] Get: 318 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-2 [467 kB] Get: 319 http://deb.debian.org/debian unstable/main arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-12+b2 [32.4 kB] Get: 320 http://deb.debian.org/debian unstable/main arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-12+b2 [37.9 kB] Get: 321 http://deb.debian.org/debian unstable/main arm64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 322 http://deb.debian.org/debian unstable/main arm64 libssw0 arm64 1.1-15+b1 [20.0 kB] Get: 323 http://deb.debian.org/debian unstable/main arm64 libssw-dev arm64 1.1-15+b1 [23.4 kB] Get: 324 http://deb.debian.org/debian unstable/main arm64 libtabixpp0t64 arm64 1.1.2-2.1+b1 [9504 B] Get: 325 http://deb.debian.org/debian unstable/main arm64 libtabixpp-dev arm64 1.1.2-2.1+b1 [9052 B] Get: 326 http://deb.debian.org/debian unstable/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [982 kB] Get: 327 http://deb.debian.org/debian unstable/main arm64 libxft2 arm64 2.3.6-1+b2 [51.6 kB] Get: 328 http://deb.debian.org/debian unstable/main arm64 libxss1 arm64 1:1.2.3-1+b2 [17.1 kB] Get: 329 http://deb.debian.org/debian unstable/main arm64 libtk8.6 arm64 8.6.15-1 [738 kB] Get: 330 http://deb.debian.org/debian unstable/main arm64 libtsl-hopscotch-map-dev all 2.3.1-1 [36.6 kB] Get: 331 http://deb.debian.org/debian unstable/main arm64 libwfa2-0 arm64 2.3.3-4+b1 [55.2 kB] Get: 332 http://deb.debian.org/debian unstable/main arm64 libvcflib2 arm64 1.0.9+dfsg1-3+b2 [165 kB] Get: 333 http://deb.debian.org/debian unstable/main arm64 libwfa2-dev arm64 2.3.3-4+b1 [74.9 kB] Get: 334 http://deb.debian.org/debian unstable/main arm64 libvcflib-dev arm64 1.0.9+dfsg1-3+b2 [77.8 kB] Get: 335 http://deb.debian.org/debian unstable/main arm64 zip arm64 3.0-14+b1 [227 kB] Get: 336 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28+b1 [158 kB] Get: 337 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 338 http://deb.debian.org/debian unstable/main arm64 r-base-core arm64 4.4.2-1 [28.0 MB] Get: 339 http://deb.debian.org/debian unstable/main arm64 r-cran-littler arm64 0.3.20-2 [102 kB] Get: 340 http://deb.debian.org/debian unstable/main arm64 littler all 0.3.20-2 [16.0 kB] Get: 341 http://deb.debian.org/debian unstable/main arm64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get: 342 http://deb.debian.org/debian unstable/main arm64 r-cran-rcpp arm64 1.0.13-1-1 [2057 kB] Get: 343 http://deb.debian.org/debian unstable/main arm64 r-cran-plyr arm64 1.8.9-1+b1 [791 kB] Get: 344 http://deb.debian.org/debian unstable/main arm64 r-cran-cli arm64 3.6.3-1 [1340 kB] Get: 345 http://deb.debian.org/debian unstable/main arm64 r-cran-glue arm64 1.8.0-1 [165 kB] Get: 346 http://deb.debian.org/debian unstable/main arm64 r-cran-rlang arm64 1.1.4-1+b1 [1708 kB] Get: 347 http://deb.debian.org/debian unstable/main arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 348 http://deb.debian.org/debian unstable/main arm64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get: 349 http://deb.debian.org/debian unstable/main arm64 r-cran-isoband arm64 0.2.7-1+b1 [1614 kB] Get: 350 http://deb.debian.org/debian unstable/main arm64 r-cran-mass arm64 7.3-61-1+b1 [1112 kB] Get: 351 http://deb.debian.org/debian unstable/main arm64 r-cran-lattice arm64 0.22-6-1+b1 [1417 kB] Get: 352 http://deb.debian.org/debian unstable/main arm64 r-cran-nlme arm64 3.1.166-1 [2326 kB] Get: 353 http://deb.debian.org/debian unstable/main arm64 r-cran-matrix arm64 1.7-1-1 [4023 kB] Get: 354 http://deb.debian.org/debian unstable/main arm64 r-cran-mgcv arm64 1.9-1-1+b1 [3218 kB] Get: 355 http://deb.debian.org/debian unstable/main arm64 r-cran-farver arm64 2.1.2-1+b1 [1397 kB] Get: 356 http://deb.debian.org/debian unstable/main arm64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 357 http://deb.debian.org/debian unstable/main arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1713 kB] Get: 358 http://deb.debian.org/debian unstable/main arm64 r-cran-munsell all 0.5.1-1 [237 kB] Get: 359 http://deb.debian.org/debian unstable/main arm64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 360 http://deb.debian.org/debian unstable/main arm64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 361 http://deb.debian.org/debian unstable/main arm64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 362 http://deb.debian.org/debian unstable/main arm64 r-cran-scales all 1.3.0-1 [677 kB] Get: 363 http://deb.debian.org/debian unstable/main arm64 r-cran-fansi arm64 1.0.5-1+b1 [626 kB] Get: 364 http://deb.debian.org/debian unstable/main arm64 r-cran-magrittr arm64 2.0.3-1+b1 [203 kB] Get: 365 http://deb.debian.org/debian unstable/main arm64 r-cran-utf8 arm64 1.2.4-1+b1 [133 kB] Get: 366 http://deb.debian.org/debian unstable/main arm64 r-cran-vctrs arm64 0.6.5-1+b1 [1378 kB] Get: 367 http://deb.debian.org/debian unstable/main arm64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get: 368 http://deb.debian.org/debian unstable/main arm64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 369 http://deb.debian.org/debian unstable/main arm64 r-cran-tibble arm64 3.2.1+dfsg-2+b1 [425 kB] Get: 370 http://deb.debian.org/debian unstable/main arm64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 371 http://deb.debian.org/debian unstable/main arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get: 372 http://deb.debian.org/debian unstable/main arm64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 373 http://deb.debian.org/debian unstable/main arm64 libvcflib-tools arm64 1.0.9+dfsg1-3+b2 [590 kB] Get: 374 http://deb.debian.org/debian unstable/main arm64 protobuf-compiler arm64 3.21.12-10+b1 [84.9 kB] Get: 375 http://deb.debian.org/debian unstable/main arm64 pv arm64 1.9.7-1 [103 kB] Get: 376 http://deb.debian.org/debian unstable/main arm64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 377 http://deb.debian.org/debian unstable/main arm64 raptor2-utils arm64 2.0.16-4+b1 [34.6 kB] Get: 378 http://deb.debian.org/debian unstable/main arm64 rasqal-utils arm64 0.9.33-2.1+b2 [43.1 kB] Get: 379 http://deb.debian.org/debian unstable/main arm64 rs arm64 20200313-1+b1 [15.2 kB] Get: 380 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.20-3+b1 [629 kB] Get: 381 http://deb.debian.org/debian unstable/main arm64 tabix arm64 1.20+ds-2 [455 kB] Get: 382 http://deb.debian.org/debian unstable/main arm64 xxd arm64 2:9.1.0861-1 [97.7 kB] Fetched 251 MB in 1s (218 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (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 ... 20082 files and directories currently installed.) Preparing to unpack .../archives/m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package flex. Preparing to unpack .../flex_2.6.4-8.2+b3_arm64.deb ... Unpacking flex (2.6.4-8.2+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../libsigsegv2_2.14-1+b2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.14-1+b2) ... Setting up readline-common (8.2-6) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up libsigsegv2:arm64 (2.14-1+b2) ... Selecting previously unselected package gawk. (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 ... 20307 files and directories currently installed.) Preparing to unpack .../0-gawk_1%3a5.2.1-2+b2_arm64.deb ... Unpacking gawk (1:5.2.1-2+b2) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../1-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../2-procps_2%3a4.0.4-6_arm64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../3-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package ucf. Preparing to unpack .../4-ucf_3.0045_all.deb ... Moving old data out of the way Unpacking ucf (3.0045) ... Selecting previously unselected package libdebuginfod-common. Preparing to unpack .../5-libdebuginfod-common_0.192-4_all.deb ... Unpacking libdebuginfod-common (0.192-4) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../6-liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../7-libpython3.12-minimal_3.12.8-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.8-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../8-libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../9-python3.12-minimal_3.12.8-3_arm64.deb ... Unpacking python3.12-minimal (3.12.8-3) ... Setting up libpython3.12-minimal:arm64 (3.12.8-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... Selecting previously unselected package python3-minimal. (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 ... 21078 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_arm64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../13-libpython3.12-stdlib_3.12.8-3_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.8-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../14-python3.12_3.12.8-3_arm64.deb ... Unpacking python3.12 (3.12.8-3) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../15-libpython3-stdlib_3.12.7-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (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 ... 22109 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_arm64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.3.2-2_arm64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../005-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-6_arm64.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.40.2-12_arm64.deb ... Unpacking bsdextrautils (2.40.2-12) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../011-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package bc. Preparing to unpack .../017-bc_1.07.1-4+b1_arm64.deb ... Unpacking bc (1.07.1-4+b1) ... Selecting previously unselected package bison. Preparing to unpack .../018-bison_2%3a3.8.2+dfsg-1+b2_arm64.deb ... Unpacking bison (2:3.8.2+dfsg-1+b2) ... Selecting previously unselected package bwa. Preparing to unpack .../019-bwa_0.7.18-1_arm64.deb ... Unpacking bwa (0.7.18-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../020-cmake-data_3.31.2-1_all.deb ... Unpacking cmake-data (3.31.2-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../021-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../022-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libarchive13t64:arm64. Preparing to unpack .../023-libarchive13t64_3.7.4-1.1_arm64.deb ... Unpacking libarchive13t64:arm64 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../024-libbrotli1_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../025-libsasl2-modules-db_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../026-libsasl2-2_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../027-libldap-2.5-0_2.5.18+dfsg-3+b1_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../028-libnghttp2-14_1.64.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../029-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../030-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../031-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../032-libcurl4t64_8.11.1-1_arm64.deb ... 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Setting up libpangocairo-1.0-0:arm64 (1.55.0+ds-3) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-3) ... Setting up libcairo-script-interpreter2:arm64 (1.18.2-2) ... Setting up libdebuginfod1t64:arm64 (0.192-4) ... Setting up libxmu6:arm64 (2:1.1.3-3+b3) ... Setting up libpython3.12-stdlib:arm64 (3.12.8-3) ... Setting up libkdb5-10t64:arm64 (1.21.3-3) ... Setting up libfontconfig-dev:arm64 (2.15.0-1.1+b1) ... Setting up python3.12 (3.12.8-3) ... Setting up libraptor2-0:arm64 (2.0.16-4+b1) ... Setting up raptor2-utils (2.0.16-4+b1) ... Setting up debhelper (13.20) ... Setting up librasqal3t64:arm64 (0.9.33-2.1+b2) ... Setting up libxaw7:arm64 (2:1.0.16-1) ... Setting up librdf0t64:arm64 (1.0.17-4+b1) ... Setting up samtools (1.20-3+b1) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-6-1+b1) ... Setting up r-cran-nlme (3.1.166-1) ... Setting up r-cran-farver (2.1.2-1+b1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libkadm5srv-mit12:arm64 (1.21.3-3) ... Setting up libtabixpp0t64:arm64 (1.1.2-2.1+b1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-cran-magrittr (2.0.3-1+b1) ... Setting up libpython3-stdlib:arm64 (3.12.7-1) ... Setting up krb5-multidev:arm64 (1.21.3-3) ... Setting up r-cran-littler (0.3.20-2) ... Setting up r-cran-rcpp (1.0.13-1-1) ... Setting up rasqal-utils (0.9.33-2.1+b2) ... Setting up elfutils (0.192-4) ... Setting up r-cran-rlang (1.1.4-1+b1) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up littler (0.3.20-2) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up r-cran-fansi (1.0.5-1+b1) ... Setting up r-cran-mass (7.3-61-1+b1) ... Setting up python3 (3.12.7-1) ... /usr/share/gtk-doc/python/gtkdoc/scan.py:44: SyntaxWarning: invalid escape sequence '\s' VAR_TYPE_MODIFIER = '(?:' + '|'.join([t + '\s+' for t in TYPE_MODIFIERS]) + ')*' /usr/share/gtk-doc/python/gtkdoc/scan.py:45: SyntaxWarning: invalid escape sequence '\s' RET_TYPE_MODIFIER = '(?:' + '|'.join([t + '\s+' for t in TYPE_MODIFIERS + ['G_CONST_RETURN']]) + ')*' /usr/share/gtk-doc/python/gtkdoc/scan.py:238: SyntaxWarning: invalid escape sequence '\(' ignore_decorators = '|' + options.ignore_decorators.replace('()', '\(\w*\)') /usr/share/gtk-doc/python/gtkdoc/scan.py:239: SyntaxWarning: invalid escape sequence '\s' optional_decorators_regex = '(?:\s+(?:%s))?' % ignore_decorators[1:] /usr/share/gtk-doc/python/gtkdoc/scan.py:487: SyntaxWarning: invalid escape sequence '\(' ignore_decorators = '|' + options.ignore_decorators.replace('()', '\(\w*\)') /usr/share/gtk-doc/python/gtkdoc/scan.py:488: SyntaxWarning: invalid escape sequence '\s' optional_decorators_regex = '(?:\s+(?:%s))?' % ignore_decorators[1:] Setting up python3-autocommand (2.2.2-3) ... Setting up r-cran-glue (1.8.0-1) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up libkrb5-dev:arm64 (1.21.3-3) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.4-1+b1) ... Setting up python3-packaging (24.2-1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up libvcflib2:arm64 (1.0.9+dfsg1-3+b2) ... Setting up r-cran-plyr (1.8.9-1+b1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1+b1) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up r-cran-matrix (1.7-1-1) ... Setting up r-cran-mgcv (1.9-1-1+b1) ... Setting up python3-lxml:arm64 (5.3.0-1+b1) ... Setting up r-cran-vctrs (0.6.5-1+b1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libgio-2.0-dev-bin (2.82.4-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2+b1) ... Setting up libcurl4-gnutls-dev:arm64 (8.11.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up r-cran-scales (1.3.0-1) ... Setting up libraptor2-dev:arm64 (2.0.16-4+b1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up libglib2.0-dev-bin (2.82.4-1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up libhts-dev:arm64 (1.20+ds-2) ... Setting up librasqal3-dev (0.9.33-2.1+b2) ... Setting up libvcflib-tools (1.0.9+dfsg1-3+b2) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up libglib2.0-dev:arm64 (2.82.4-1) ... Setting up librdf0-dev (1.0.17-4+b1) ... Setting up libtabixpp-dev:arm64 (1.1.2-2.1+b1) ... Setting up libcairo2-dev:arm64 (1.18.2-2) ... Setting up libvcflib-dev:arm64 (1.0.9+dfsg1-3+b2) ... Setting up libheif-plugin-dav1d:arm64 (1.19.3-1) ... Setting up libheif-plugin-libde265:arm64 (1.19.3-1) ... Setting up libheif1:arm64 (1.19.3-1) ... Setting up libgd3:arm64 (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-2+b1) ... Setting up graphviz (2.42.4-2+b1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xsl (1.79.2+dfsg-7) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xml (4.5-13) ... Setting up docbook (4.5-11) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-to-man (1:2.0.0-47+b1) ... Setting up gtk-doc-tools (1.34.0-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/vg-1.59.0+ds/ && 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 > ../vg_1.59.0+ds-0.1_source.changes dpkg-buildpackage: info: source package vg dpkg-buildpackage: info: source version 1.59.0+ds-0.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Bastian Germann dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' find /build/reproducible-path/vg-1.59.0+ds/include/ -type f -a '!' -name vg_git_version.hpp -delete dh_auto_clean || true make -j12 clean make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now rm -f -r bin/unittest rm -f -r lib rm -f -r obj/unittest/support rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/pic/io rm -f -r obj/io rm -f -r obj/pic/algorithms rm -f -r obj/algorithms rm -f -r obj/config rm -f -r obj/pic rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd C && make clean cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make clean cd quicktree_1.1 && make clean rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[2]: *** [Makefile:854: clean] Error 2 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_clean: error: make -j12 clean returned exit code 2 make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' rm -Rf ./deps/DYNAMIC/build/CMakeFiles dh_clean make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' dh_autoreconf --sourcedirectory=/build/reproducible-path/vg-1.59.0+ds/deps/vowpal_wabbit make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_configure debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' mkdir -p /build/reproducible-path/vg-1.59.0+ds/debian/help find . -type d -name simde | xargs rm -Rf dh_auto_build -- all test/build_graph bin/shuf make -j12 "INSTALL=install --strip-program=true" all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" ./install.sh /build/reproducible-path/vg-1.59.0+ds . ./source_me.sh && cd deps/ssw/src && make && ar rs /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && cd deps/libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="-std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make && make install . ./source_me.sh && cd deps/kff-cpp-api && rm -Rf build && mkdir build && cd build && cmake .. && make && cp kff_io.hpp /build/reproducible-path/vg-1.59.0+ds/include && mv libkff.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cd deps/gssw && make && cp lib/libgssw.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp src/gssw.h /build/reproducible-path/vg-1.59.0+ds/include/ . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.59.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS/ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.59.0+ds/include/ rm -f lib/cleaned_old_protobuf* g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c cp deps/BBHash/BooPHF.h /build/reproducible-path/vg-1.59.0+ds/include make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cp -r deps/sparsepp/sparsepp include/ cd externalTools && make all cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi WARNING: .git/hooks directory does not exists. rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* The pre-commit hook is not installed. make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all rm -Rf include/dynamic.hpp include/dynamic if [ ! -d obj ]; then mkdir -p obj; fi make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c if [ ! -d lib ]; then mkdir -p lib; fi rm -Rf include/google/protobuf deps/protobuf # annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers find bin obj lib -type f -delete touch lib/cleaned_old_protobuf_v003 if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' . ./source_me.sh && cp -r deps/mio/include/mio /build/reproducible-path/vg-1.59.0+ds/include/ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d lib ]; then mkdir -p lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/union_find.cpp -o obj/union_find.o CMake Deprecation Warning at CMakeLists.txt:1 (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. . ./source_me.sh && cp -r deps/atomic_queue/include/atomic_queue/* /build/reproducible-path/vg-1.59.0+ds/include/ if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi CMake Deprecation Warning at CMakeLists.txt:1 (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. -- Setting build type to 'Release' as none was specified. if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o . ./source_me.sh && cp -r deps/ips4o/ips4o* /build/reproducible-path/vg-1.59.0+ds/include/ -- The C compiler identification is GNU 14.2.0 cd ./deps/lru_cache && cp *.h* /build/reproducible-path/vg-1.59.0+ds/include/ -- The C compiler identification is GNU 14.2.0 cp deps/sha1/*.h* /build/reproducible-path/vg-1.59.0+ds/include/ cp deps/progress_bar/progress_bar.hpp /build/reproducible-path/vg-1.59.0+ds/include mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/dozeu && cp deps/dozeu/*.h /build/reproducible-path/vg-1.59.0+ds/include/dozeu/ -- The C compiler identification is GNU 14.2.0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o -- The CXX compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info src/gssw.c: In function ‘gssw_graph_print’: -- The CXX compiler identification is GNU 14.2.0 src/gssw.c:1947:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1947 | fprintf(stdout, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1951:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1951:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_stderr’: src/gssw.c:1963:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1963 | fprintf(stderr, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1967:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1967:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_score_matrices’: src/gssw.c:1978:31: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1978 | fprintf(out, "node %llu\n", n->id); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o -- Detecting C compiler ABI info src/gssw.c: In function ‘gssw_print_graph_cigar’: src/gssw.c:3623:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 3623 | fprintf(out, "%llu[", nc->node->id); | ~~~^ ~~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -- The C compiler identification is GNU 14.2.0 src/gssw.c: In function ‘gssw_create_seed_byte’: src/gssw.c:5095:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5095 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_word’: -- Detecting CXX compiler ABI info src/gssw.c:5130:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5130 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- Detecting C compiler ABI info - done -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting C compiler ABI info - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done libhandlegraph is root project or external_project -- Configuring done (0.7s) -- Detecting CXX compiler ABI info - done -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build -- Configuring done (0.8s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build -- Detecting C compiler ABI info - done make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -- Detecting CXX compile features - done /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend Building in Release modemake[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Configuring done (0.8s) make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC -B/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build --check-build-system CMakeFiles/Makefile.cmake 0 [ 2%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build//CMakeFiles/progress.marks [ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/depend gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/debug.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 6%] Building CXX object CMakeFiles/debug.dir/debug.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/debug.dir/debug.cpp.o -MF CMakeFiles/debug.dir/debug.cpp.o.d -o CMakeFiles/debug.dir/debug.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/debug.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v1.dir/DependInfo.cmake "--color=" gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 12%] Building CXX object CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -MF CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o.d -o CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_lz77_v1.cpp [ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dfs.cpp gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz -- Performing Test HAVE_CXA_DEMANGLE rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' diff: include/vg_environment_version.hpp: No such file or directory . ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:102 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm ln -s `which shuf` bin/shuf . ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/reproducible-path/vg-1.59.0+ds/include/ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' [ 8%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o cp inc/avl.h ../lib/avl.h.tmp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/handle_graph.cpp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h -- Looking for C++ include cstdio - found cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot cp inc/stJson.h ../lib/stJson.h.tmp src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h -- Configuring done (2.1s) cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Generating done (0.1s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 [ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_metadata.cpp make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" [ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4975:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ src/gssw.c:4971:19: note: length computed here 4971 | int32_t len = strlen(seq); | ^~~~~~~~~~~ impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_handle_graph.cpp [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [24, 248] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 8 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [25, 249] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 9 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [26, 250] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 10 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [27, 251] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 11 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [28, 252] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 12 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [29, 253] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 13 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [30, 254] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 14 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [24, 248] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 8 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [25, 249] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 9 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [26, 250] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 10 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [27, 251] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 11 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [28, 252] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 12 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [29, 253] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 13 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [30, 254] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 14 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [24, 248] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 8 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [25, 249] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 9 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [26, 250] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 10 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [27, 251] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 11 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [28, 252] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 12 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [29, 253] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 13 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [30, 254] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 14 into destination object ‘buff’ of size 8 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 28%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp [ 31%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/serializable.cpp [ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp [ 37%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp [ 40%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/types.cpp [ 42%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/copy_graph.cpp [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/append_graph.cpp [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/are_equivalent.cpp In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [24, 248] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 8 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [25, 249] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 9 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [26, 250] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 10 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [27, 251] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 11 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [28, 252] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 12 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [29, 253] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 13 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [30, 254] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 14 into destination object ‘buff’ of size 8 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_tips.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 18%] Linking CXX executable debug /usr/bin/cmake -E cmake_link_script CMakeFiles/debug.dir/link.txt --verbose=1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/debug.dir/link.d CMakeFiles/debug.dir/debug.cpp.o -o debug make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 18%] Built target debug make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v2.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -MF CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o.d -o CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_lz77_v2.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Linking CXX static library libkff.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 33%] Built target kff make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 50%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/topological_sort.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 57%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/apply_orientations.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1358:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:380:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1285:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 448 | *word &= | ^~~~~ [ 60%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:765:75: note: declared here 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:773:68: note: declared here 773 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 62%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.cpp impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘stConnectedComponent_destruct’, inlined from ‘stConnectivity_addEdge’ at impl/sonLibConnectivity.c:238:3: impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ [ 65%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 68%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 66%] Linking CXX executable kff_example [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp [ 71%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o [ 66%] Built target kff_example make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 83%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dijkstra.cpp [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_acyclic.cpp [100%] Linking CXX executable reader_bench g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [100%] Built target reader_bench make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/reverse_complement.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibTreap.c: In function ‘stTreap_remove’: impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] 331 | stTreap *p = rmnode->parent; | ^ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:544:23, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:509:28, inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp [ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/h0_lz77.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_bwt.dir/DependInfo.cmake "--color=" [ 31%] Building CXX object CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -MF CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o.d -o CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/h0_lz77.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 37%] Building CXX object CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -MF CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o.d -o CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_bwt.cpp [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 43%] Linking CXX executable rle_lz77_v1 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v1.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rle_lz77_v1.dir/link.d CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -o rle_lz77_v1 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 43%] Built target rle_lz77_v1 make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC 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-fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -MF CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o.d -o CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/cw-bwt.cpp make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/benchmark.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 56%] Building CXX object CMakeFiles/benchmark.dir/benchmark.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/benchmark.dir/benchmark.cpp.o -MF CMakeFiles/benchmark.dir/benchmark.cpp.o.d -o CMakeFiles/benchmark.dir/benchmark.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/benchmark.cpp make -f CMakeFiles/wm_string.dir/build.make CMakeFiles/wm_string.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/wm_string.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/wm_string.dir/build.make CMakeFiles/wm_string.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 62%] Building CXX object CMakeFiles/wm_string.dir/wm_string.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/wm_string.dir/wm_string.cpp.o -MF CMakeFiles/wm_string.dir/wm_string.cpp.o.d -o CMakeFiles/wm_string.dir/wm_string.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/wm_string.cpp [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm [ 68%] Linking CXX executable rle_lz77_v2 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp /usr/bin/g++ -fPIC -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file=CMakeFiles/handlegraph_shared.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rle_lz77_v2.dir/link.d CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -o rle_lz77_v2 /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 68%] Built target rle_lz77_v2 [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.a -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/util.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/buildable_snarl_decomposition.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/strongly_connected_components.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/split_strands.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/reverse_complement.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_acyclic.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal/dfs.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/extend.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' rm -f /build/reproducible-path/vg-1.59.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" && export LDFLAGS="-Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig: cmake -DCMAKE_CXX_STANDARD=14 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;/" -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make clean && VERBOSE=1 make && make install -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Building libvgio for C++ 14 -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Could NOT find Protobuf (missing: Protobuf_DIR) No installed Protobuf has registered itself with CMake. -- Found Protobuf: /usr/lib/aarch64-linux-gnu/libprotobuf.so (found version "3.21.12") Found Protobuf using FindProtobuf.cmake -- Found Threads: TRUE Using real Threads library -- Checking for module 'htslib' -- Found htslib, version 1.20 -- Checking for module 'jansson' -- Found jansson, version 2.14 Using installed libhandlegraph -- Configuring done (1.3s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/test_libvgio.dir/build.make CMakeFiles/test_libvgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 2%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 5%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/vg.pb.cc [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 75%] Linking CXX executable rle_bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_bwt.dir/link.txt --verbose=1 [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rle_bwt.dir/link.d CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 75%] Built target rle_bwt [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I .//../sonLib/lib/ -c impl/*.c [ 81%] Linking CXX executable h0_lz77 /usr/bin/cmake -E cmake_link_script CMakeFiles/h0_lz77.dir/link.txt --verbose=1 [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/h0_lz77.dir/link.d CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -o h0_lz77 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 81%] Built target h0_lz77 [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 87%] Linking CXX executable wm_string /usr/bin/cmake -E cmake_link_script CMakeFiles/wm_string.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/wm_string.dir/link.d CMakeFiles/wm_string.dir/wm_string.cpp.o -o wm_string make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 87%] Built target wm_string [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 93%] Linking CXX executable cw-bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cw-bwt.dir/link.d "CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o" -o cw-bwt make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 93%] Built target cw-bwt [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp [100%] Linking CXX executable benchmark /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/benchmark.dir/link.d CMakeFiles/benchmark.dir/benchmark.cpp.o -o benchmark make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [100%] Built target benchmark make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' # Do the copy of the main file last so we can tell if this recipe failed and redo it. # Otherwise we get dynamic.hpp without its deps mkdir -p include/dynamic && cp -r /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include/dynamic/* include/dynamic/ [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o cd 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-I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp [ 8%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 11%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" [ 14%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 17%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/vg.pb.cc [ 20%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp [ 29%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 32%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c 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/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' [ 38%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 41%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp [ 44%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp [ 47%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 50%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp [ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 55%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp [100%] Linking CXX static library libsdsl.a cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/simple_sds.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.59.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 [ 58%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ 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make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp -- Installing: 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/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp -- 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/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.59.0+ds/include'. The library files are located in '/build/reproducible-path/vg-1.59.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gcsa2 && make directories && make lib/libgcsa2.a && mv lib/libgcsa2.a /build/reproducible-path/vg-1.59.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' mkdir -p bin mkdir -p lib mkdir -p obj make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp [ 61%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp [ 64%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp [ 67%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp [ 70%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp [ 73%] Building CXX object 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-I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp [ 79%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/registry.cpp.o -MF CMakeFiles/vgio_static.dir/src/registry.cpp.o.d -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp [ 82%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp [ 85%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp [ 88%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 91%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp [ 94%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wl,--dependency-file=CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/lib/aarch64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 94%] Built target vgio /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwt && make clean && make && mv lib/libgbwt.a /build/reproducible-path/vg-1.59.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' rm -rf bin lib obj rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp [ 97%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 50%] Built target vgio make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/json2pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' . ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' [ ! -e bdsg/obj ] || rm -r bdsg/obj [ ! -e lib ] || rm -r lib [ ! -e bin ] || rm -r bin make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' ar rcs lib/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/merge_gbwt obj/merge_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/benchmark obj/benchmark.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/metadata_tool obj/metadata_tool.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/remove_seq obj/remove_seq.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 rm obj/build_ri.o obj/metadata_tool.o obj/benchmark.o obj/merge_gbwt.o obj/remove_seq.o obj/build_gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv lib/libgbwtgraph.a /build/reproducible-path/vg-1.59.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' rm -rf bin lib obj rm -f *.o *.a gfa2gbwt cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' rm -f test_utils test_gbwtgraph test_cached_gbwtgraph test_gfa test_gbz test_minimizer test_index test_algorithms test_path_cover *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwtgraph.o src/cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwtgraph.o src/gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz.o src/gbz.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa.o src/gfa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/minimizer.o src/minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_cover.o src/path_cover.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp ar rcs lib/libgbwtgraph.a obj/algorithms.o obj/cached_gbwtgraph.o obj/gbwtgraph.o obj/gbz.o obj/gfa.o obj/internal.o obj/minimizer.o obj/path_cover.o obj/utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gfa2gbwt obj/gfa2gbwt.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gbz_stats obj/gbz_stats.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/kmer_freq obj/kmer_freq.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 rm obj/kmer_freq.o obj/gbz_stats.o obj/gfa2gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/back_translating_alignment_emitter.o src/back_translating_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/clip.o src/clip.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/contracting_graph.o src/contracting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/explainer.o src/explainer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/flat_file_back_translation.o src/flat_file_back_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gbwt_extender.o src/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gbwtgraph_helper.o src/gbwtgraph_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gcsa_helper.o src/gcsa_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/job_schedule.o src/job_schedule.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/kff.o src/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/kmp.o src/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mem_accelerator.o src/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper_from_chains.o src/minimizer_mapper_from_chains.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/recombinator.o src/recombinator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarl_distance_index.o src/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarl_seed_clusterer.o src/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/sparse_union_find.o src/sparse_union_find.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subpath_overlay.o src/subpath_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_clusters.o src/traversal_clusters.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/zstdutil.o src/zstdutil.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/back_translate.o src/algorithms/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/chain_items.o src/algorithms/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/component.o src/algorithms/component.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwt.o src/algorithms/find_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwtgraph.o src/algorithms/find_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/find_translation.o src/algorithms/find_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/intersect_path_offsets.o src/algorithms/intersect_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/locally_expand_graph.o src/algorithms/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/min_cut_graph.o src/algorithms/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/pad_band.o src/algorithms/pad_band.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/prune_to_connecting_graph.o src/algorithms/prune_to_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_params_json.o src/io/register_loader_params_json.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbz.o src/io/register_loader_saver_gbz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbzgraph.o src/io/register_loader_saver_gbzgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gfa.o src/io/register_loader_saver_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/back_translate.o src/unittest/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/chain_items.o src/unittest/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/component_paths.o src/unittest/component_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/gbwt_extender.o src/unittest/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/index_helpers.o src/unittest/index_helpers.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/kff.o src/unittest/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/kmp.o src/unittest/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/locally_expand_graph.o src/unittest/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mem_accelerator.o src/unittest/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/min_cut_graph.o src/unittest/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/protobuf.o src/unittest/protobuf.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/snarl_distance_index.o src/unittest/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/snarl_seed_clusterer.o src/unittest/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/transcriptome.o src/unittest/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/chain_main.o src/subcommand/chain_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/clip_main.o src/subcommand/clip_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/haplotypes_main.o src/subcommand/haplotypes_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:147:31: required from here 147 | gs.stream_sort(gam_in, cout, index.get()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/any.h:38, from /usr/include/google/protobuf/generated_message_util.h:52, from /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4: /usr/include/google/protobuf/message_lite.h:381:7: note: declared here 381 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/options.o src/subcommand/options.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/config/allocator_config_jemalloc.o src/config/allocator_config_jemalloc.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/back_translating_alignment_emitter.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/clip.o obj/cluster.o obj/constructor.o obj/contracting_graph.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/explainer.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flat_file_back_translation.o obj/flow_sort.o obj/funnel.o obj/gbwt_extender.o obj/gbwt_helper.o obj/gbwtgraph_helper.o obj/gcsa_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/job_schedule.o obj/kff.o obj/kmer.o obj/kmp.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/mem_accelerator.o obj/memoizing_graph.o obj/memusage.o obj/minimizer_mapper.o obj/minimizer_mapper_from_chains.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/recombinator.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarl_distance_index.o obj/snarl_seed_clusterer.o obj/snarls.o obj/source_sink_overlay.o obj/sparse_union_find.o obj/splicing.o obj/split_strand_graph.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/subpath_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_clusters.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/zstdutil.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/back_translate.o obj/algorithms/chain_items.o obj/algorithms/component.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/find_gbwt.o obj/algorithms/find_gbwtgraph.o obj/algorithms/find_translation.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/intersect_path_offsets.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/locally_expand_graph.o obj/algorithms/merge.o obj/algorithms/min_cut_graph.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/pad_band.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/prune_to_connecting_graph.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_params_json.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gbz.o obj/io/register_loader_saver_gbzgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_gfa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o test/build_graph test/build_graph.cpp -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/aarch64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o bin/vg obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/back_translate.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chain_items.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/component_paths.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gbwt_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_helpers.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/kff.o obj/unittest/kmp.o obj/unittest/locally_expand_graph.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/mem_accelerator.o obj/unittest/min_cut_graph.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/protobuf.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/sequence_complexity.o obj/unittest/snarl_distance_index.o obj/unittest/snarl_seed_clusterer.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/transcriptome.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chain_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/clip_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/haplotypes_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/options.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o obj/config/allocator_config_jemalloc.o -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/aarch64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic -lpthread -lm make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' cp bin/vg debian/help/ PATH=$PATH:/build/reproducible-path/vg-1.59.0+ds/debian/help \ LD_PRELOAD= help2man \ --no-discard-stderr \ --no-info \ --help-option=help \ --version-option=version \ --name='tools for working with genome variation graphs' \ vg > debian/vg.1 make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build -- docs make -j12 "INSTALL=install --strip-program=true" docs make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now doxygen warning: Tag 'TCL_SUBST' at line 237 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 1001 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_TIMESTAMP' at line 1136 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'FORMULA_TRANSPARENT' at line 1417 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'LATEX_SOURCE_CODE' at line 1702 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'RTF_SOURCE_CODE' at line 1776 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOCBOOK_PROGRAMLISTING' at line 1874 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 2054 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 2067 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 2076 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTNAME' at line 2118 of file 'Doxyfile' has become obsolete. 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To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: tag INPUT: input source 'src/unittest/driver.cpp' does not exist warning: tag INPUT: input source 'src/unittest/driver.hpp' does not exist warning: tag INPUT: input source 'deps/libbdsg/src' does not exist warning: tag INPUT: input source 'deps/libbdsg/include/bdsg' does not exist warning: source 'src/unittest/driver.cpp' is not a readable file or directory... skipping. warning: source 'src/unittest/driver.hpp' is not a readable file or directory... skipping. warning: source 'deps/libbdsg/src' is not a readable file or directory... skipping. warning: source 'deps/libbdsg/include/bdsg' is not a readable file or directory... skipping. Adding custom extension mapping: 'proto' will be treated as language 'c++' Doxygen version used: 1.9.8 Notice: Output directory 'doc/doxygen' does not exist. I have created it for you. Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/src Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/src/algorithms Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/src/io Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/src/subcommand Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps Reading and parsing tag files Parsing files Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/aligner.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/aligner.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/aligner.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/aligner.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/alignment.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/alignment.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/alignment.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/alignment.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/annotation.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/annotation.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/augment.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/augment.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/augment.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/augment.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/back_translating_alignment_emitter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/back_translating_alignment_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/back_translating_alignment_emitter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/back_translating_alignment_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/banded_global_aligner.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/banded_global_aligner.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/banded_global_aligner.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/banded_global_aligner.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/benchmark.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/benchmark.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/benchmark.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/benchmark.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/build_index.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/build_index.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/build_index.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/build_index.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/cactus.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/cactus.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/cactus.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/cactus.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/cactus_snarl_finder.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/cactus_snarl_finder.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/cactus_snarl_finder.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/cactus_snarl_finder.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/chunker.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/chunker.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/chunker.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/chunker.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/clip.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/clip.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/clip.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/clip.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/cluster.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/cluster.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/cluster.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/cluster.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/colors.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/colors.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/constructor.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/constructor.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/constructor.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/constructor.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/contracting_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/contracting_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/contracting_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/contracting_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/convert.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/convert.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/crash.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/crash.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/crash.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/crash.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/dagified_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/dagified_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/dagified_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/dagified_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/deconstructor.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/deconstructor.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/deconstructor.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/deconstructor.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/deletion_aligner.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/deletion_aligner.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/deletion_aligner.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/deletion_aligner.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/dinucleotide_machine.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/dinucleotide_machine.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/dinucleotide_machine.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/dinucleotide_machine.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/dozeu_interface.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/dozeu_interface.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/dozeu_interface.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/dozeu_interface.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/dozeu_pinning_overlay.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/dozeu_pinning_overlay.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/dozeu_pinning_overlay.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/dozeu_pinning_overlay.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/endianness.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/endianness.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/entropy.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/entropy.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/entropy.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/entropy.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/explainer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/explainer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/explainer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/explainer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/extra_node_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/extra_node_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/extra_node_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/extra_node_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/feature_set.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/feature_set.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/feature_set.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/feature_set.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/filter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/filter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/filter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/filter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/flat_file_back_translation.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/flat_file_back_translation.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/flat_file_back_translation.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/flat_file_back_translation.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/flow_sort.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/flow_sort.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/flow_sort.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/flow_sort.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/funnel.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/funnel.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/funnel.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/funnel.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/gbwt_extender.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/gbwt_extender.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/gbwt_extender.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/gbwt_extender.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/gbwt_helper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/gbwt_helper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/gbwt_helper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/gbwt_helper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/gbwtgraph_helper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/gbwtgraph_helper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/gbwtgraph_helper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/gbwtgraph_helper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/gbzgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/gbzgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/gcsa_helper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/gcsa_helper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/gcsa_helper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/gcsa_helper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/genome_state.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/genome_state.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/genome_state.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/genome_state.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/genotypekit.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/genotypekit.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/genotypekit.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/genotypekit.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/genotyper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/genotyper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/genotyper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/genotyper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/gfa.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/gfa.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/gfa.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/gfa.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/gff_reader.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/gff_reader.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/gff_reader.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/gff_reader.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/graph_caller.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/graph_caller.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/graph_caller.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/graph_caller.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/graph_synchronizer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/graph_synchronizer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/graph_synchronizer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/graph_synchronizer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/handle.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/handle.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/haplotype_extracter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/haplotype_extracter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/haplotype_extracter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/haplotype_extracter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/haplotype_indexer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/haplotype_indexer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/haplotype_indexer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/haplotype_indexer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/haplotypes.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/haplotypes.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/haplotypes.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/haplotypes.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/hash_map.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/hash_map.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/hts_alignment_emitter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/hts_alignment_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/hts_alignment_emitter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/hts_alignment_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/identity_overlay.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/identity_overlay.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/identity_overlay.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/identity_overlay.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/incremental_subgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/incremental_subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/incremental_subgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/incremental_subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/index_registry.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/index_registry.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/index_registry.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/index_registry.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/indexed_vg.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/indexed_vg.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/indexed_vg.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/indexed_vg.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/integrated_snarl_finder.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/integrated_snarl_finder.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/integrated_snarl_finder.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/integrated_snarl_finder.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/job_schedule.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/job_schedule.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/job_schedule.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/job_schedule.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/kff.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/kff.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/kff.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/kff.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/kmer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/kmer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/kmer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/kmer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/kmp.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/kmp.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/kmp.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/kmp.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mapper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mapper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mapper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mapper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mcmc_caller.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mcmc_caller.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mcmc_caller.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mcmc_caller.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mcmc_genotyper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mcmc_genotyper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mcmc_genotyper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mcmc_genotyper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mem.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mem.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mem.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mem.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mem_accelerator.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mem_accelerator.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mem_accelerator.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mem_accelerator.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/memoizing_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/memoizing_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/memoizing_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/memoizing_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/memusage.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/memusage.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/memusage.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/memusage.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/minimizer_mapper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/minimizer_mapper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/minimizer_mapper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/minimizer_mapper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/minimizer_mapper_from_chains.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/minimizer_mapper_from_chains.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/msa_converter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/msa_converter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/msa_converter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/msa_converter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_emitter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_emitter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_mapper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_mapper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_mapper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_mapper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/name_mapper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/name_mapper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/name_mapper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/name_mapper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/nested_traversal_finder.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/nested_traversal_finder.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/nested_traversal_finder.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/nested_traversal_finder.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/nodeside.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/nodeside.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/nodetraversal.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/nodetraversal.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/null_masking_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/null_masking_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/null_masking_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/null_masking_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/option.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/option.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/option.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/option.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/packer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/packer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/packer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/packer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path_component_index.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path_component_index.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path_component_index.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path_component_index.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path_index.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path_index.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path_index.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path_index.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path_subgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path_subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path_subgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path_subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/phase_unfolder.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/phase_unfolder.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/phase_unfolder.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/phase_unfolder.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/phased_genome.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/phased_genome.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/phased_genome.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/phased_genome.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/pictographs.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/pictographs.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/position.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/position.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/position.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/position.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/preflight.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/preflight.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/preflight.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/preflight.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/progressive.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/progressive.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/progressive.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/progressive.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/qual_adj_xdrop_aligner.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/qual_adj_xdrop_aligner.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/rare_variant_simplifier.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/rare_variant_simplifier.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/rare_variant_simplifier.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/rare_variant_simplifier.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/readfilter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/readfilter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/readfilter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/readfilter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/recombinator.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/recombinator.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/recombinator.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/recombinator.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/region.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/region.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/region.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/region.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/region_expander.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/region_expander.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/region_expander.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/region_expander.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/reverse_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/reverse_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/reverse_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/reverse_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/sampler.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/sampler.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/sampler.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/sampler.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/scanner.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/scanner.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/scanner.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/scanner.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/sequence_complexity.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/sequence_complexity.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/small_bitset.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/small_bitset.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/small_snarl_simplifier.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/small_snarl_simplifier.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/small_snarl_simplifier.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/small_snarl_simplifier.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarl_caller.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarl_caller.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarl_caller.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarl_caller.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarl_distance_index.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarl_distance_index.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarl_distance_index.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarl_distance_index.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarl_seed_clusterer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarl_seed_clusterer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarl_seed_clusterer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarl_seed_clusterer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarls.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarls.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarls.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarls.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/source_sink_overlay.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/source_sink_overlay.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/source_sink_overlay.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/source_sink_overlay.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/sparse_union_find.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/sparse_union_find.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/sparse_union_find.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/sparse_union_find.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/splicing.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/splicing.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/splicing.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/splicing.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/split_strand_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/split_strand_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/split_strand_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/split_strand_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/ssw_aligner.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/ssw_aligner.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/ssw_aligner.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/ssw_aligner.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/statistics.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/statistics.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/statistics.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/statistics.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/stream_index.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/stream_index.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/stream_index.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/stream_index.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/stream_sorter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/stream_sorter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/stream_sorter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/stream_sorter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subgraph_overlay.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subgraph_overlay.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subgraph_overlay.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subgraph_overlay.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subpath_overlay.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subpath_overlay.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subpath_overlay.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subpath_overlay.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/surjecting_alignment_emitter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/surjecting_alignment_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/surjecting_alignment_emitter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/surjecting_alignment_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/surjector.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/surjector.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/surjector.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/surjector.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/swap_remove.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/swap_remove.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/transcriptome.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/transcriptome.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/transcriptome.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/transcriptome.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/translator.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/translator.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/translator.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/translator.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/traversal_clusters.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/traversal_clusters.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/traversal_clusters.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/traversal_clusters.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/traversal_finder.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/traversal_finder.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/traversal_finder.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/traversal_finder.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/traversal_support.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/traversal_support.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/traversal_support.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/traversal_support.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/tree_subgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/tree_subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/tree_subgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/tree_subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/types.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/types.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/utility.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/utility.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/utility.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/utility.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/variant_adder.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/variant_adder.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/variant_adder.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/variant_adder.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/variant_recall.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/variant_recall.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/variant_recall.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/variant_recall.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vcf_buffer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vcf_buffer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vcf_buffer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vcf_buffer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vectorizer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vectorizer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vectorizer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vectorizer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/version.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/version.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/version.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/version.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vg.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vg.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vg.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vg.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vg_set.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vg_set.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vg_set.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vg_set.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/viz.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/viz.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/viz.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/viz.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/wang_hash.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/wang_hash.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/watchdog.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/watchdog.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/watchdog.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/watchdog.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/xdrop_aligner.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/xdrop_aligner.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/zstdutil.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/zstdutil.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/zstdutil.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/zstdutil.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/a_star.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/a_star.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/alignment_path_offsets.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/alignment_path_offsets.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/alignment_path_offsets.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/alignment_path_offsets.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/approx_path_distance.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/approx_path_distance.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/approx_path_distance.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/approx_path_distance.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/back_translate.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/back_translate.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/back_translate.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/back_translate.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/chain_items.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/chain_items.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/chain_items.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/chain_items.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/component.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/component.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/component.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/component.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/count_covered.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/count_covered.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/coverage_depth.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/coverage_depth.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/coverage_depth.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/coverage_depth.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/dfs.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/dfs.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/dfs.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/dfs.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/disjoint_components.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/disjoint_components.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/disjoint_components.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/disjoint_components.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_head.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_head.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_head.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_head.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_tail.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_tail.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_tail.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_tail.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/expand_context.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/expand_context.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/expand_context.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/expand_context.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_connecting_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_connecting_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_connecting_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_connecting_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_containing_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_containing_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_containing_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_containing_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_extending_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_extending_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_extending_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_extending_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwt.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwt.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwt.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwt.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwtgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwtgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwtgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwtgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_translation.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_translation.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_translation.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_translation.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/gfa_to_handle.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/gfa_to_handle.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/gfa_to_handle.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/gfa_to_handle.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/id_sort.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/id_sort.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/id_sort.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/id_sort.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/intersect_path_offsets.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/intersect_path_offsets.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/intersect_path_offsets.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/intersect_path_offsets.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/jump_along_path.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/jump_along_path.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/jump_along_path.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/jump_along_path.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/k_widest_paths.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/k_widest_paths.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/k_widest_paths.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/k_widest_paths.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/kmer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/kmer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/kmer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/kmer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/locally_expand_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/locally_expand_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/locally_expand_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/locally_expand_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/merge.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/merge.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/merge.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/merge.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/min_cut_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/min_cut_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/min_cut_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/min_cut_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/nearest_offsets_in_paths.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/nearest_offsets_in_paths.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/nearest_offsets_in_paths.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/nearest_offsets_in_paths.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/next_pos_chars.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/next_pos_chars.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/next_pos_chars.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/next_pos_chars.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/normalize.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/normalize.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/normalize.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/normalize.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/pad_band.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/pad_band.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/pad_band.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/pad_band.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/path_string.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/path_string.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/path_string.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/path_string.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune_to_connecting_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune_to_connecting_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune_to_connecting_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune_to_connecting_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/ref_path_distance.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/ref_path_distance.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/ref_path_distance.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/ref_path_distance.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/shortest_cycle.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/shortest_cycle.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/shortest_cycle.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/shortest_cycle.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/simplify_siblings.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/simplify_siblings.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/simplify_siblings.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/simplify_siblings.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/sorted_id_ranges.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/sorted_id_ranges.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/sorted_id_ranges.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/sorted_id_ranges.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/subgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/subgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/three_edge_connected_components.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/three_edge_connected_components.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/three_edge_connected_components.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/three_edge_connected_components.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/walk.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/walk.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/walk.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/walk.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/converted_hash_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/converted_hash_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/json_stream_helper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/json_stream_helper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/load_proto_to_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/load_proto_to_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/load_proto_to_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/load_proto_to_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_libvg_io.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_libvg_io.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_libvg_io.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_libvg_io.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_params_json.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_params_json.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_params_json.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_params_json.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_distance_index.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_distance_index.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_distance_index.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_distance_index.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwt.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwt.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwt.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwt.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwtgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwtgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwtgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwtgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbz.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbz.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbz.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbz.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbzgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbzgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbzgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbzgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gcsa.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gcsa.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gcsa.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gcsa.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gfa.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gfa.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gfa.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gfa.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_hash_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_hash_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_hash_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_hash_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_lcp.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_lcp.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_lcp.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_lcp.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_minimizer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_minimizer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_minimizer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_minimizer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_packed_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_packed_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_packed_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_packed_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_r_index.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_r_index.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_r_index.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_r_index.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_snarl_manager.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_snarl_manager.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_snarl_manager.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_snarl_manager.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_vg.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_vg.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_vg.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_vg.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_xg.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_xg.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_xg.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_xg.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/save_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/save_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/add_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/add_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/align_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/align_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/annotate_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/annotate_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/augment_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/augment_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/autoindex_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/autoindex_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/benchmark_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/benchmark_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/call_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/call_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/chain_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/chain_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/chunk_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/chunk_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/circularize_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/circularize_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/clip_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/clip_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/cluster_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/cluster_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/combine_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/combine_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/concat_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/concat_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/construct_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/construct_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/convert_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/convert_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/deconstruct_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/deconstruct_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/depth_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/depth_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/dotplot_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/dotplot_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/explode_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/explode_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/filter_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/filter_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/find_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/find_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gamcompare_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gamcompare_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gampcompare_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gampcompare_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gamsort_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gamsort_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gbwt_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gbwt_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/genotype_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/genotype_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/giraffe_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/giraffe_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/haplotypes_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/haplotypes_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/help_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/help_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/ids_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/ids_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/index_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/index_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/inject_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/inject_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/join_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/join_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/kmers_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/kmers_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/map_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/map_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/mcmc_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/mcmc_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/minimizer_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/minimizer_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/mod_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/mod_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/mpmap_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/mpmap_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/msga_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/msga_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/options.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/options.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/options.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/options.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/pack_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/pack_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/paths_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/paths_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/prune_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/prune_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/rna_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/rna_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/sift_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/sift_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/sim_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/sim_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/simplify_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/simplify_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/snarls_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/snarls_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/sort_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/sort_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/stats_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/stats_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/subcommand.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/subcommand.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/subcommand.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/subcommand.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/surject_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/surject_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/test_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/test_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/trace_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/trace_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/translate_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/translate_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/validate_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/validate_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/vectorize_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/vectorize_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/version_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/version_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/view_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/view_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/viz_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/viz_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/xg/src/xg.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/xg/src/xg.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/xg/src/xg.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/xg/src/xg.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/append_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/append_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/apply_orientations.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/apply_orientations.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/are_equivalent.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/are_equivalent.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/copy_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/copy_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dfs.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dfs.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dijkstra.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dijkstra.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_tips.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_tips.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_acyclic.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_acyclic.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_metadata.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_metadata.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/reverse_complement.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/reverse_complement.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/serializable.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/serializable.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/topological_sort.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/topological_sort.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/types.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/types.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/buildable_snarl_decomposition.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/buildable_snarl_decomposition.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_metadata.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_metadata.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/named_node_back_translation.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/named_node_back_translation.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/path_metadata.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/path_metadata.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/snarl_decomposition.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/snarl_decomposition.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/types.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/types.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/util.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/util.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/bin2ascii.h... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/bin2ascii.h... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/alignment_io.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/alignment_io.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/blocked_gzip_input_stream.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/blocked_gzip_input_stream.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/blocked_gzip_output_stream.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/blocked_gzip_output_stream.hpp... Preprocessing /build/reproducibl/build/reproducible-path/vg-1.59.0+ds/src/qual_adj_xdrop_aligner.cpp:2: warning: the name 'qual_adj_xdrop_aliigner.cpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.59.0+ds/src/xdrop_aligner.cpp:2: warning: the name 'xdrop_aliigner.cpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_containing_graph.hpp:5: warning: the name 'extract_containing_graphs.hpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_extending_graph.hpp:5: warning: the name 'extract_extending_graphs.hpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp:2: warning: the name 'unchop.cpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/handle_graph.cpp:5: warning: the name 'handle_graphs.cpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/stream_multiplexer.hpp:5: warning: the name 'stream_multiplexer.chpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp:33: warning: Detected potential recursive class relation between class handlegraph::return_type_of and base class handlegraph::return_type_of< decltype(&std::remove_reference< Function >::type::operator())>! /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp:33: warning: Detected potential recursive class relation between class handlegraph::return_type_of and base class return_type_of< decltype(&std::remove_reference< Function >::type::operator())>! /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp:33: warning: Detected potential recursive class relation between class handlegraph::return_type_of and base class handlegraph::return_type_of< decltype(&std::remove_reference< Function >::type::operator())>! /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp:33: warning: Detected potential recursive class relation between class handlegraph::return_type_of and base class return_type_of< decltype(&std::remove_reference< Function >::type::operator())>! /build/reproducible-path/vg-1.59.0+ds/src/alignment.hpp:307: warning: no matching file member found for void vg::parse_bed_regions(std::istream &bedstream, const handlegraph::PathPositionHandleGraph *graph, vector< vg::Alignment > *out_alignments) Possible candidates: 'void parse_bed_regions(istream &bedstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)' at line 1901 of file /build/reproducible-path/vg-1.59.0+ds/src/alignment.cpp 'void parse_bed_regions(istream &bedstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)' at line 1910 of file /build/reproducible-path/vg-1.59.0+ds/src/alignment.cpp 'void parse_bed_regions(const string &bed_path, vector< Region > &out_regions, vector< string > *out_names)' at line 28 of file /build/reproducible-path/vg-1.59.0+ds/src/region.cpp /build/reproducible-path/vg-1.59.0+ds/src/alignment.hpp:310: warning: no matching file member found for void vg::parse_gff_regions(istream >fstream, const handlegraph::PathPositionHandleGraph *graph, vector< vg::Alignment > *out_alignments) Possible candidates: 'void parse_gff_regions(istream &gffstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)' at line 2179 of file /build/reproducible-path/vg-1.59.0+ds/src/alignment.cpp 'void parse_gff_regions(istream &gffstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)' at line 2188 of file /build/reproducible-path/vg-1.59.0+ds/src/alignment.cpp /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/registry.hpp:67: warning: no matching file member found for load_function_t vg::io::wrap_bare_loader(function< void *(istream &)> istream_loader) Possible candidates: 'auto wrap_bare_loader(function< void *(istream &)> istream_loader) -> load_function_t' at line 105 of file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp e-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/edit.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/edit.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/fdstream.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/fdstream.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/hfile_cppstream.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/hfile_cppstream.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/hfile_internal.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/hfile_internal.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/json2pb.h... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/json2pb.h... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/loader.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/loader.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/message_emitter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/message_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/protobuf_emitter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/protobuf_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/registry.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/registry.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/stream.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/stream.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/stream_multiplexer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/stream_multiplexer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/vpkg.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/vpkg.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Associating documentation with modules... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Computing module relations... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating file documentation... Generating docs for file deps/libhandlegraph/src/append_graph.cpp... Generating docs for file deps/libhandlegraph/src/apply_orientations.cpp... Generating docs for file deps/libhandlegraph/src/are_equivalent.cpp... Generating docs for file deps/libhandlegraph/src/chop.cpp... Generating docs for file deps/libhandlegraph/src/copy_graph.cpp... Generating docs for file deps/libhandlegraph/src/count_walks.cpp... Generating docs for file deps/libhandlegraph/src/dagify.cpp... Generating docs for file deps/libhandlegraph/src/deletable_handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/dijkstra.cpp... Generating docs for file deps/libhandlegraph/src/eades_algorithm.cpp... Generating docs for file deps/libhandlegraph/src/extend.cpp... Generating docs for file deps/libhandlegraph/src/find_shortest_paths.cpp... Generating docs for file deps/libhandlegraph/src/find_tips.cpp... Generating docs for file deps/libhandlegraph/src/handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/buildable_snarl_decomposition.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/iteratee.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/mutable_path_metadata.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/named_node_back_translation.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/path_metadata.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/serializable.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/snarl_decomposition.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/util.hpp... Generating docs for file deps/libhandlegraph/src/is_acyclic.cpp... Generating docs for file deps/libhandlegraph/src/is_single_stranded.cpp... Generating docs for file deps/libhandlegraph/src/mutable_handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/mutable_path_handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/mutable_path_metadata.cpp... Generating docs for file deps/libhandlegraph/src/path_handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/path_metadata.cpp... Generating docs for file deps/libhandlegraph/src/path_position_handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/ranked_handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/reverse_complement.cpp... Generating docs for file deps/libhandlegraph/src/serializable.cpp... Generating docs for file deps/libhandlegraph/src/snarl_decomposition.cpp... Generating docs for file deps/libhandlegraph/src/split_strands.cpp... Generating docs for file deps/libhandlegraph/src/strongly_connected_components.cpp... Generating docs for file deps/libhandlegraph/src/topological_sort.cpp... Generating docs for file deps/libhandlegraph/src/trivially_serializable.cpp... Generating docs for file deps/libhandlegraph/src/types.cpp... Generating docs for file deps/libhandlegraph/src/weakly_connected_components.cpp... Generating docs for file deps/libvgio/deps/vg.proto... Generating docs for file deps/libvgio/include/vg/io/alignment_emitter.hpp... Generating docs for file deps/libvgio/include/vg/io/alignment_io.hpp... Generating docs for file deps/libvgio/include/vg/io/basic_stream.hpp... Generating docs for file deps/libvgio/include/vg/io/blocked_gzip_input_stream.hpp... Generating docs for file deps/libvgio/include/vg/io/blocked_gzip_output_stream.hpp... Generating docs for file deps/libvgio/include/vg/io/edit.hpp... Generating docs for file deps/libvgio/include/vg/io/fdstream.hpp... Generating docs for file deps/libvgio/include/vg/io/gafkluge.hpp... Generating docs for file deps/libvgio/include/vg/io/hfile_cppstream.hpp... Generating docs for file deps/libvgio/include/vg/io/hfile_internal.hpp... Generating docs for file deps/libvgio/include/vg/io/json2pb.h... Generating docs for file deps/libvgio/include/vg/io/loader.hpp... Generating docs for file deps/libvgio/include/vg/io/message_emitter.hpp... Generating docs for file deps/libvgio/include/vg/io/message_iterator.hpp... Generating docs for file deps/libvgio/include/vg/io/protobuf_emitter.hpp... Generating docs for file deps/libvgio/include/vg/io/protobuf_iterator.hpp... Generating docs for file deps/libvgio/include/vg/io/registry.hpp... Generating docs for file deps/libvgio/include/vg/io/stream.hpp... Generating docs for file deps/libvgio/include/vg/io/stream_multiplexer.hpp... Generating docs for file deps/libvgio/include/vg/io/vpkg.hpp... Generating docs for file deps/libvgio/src/alignment_emitter.cpp... Generating docs for file deps/libvgio/src/alignment_io.cpp... Generating docs for file deps/libvgio/src/basic_stream.cpp... Generating docs for file deps/libvgio/src/bin2ascii.h... Generating docs for file deps/libvgio/src/blocked_gzip_input_stream.cpp... Generating docs for file deps/libvgio/src/blocked_gzip_output_stream.cpp... Generating docs for file deps/libvgio/src/edit.cpp... Generating docs for file deps/libvgio/src/hfile_cppstream.cpp... Generating docs for file deps/libvgio/src/json2pb.cpp... Generating docs for file deps/libvgio/src/message_emitter.cpp... Generating docs for file deps/libvgio/src/message_iterator.cpp... Generating docs for file deps/libvgio/src/registry.cpp... Generating docs for file deps/libvgio/src/stream.cpp... Generating docs for file deps/libvgio/src/stream_multiplexer.cpp... Generating docs for file deps/libvgio/src/vpkg.cpp... Generating docs for file deps/xg/src/xg.cpp... 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Generating docs for compound vg::path_mapping_t... Generating docs for compound vg::path_t... Generating docs for compound vg::PathBasedTraversalFinder... Generating docs for compound vg::PathBranch... Generating docs for compound vg::PathChunker... Generating docs for compound vg::PathComponentIndex... Generating docs for compound vg::PathIndex... Generating docs for compound vg::PathNode... Generating docs for compound vg::PathOrientedDistanceMeasurer... Generating docs for compound vg::PathRestrictedTraversalFinder... Generating docs for compound vg::Paths... Generating docs for compound vg::PathSubgraph... Generating docs for compound vg::PathSubgraphOverlay... Generating docs for compound vg::PathTraversalFinder... Generating docs for compound vg::PhasedGenome... Generating docs for nested compound vg::PhasedGenome::Haplotype... Generating docs for nested compound vg::PhasedGenome::HaplotypeNode... Generating docs for nested compound vg::PhasedGenome::iterator... Generating docs for compound vg::PhaseUnfolder... Generating docs for compound vg::Pictographs... Generating docs for compound vg::Pileup... Generating docs for compound vg::PoissonSupportSnarlCaller... Generating docs for nested compound vg::PoissonSupportSnarlCaller::PoissonCallInfo... Generating docs for compound vg::Position... Generating docs for compound vg::position_t... Generating docs for compound vg::PositionIDScanner... Generating docs for compound vg::ProblemDumpExplainer... Generating docs for compound vg::Progressive... Generating docs for compound vg::QualAdjAligner... Generating docs for compound vg::QualAdjXdropAligner... Generating docs for compound vg::Range... Generating docs for compound vg::RareVariantSimplifier... Generating docs for compound vg::RatioSupportSnarlCaller... Generating docs for compound vg::read_alignment_index_t... Generating docs for compound vg::ReadFilter... Generating docs for compound vg::ReadMasker... Generating docs for compound vg::ReadRestrictedTraversalFinder... Generating docs for compound vg::RebuildJob... Generating docs for compound vg::RebuildParameters... Generating docs for compound vg::Recombinator... Generating docs for nested compound vg::Recombinator::LocalHaplotype... Generating docs for nested compound vg::Recombinator::Parameters... Generating docs for nested compound vg::Recombinator::Statistics... Generating docs for compound vg::RecombinatorHaplotype... Generating docs for compound vg::Region... Generating docs for compound vg::RegionExpander... Generating docs for compound vg::ReplaceLocalHaplotypeCommand... Generating docs for compound vg::ReplaceSnarlHaplotypeCommand... Generating docs for compound vg::RepresentativeTraversalFinder... Generating docs for compound vg::ReverseGraph... Generating docs for compound vg::RewindPlanException... Generating docs for compound vg::Sampler... Generating docs for compound vg::SeqComplexity... Generating docs for compound vg::ShuffledPairs... Generating docs for nested compound vg::ShuffledPairs::iterator... Generating docs for compound vg::SimpleConsistencyCalculator... Generating docs for compound vg::SimpleTraversalSupportCalculator... Generating docs for compound vg::SizeLimitExceededException... Generating docs for compound vg::SmallBitset... Generating docs for compound vg::SmallSnarlSimplifi/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto:268: warning: Unsupported xml/html tag found /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto:268: warning: Unsupported xml/html tag found er... Generating docs for compound vg::Snarl... Generating docs for compound vg::SnarlCaller... Generating docs for nested compound vg::SnarlCaller::CallInfo... Generating docs for compound vg::SnarlDistanceIndexClusterer... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::Cluster... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::ClusterHead... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::ClusteringProblem... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::Seed... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::SeedCache... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild... Generating docs for compound vg::SnarlFinder... Generating docs for compound vg::SnarlGraph... Generating docs for compound vg::SnarlManager... Generating docs for nested compound vg::SnarlManager::SnarlRecord... Generating docs for compound vg::SnarlMinDistance... Generating docs for compound vg::SnarlOrientedDistanceMeasurer... Generating docs for compound vg::SnarlState... Generating docs for compound vg::SnarlTraversal... Generating docs for compound vg::SourceSinkOverlay... Generating docs for compound vg::SparseUnionFind... Generating docs for compound vg::SplicedHTSAlignmentEmitter... Generating docs for compound vg::SpliceRegion... Generating docs for compound vg::SpliceStats... Generating docs for compound vg::SSWAligner... Generating docs for compound vg::state_hash... Generating docs for compound vg::StrandSplitGraph... Generating docs for compound vg::StreamIndex... Generating docs for compound vg::StreamIndexBase... Generating docs for compound vg::StreamSorter... Generating docs for compound vg::string_hash_map... Generating docs for compound vg::string_hash_set... Generating docs for compound vg::SubgraphOverlay... Generating docs for compound vg::SubHandleGraph... Generating docs for compound vg::Subpath... Generating docs for compound vg::subpath_t... Generating docs for compound vg::SubpathOverlay... Generating docs for compound vg::SummaryStatistics... Generating docs for compound vg::Support... Generating docs for compound vg::SupportAugmentedGraph... Generating docs for compound vg::SupportBasedSnarlCaller... Generating docs for compound vg::SupportRestrictedTraversalFinder... Generating docs for compound vg::SurjectingAlignmentEmitter... Generating docs for compound vg::Surjector... Generating docs for compound vg::SwapHaplotypesCommand... Generating docs for compound vg::TargetValueSearch... Generating docs for compound vg::TipAnchoredMaxDistance... Generating docs for compound vg::Transcript... Generating docs for compound vg::Transcriptome... Generating docs for compound vg::TranscriptPath... Generating docs for compound vg::Translation... Generating docs for compound vg::Translator... Generating docs for compound vg::TraversalFinder... Generating docs for compound vg::TraversalSupportCalculator... Generating docs for compound vg::TraversalSupportFinder... Generating docs for compound vg::Tree... Generating docs for compound vg::TreeNode... Generating docs for compound vg::TreeSubgraph... Generating docs for compound vg::TrivialTraversalFinder... Generating docs for compound vg::truncated_normal_distribution... Generating docs for compound vg::TVSClusterer... Generating docs for compound vg::uniform_int_distribution... Generating docs for compound vg::uniform_real_distribution... Generating docs for compound vg::VariantAdder... Generating docs for compound vg::VcfBuffer... Generating docs for compound vg::VCFGenotyper... Generating docs for compound vg::VCFOutputCaller... Generating docs for compound vg::VcfRecordConverter... Generating docs for compound vg::VcfRecordFilter... Generating docs for compound vg::VCFTraversalFinder... Generating docs for compound vg::VectorView... Generating docs for nested compound vg::VectorView::const_iterator... Generating docs for compoun/build/reproducible-path/vg-1.59.0+ds/src/vg.hpp:881: warning: explicit link request to 'matches' could not be resolved /build/reproducible-path/vg-1.59.0+ds/src/vg.hpp:881: warning: explicit link request to 'mismatches' could not be resolved d vg::VectorViewInverse... Generating docs for compound vg::Version... Generating docs for compound vg::VG... Generating docs for nested compound vg::VG::Plan... Generating docs for compound vg::VGIndexes... Generating docs for compound vg::VGset... Generating docs for compound vg::Visit... Generating docs for compound vg::Viz... Generating docs for compound vg::wang_hash... Generating docs for compound vg::wang_hash< handle_t >... Generating docs for compound vg::wang_hash< handlegraph::net_handle_t >... Generating docs for compound vg::wang_hash< NodeSide >... Generating docs for compound vg::wang_hash< NodeTraversal >... Generating docs for compound vg::wang_hash< path_handle_t >... Generating docs for compound vg::wang_hash< std::pair< A, B > >... Generating docs for compound vg::wang_hash< T * >... Generating docs for compound vg::wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >... Generating docs for compound vg::Watchdog... Generating docs for nested compound vg::Watchdog::thread_state_t... Generating docs for compound vg::WFAAlignment... Generating docs for compound vg::WFAExtender... Generating docs for nested compound vg::WFAExtender::ErrorModel... Generating docs for nested compound vg::WFAExtender::ErrorModel::Event... Generating docs for compound vg::WFANode... Generating docs for compound vg::WFAPoint... Generating docs for compound vg::WFATree... Generating docs for nested compound vg::WFATree::ScoreProperties... Generating docs for compound vg::WideningPRNG... Generating docs for compound vg::WindowedVcfBuffer... Generating docs for compound vg::WrappingPositionScanner... Generating docs for compound vg::XdropAligner... Generating docs for namespace vg::algorithms Generating docs for compound vg::algorithms::Anchor... Generating docs for compound vg::algorithms::Edge... Generating docs for compound vg::algorithms::GFADuplicatePathError... Generating docs for compound vg::algorithms::GFAFormatError... Generating docs for compound vg::algorithms::GFAIDMapInfo... Generating docs for compound vg::algorithms::GFAParser... Generating docs for compound vg::algorithms::Graph... Generating docs for compound vg::algorithms::kmer_t... Generating docs for compound vg::algorithms::Node... Generating docs for compound vg::algorithms::TracedScore... Generating docs for compound vg::algorithms::walk_t... Generating docs for namespace vg::io Generating docs for compound vg::io::AlignmentEmitter... Generating docs for compound vg::io::BlockedGzipInputStream... Generating docs for compound vg::io::BlockedGzipOutputStream... Generating docs for compound vg::io::ConvertedHashGraph... Generating docs for compound vg::io::fdinbuf... Generating docs for compound vg::io::fdistream... Generating docs for compound vg::io::fdostream... Generating docs for compound vg::io::fdoutbuf... Generating docs for compound vg::io::GafAlignmentEmitter... Generating docs for compound vg::io::hFILE_cppstream... Generating docs for compound vg::io::JSONStreamHelper... Generating docs for compound vg::io::MessageEmitter... Generating docs for compound vg::io::MessageIterator... Generating docs for compound vg::io::NullAlignmentEmitter... Generating docs for compound vg::io::ProtobufEmitter... Generating docs for compound vg::io::ProtobufIterator... Generating docs for compound vg::io::Registry... Generating docs for nested compound vg::io::Registry::Tables... Generating docs for compound vg::io::streaminbuf... Generating docs for compound vg::io::streamistream... Generating docs for compound vg::io::StreamMultiplexer... Generating docs for compound vg::io::TSVAlignmentEmitter... Generating docs for compound vg::io::VGAlignmentEmitter... Generating docs for compound vg::io::VPKG... Generating docs for namespace vg::subcommand Generating docs for compound vg::subcommand::ArgSpec... Generating docs for compound vg::subcommand::BaseArgSpec... Generating docs for compound vg::subcommand::BaseOptionGroup... Generating docs for compound vg::subcommand::BaseValuation... Generating docs for compound vg::subcommand::FlagArgSpec../build/reproducible-path/vg-1.59.0+ds/src/banded_global_aligner.hpp:88: warning: Unsupported xml/html tag found . Generating docs for compound vg::subcommand::GroupedOptionGroup... Generating docs for compound vg::subcommand::OptionGroup... Generating docs for compound vg::subcommand::Preset... Generating docs for compound vg::subcommand::RangeArgSpec... Generating docs for compound vg::subcommand::Subcommand... Generating docs for compound vg::subcommand::TickChainLink... Generating docs for compound vg::subcommand::Valuation... Generating docs for compound vg::subcommand::ValueArgSpec... Generating docs for namespace vg::temp_file Generating docs for compound vg::temp_file::Handler... Generating docs for namespace xg Generating docs for compound xg::XG... Generating docs for compound xg::XGFormatError... Generating docs for compound xg::XGPath... Generating docs for namespace xg::temp_file Generating docs for compound xg::temp_file::Handler... Generating docs for namespace zstdutil Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating topic index... Generating module index... Generating module member index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Generating XML output... Generating XML output for class vg::AbstractReadSampler Generating XML output for class vg::Genotyper::Affinity Generating XML output for class vg::AliasGraph Generating XML output for class vg::Aligner Generating XML output for class vg::AlignerClient Generating XML output for class vg::Alignment Generating XML output for class vg::alignment_index_t Generating XML output for class vg::AlignmentChainModel Generating XML output for class vg::AlignmentChainModelVertex Generating XML output for class vg::io::AlignmentEmitter Generating XML output for class vg::AlignmentValidity Generating XML output for class vg::BandedGlobalAligner::AltTracebackStack Generating XML output for class vg::algorithms::Anchor Generating XML output for class vg::Annotation Generating XML output for class vg::AppendHaplotypeCommand Generating XML output for class vg::subcommand::ArgSpec Generating XML output for class vg::AugmentedGraph Generating XML output for class vg::BandedGlobalAligner::BABuilder Generating XML output for class vg::BackTranslatingAlignmentEmitter Generating XML output for class vg::BandedGlobalAligner::BAMatrix Generating XML output for class vg::BandedGlobalAligner Generating XML output for class vg::BaseAligner Generating XML output for class vg::subcommand::BaseArgSpec Generating XML output for class vg::BaseMapper Generating XML output for class vg::BaseOption Generating XML output for class vg::subcommand::BaseOptionGroup Generating XML output for class vg::BasePileup Generating XML output for class vg::subcommand::BaseValuation Generating XML output for class vg::BBEdgeHash Generating XML output for class vg::BenchmarkResult Generating XML output for class vg::BitString Generating XML output for class vg::BitStringTree Generating XML output for class vg::io::BlockedGzipInputStream Generating XML output for class vg::io::BlockedGzipOutputStream Generating XML output for class handlegraph::BoolReturningWrapper Generating XML output for class handlegraph::BoolReturningWrapper< Iteratee, false > Generating XML output for class handlegraph::BoolReturningWrapper< Iteratee, true > Generating XML output for class vg::BREAKPOINT Generating XML output for class handlegraph::BuildableSnarlDecomposition Generating XML output for class vg::CachedPackedTraversalSupportFinder Generating XML output for class vg::IndexedVG::CacheEntry Generating XML output for class vg::CactusSide Generating XML output for class vg::CactusSnarlFinder Generating XML output for class vg::SnarlCaller::CallInfo Generating XML output for class vg::NestedFlowCaller::CallRecord Generating XML outp/build/reproducible-path/vg-1.59.0+ds/src/filter.cpp:939: warning: Unsupported xml/html tag found ut for class vg::ChainIterator Generating XML output for class vg::SnarlDistanceIndexClusterer::Cluster Generating XML output for class vg::SnarlDistanceIndexClusterer::ClusterHead Generating XML output for class vg::SnarlDistanceIndexClusterer::ClusteringProblem Generating XML output for class vg::Colors Generating XML output for class compare_gaf Generating XML output for class vg::CompletedTranscriptPath Generating XML output for class vg::ComponentMinDistanceClusterer Generating XML output for class vg::Configurable Generating XML output for class vg::ConfigurableParser Generating XML output for class vg::Connection Generating XML output for class vg::connection_t Generating XML output for class vg::ConsistencyCalculator Generating XML output for class vg::VectorView::const_iterator Generating XML output for class vg::ConstructedChunk Generating XML output for class vg::Constructor Generating XML output for class vg::ContractingGraph Generating XML output for class vg::io::ConvertedHashGraph Generating XML output for class vg::count_back_inserter Generating XML output for class vg::Counts Generating XML output for class vg::DagifiedGraph Generating XML output for class vg::Deconstructor Generating XML output for class vg::BandedGlobalAligner::AltTracebackStack::Deflection Generating XML output for class handlegraph::DeletableHandleGraph Generating XML output for class vg::DeleteHaplotypeCommand Generating XML output for class vg::DeletionAligner Generating XML output for class vg::DiagramExplainer Generating XML output for class vg::DinucleotideMachine Generating XML output for class vg::discrete_distribution Generating XML output for class vg::DistanceHeuristic Generating XML output for class vg::DotDumpExplainer Generating XML output for class vg::DozeuInterface Generating XML output for class vg::DozeuPinningOverlay Generating XML output for class vg::MEMClusterer::DPScoreComparator Generating XML output for class vg::algorithms::Edge Generating XML output for class vg::Edge Generating XML output for class vg::EdgePileup Generating XML output for class vg::Edit Generating XML output for class vg::edit_t Generating XML output for class vg::EditedTranscriptPath Generating XML output for class vg::endianness Generating XML output for class vg::WFAExtender::ErrorModel Generating XML output for class vg::WFAExtender::ErrorModel::Event Generating XML output for class vg::ExhaustiveTraversalFinder Generating XML output for class vg::Exon Generating XML output for class handlegraph::ExpandingOverlayGraph Generating XML output for class vg::Explainer Generating XML output for class vg::ExtraNodeGraph Generating XML output for class vg::IncrementalSubgraph::FCmp Generating XML output for class vg::io::fdinbuf Generating XML output for class vg::io::fdistream Generating XML output for class vg::io::fdostream Generating XML output for class vg::io::fdoutbuf Generating XML output for class vg::FeatureSet::Feature Generating XML output for class vg::FeatureSet Generating XML output for class vg::Filter Generating XML output for class vg::Funnel::FilterPerformance Generating XML output for class vg::FixedGenotypePriorCalculator Generating XML output for class vg::subcommand::FlagArgSpec Generating XML output for class vg::FlatFileBackTranslation Generating XML output for class vg::FlowCaller Generating XML output for class vg::FlowSort Generating XML output for class vg::FlowTraversalFinder Generating XML output for class vg::FragmentLengthDistribution Generating XML output for class vg::FragmentLengthStatistics Generating XML output for class vg::Funnel Generating XML output for class vg::io::GafAlignmentEmitter Generating XML output for class GafFile Generating XML output for class vg::GAFOutputCaller Generating XML output for class gafkluge::GafRecord Generating XML output for class gafkluge::GafStep Generating XML output for class vg::GaplessExtender Generating XML output for class vg::GaplessExtension Generating XML output for class haplo::gbwt_thread_t Generating XML output for class GBWTConfig Generating XML output for class vg::GBWTHandler Generating XML output for class haplo::GBWTScoreProvider Generating XML output for class vg::GBWTTraversalFinder Generating XML output for class vg::GBZGraph Generating XML output for class vg::GenomeState Generating XML output for class vg::GenomeStateCommand Generating XML output for class vg::Genotype Generating XML output for class vg::GenotypeLikelihoodCalculator Generating XML output for class vg::GenotypePriorCalculator Generating XML output for class vg::Genotyper Generating XML output for class vg::algorithms::GFADuplicatePathError Generating XML output for class vg::algorithms::GFAFormatError Generating XML output for class vg::GFAHandleGraph Generating XML output for class vg::algorithms::GFAIDMapInfo Generating XML output for class vg::algorithms::GFAParser Generating XML output for class vg::GFFReader Generating XML output for class vg::GFFRecord Generating XML output for class GiraffeMainOptions Generating XML output for class vg::algorithms::Graph Generating XML output for class vg::Graph Generating XML output for class vg::DozeuInterface::graph_pos_s Generating XML output for class vg::GraphCaller Generating XML output for class GraphHandler Generating XML output for class vg::GraphSynchronizer Generating XML output for class greater_gaffile Generating XML output for class vg::GreedyMinDistanceClusterer Generating XML output for class vg::subcommand::GroupedOptionGroup Generating XML output for class vg::FlowSort::Growth Generating XML output for class vg::GSSWAligner Generating XML output for class handlegraph::handle_t Generating XML output for class handlegraph::HandleGraph Generating XML output for class vg::HandleGraphNodeSet Generating XML output for class vg::HandleGraphSnarlFinder Generating XML output for class vg::temp_file::Handler Generating XML output for class xg::temp_file::Handler Generating XML output for class haplo::haplo_DP Generating XML output for class haplo::haplo_DP_column Generating XML output for class haplo::haplo_DP_rectangle Generating XML output for class vg::PhasedGenome::Haplotype Generating XML output for class vg::HaplotypeIndexer Generating XML output for class vg::PhasedGenome::HaplotypeNode Generating XML output for class vg::HaplotypePartitioner Generating XML output for class vg::Haplotypes Generating XML output for class HaplotypesConfig Generating XML output for class std::hash< const vg::Snarl > Generating XML output for class std::hash< handlegraph::edge_t > Generating XML output for class std::hash< handlegraph::handle_t > Generating XML output for class std::hash< handlegraph::net_handle_t > Generating XML output for class std::hash< handlegraph::path_handle_t > Generating XML output for class std::hash< handlegraph::step_handle_t > Generating XML output for class std::hash< pair< A, B > > Generating XML output for class std::hash< std::tuple< TT... > > Generating XML output for class std::hash< vg::NodeSide > Generating XML output for class std::hash< vg::NodeTraversal > Generating XML output for class vg::Genotyper::hash_ambiguous_allele_set Generating XML output for class vg::hash_map Generating XML output for class vg::hash_map< K *, V > Generating XML output for class vg::Genotyper::hash_node_traversal Generating XML output for class vg::Genotyper::hash_oriented_edge Generating XML output for class vg::hash_set Generating XML output for class vg::hash_set< K * > Generating XML output for class haplo::hDP_gbwt_graph_accessor Generating XML output for class vg::Haplotypes::Header Generating XML output for class hFILE_backend Generating XML output for class vg::io::hFILE_cppstream Generating XML output for class vg::MEMClusterer::HitEdge Generating XML output for class vg::MEMClusterer::HitGraph Generating XML output for class vg::MEMClusterer::HitNode Generating XML output for class vg::HTSAlignmentEmitter Generating XML output for class vg::HTSWriter Generating XML output for class vg::IdentityOverlay Generating XML output for class vg::IDScanner Generating XML output for class vg::IncrementalSubgraph Generating XML output for class vg::IncrementIter Generating XML output for class vg::IndexedVG Generating XML output for class vg::IndexFile Generating XML output for class vg::IndexingParameters Generating XML output for class vg::IndexingPlan Generating XML output for class vg::IndexRecipe Generating XML output for class vg::IndexRegistry Generating XML output for class vg::InsertHaplotypeCommand Generating XML output for class vg::InsufficientInputException Generating XML output for class haplo::int_itvl_t Generating XML output for class vg::IntegratedSnarlFinder Generating XML output for class vg::is_instantiation_of Generating XML output for class vg::is_instantiation_of< Predicate< PredicateArgs... >, Predicate > Generating XML output for class vg::Funnel::Item Generating XML output for class handlegraph::PathForEachSocket::iterator Generating XML output for class vg::PhasedGenome::iterator Generating XML output for class vg::ShuffledPairs::iterator Generating XML output for class std::iterator_traits< vg::PhasedGenome::iterator > Generating XML output for class vg::IncrementalSubgraph::IterFCmp Generating XML output for class j2pb_error Generating XML output for class job_type Generating XML output for class vg::JobSchedule Generating XML output for class vg::JoinedSpliceGraph Generating XML output for class json_autoptr Generating XML output for class vg::io::JSONStreamHelper Generating XML output for class vg::kff_recoding_t Generating XML output for class vg::algorithms::kmer_t Generating XML output for class vg::kmer_t Generating XML output for class vg::KmerMatch Generating XML output for class vg::KmerPosition Generating XML output for class vg::LazyRNG Generating XML output for class vg::LegacyCaller Generating XML output for class haplo::linear_haplo_structure Generating XML output for class haplo::LinearScoreProvider Generating XML output for class haplo::linear_haplo_structure::linearUnrepresentable Generating XML output for class vg::Recombinator::LocalHaplotype Generating XML output for class vg::LocationSupport Generating XML output for class vg::GraphSynchronizer::Lock Generating XML output for class vg::Locus Generating XML output for class vg::Mapper Generating XML output for class vg::Mapping Generating XML output for class vg::mapping_t Generating XML output for class vg::MappingHash Generating XML output for class MappingRun Generating XML output for class vg::NGSSimulator::MarkovDistribution Generating XML output for class vg::MatchPos Generating XML output for class vg::MaximalExactMatch Generating XML output for class vg::MCMCCaller Generating XML output for class vg::MCMCGenotyper Generating XML output for class vg::MEMAccelerator Generating XML output for class vg::MEMChainModel Generating XML output for class vg::MEMChainModelVertex Generating XML output for class vg::MEMClusterer Generating XML output for class vg::MemoizingGraph Generating XML output for class vg::IntegratedSnarlFinder::MergedAdjacencyGraph Generating XML output for class vg::io::MessageEmitter Generating XML output for class vg::io::MessageIterator Generating XML output for class vg::MinDistanceClusterer Generating XML output for class vg::MinimizerMapper::Minimizer Generating XML output for class vg::MinimizerMapper Generating XML output for class vg::MIPayload Generating XML output for class vg::MIPayloadValues Generating XML output for class vg::MSAConverter Generating XML output for class vg::multipath_alignment_t Generating XML output for class vg::MultipathAlignment Generating XML output for class vg::MultipathAlignmentEmitter Generating XML output for class vg::MultipathAlignmentGraph Generating XML output for class vg::MultipathMapper Generating XML output for class vg::MultipathProblem Generating XML output for class handlegraph::MutableHandleGraph Generating XML output for class handlegraph::MutablePathDeletableHandleGraph Generating XML output for class handlegraph::MutablePathHandleGraph Generating XML output for class handlegraph::MutablePathMetadata Generating XML output for class handlegraph::MutablePathMutableHandleGraph Generating XML o/build/reproducible-path/vg-1.59.0+ds/src/packer.hpp:61: warning: Unsupported xml/html tag found utput for class handlegraph::NamedNodeBackTranslation Generating XML output for class vg::NameMapper Generating XML output for class vg::NestedCachedPackedTraversalSupportFinder Generating XML output for class vg::NestedFlowCaller Generating XML output for class vg::NestedTraversalFinder Generating XML output for class vg::Deconstructor::NestingInfo Generating XML output for class handlegraph::net_handle_t Generating XML output for class vg::NetGraph Generating XML output for class vg::NGSSimulator Generating XML output for class vg::NoAlignmentInBandException Generating XML output for class vg::algorithms::Node Generating XML output for class vg::Node Generating XML output for class vg::NodePileup Generating XML output for class vg::NodeSide Generating XML output for class vg::NodeTraversal Generating XML output for class vg::normal_distribution Generating XML output for class vg::io::NullAlignmentEmitter Generating XML output for class vg::NullClusterer Generating XML output for class vg::NullMaskingGraph Generating XML output for class handlegraph::number_bool_packing Generating XML output for class vg::Option Generating XML output for class vg::Option< vector< Item >, Parser > Generating XML output for class vg::subcommand::OptionGroup Generating XML output for class vg::OptionInterface Generating XML output for class vg::OptionValueParser Generating XML output for class vg::OptionValueParser< vector< Item > > Generating XML output for class vg::DozeuInterface::OrderedGraph Generating XML output for class vg::OrientedDistanceClusterer Generating XML output for class vg::OrientedDistanceMeasurer Generating XML output for class vg::PackedTraversalSupportFinder Generating XML output for class vg::Packer Generating XML output for class vg::Packers Generating XML output for class vg::Funnel::PaintableSpace Generating XML output for class vg::pair_hash_map Generating XML output for class vg::pair_hash_set Generating XML output for class vg::PairedEndMapper Generating XML output for class vg::ParallelKFFReader Generating XML output for class vg::HaplotypePartitioner::Parameters Generating XML output for class vg::Recombinator::Parameters Generating XML output for class vg::ParentGenotypeInfo Generating XML output for class vg::Path Generating XML output for class handlegraph::path_handle_t Generating XML output for class vg::path_mapping_t Generating XML output for class vg::path_t Generating XML output for class vg::PathBasedTraversalFinder Generating XML output for class vg::PathBranch Generating XML output for class vg::PathChunker Generating XML output for class vg::PathComponentIndex Generating XML output for class handlegraph::PathForEachSocket Generating XML output for class handlegraph::PathHandleGraph Generating XML output for class vg::PathIndex Generating XML output for class vg::MatchPos::PathList Generating XML output for class handlegraph::PathMetadata Generating XML output for class vg::PathNode Generating XML output for class vg::PathOrientedDistanceMeasurer Generating XML output for class handlegraph::PathPositionHandleGraph Generating XML output for class vg::PathRestrictedTraversalFinder Generating XML output for class vg::Paths Generating XML output for class vg::PathSubgraph Generating XML output for class vg::PathSubgraphOverlay Generating XML output for class vg::PathTraversalFinder Generating XML output for class vg::PhasedGenome Generating XML output for class vg::PhaseUnfolder Generating XML output for class vg::Pictographs Generating XML output for class vg::Pileup Generating XML output for class vg::VG::Plan Generating XML output for class vg::PoissonSupportSnarlCaller::PoissonCallInfo Generating XML output for class vg::PoissonSupportSnarlCaller Generating XML output for class vg::Position Generating XML output for class vg::position_t Generating XML output for class vg::PositionIDScanner Generating XML output for class vg::subcommand::Preset Generating XML output for class vg::ProblemDumpExplainer Generating XML output for class vg::Progressive Generating XML output for class vg::io::ProtobufEm/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto:268: warning: Unsupported xml/html tag found /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto:268: warning: Unsupported xml/html tag found itter Generating XML output for class vg::io::ProtobufIterator Generating XML output for class PruningParameters Generating XML output for class vg::QualAdjAligner Generating XML output for class vg::QualAdjXdropAligner Generating XML output for class vg::Range Generating XML output for class vg::subcommand::RangeArgSpec Generating XML output for class handlegraph::RankedHandleGraph Generating XML output for class vg::RareVariantSimplifier Generating XML output for class vg::RatioSupportSnarlCaller Generating XML output for class vg::read_alignment_index_t Generating XML output for class vg::ReadFilter Generating XML output for class vg::ReadMasker Generating XML output for class vg::ReadRestrictedTraversalFinder Generating XML output for class vg::RebuildJob Generating XML output for class vg::RebuildParameters Generating XML output for class vg::Recombinator Generating XML output for class vg::RecombinatorHaplotype Generating XML output for class ReferenceInterval Generating XML output for class vg::Region Generating XML output for class vg::RegionExpander Generating XML output for class vg::io::Registry Generating XML output for class vg::ReplaceLocalHaplotypeCommand Generating XML output for class vg::ReplaceSnarlHaplotypeCommand Generating XML output for class vg::RepresentativeTraversalFinder Generating XML output for class handlegraph::return_type_of Generating XML output for class handlegraph::return_type_of< Returns(*)(Args...)> Generating XML output for class handlegraph::return_type_of< Returns(Owner::*)(Args...) const > Generating XML output for class handlegraph::return_type_of< Returns(Owner::*)(Args...)> Generating XML output for class vg::ReverseGraph Generating XML output for class vg::RewindPlanException Generating XML output for class haplo::haploMath::RRMemo Generating XML output for class vg::Sampler Generating XML output for class vg::WFATree::ScoreProperties Generating XML output for class haplo::ScoreProvider Generating XML output for class ScoringOptions Generating XML output for class vg::SnarlDistanceIndexClusterer::Seed Generating XML output for class vg::SnarlDistanceIndexClusterer::SeedCache Generating XML output for class vg::SeqComplexity Generating XML output for class handlegraph::Serializable Generating XML output for class handlegraph::SerializableHandleGraph Generating XML output for class vg::ShuffledPairs Generating XML output for class vg::SimpleConsistencyCalculator Generating XML output for class vg::SimpleTraversalSupportCalculator Generating XML output for class vg::SizeLimitExceededException Generating XML output for class vg::SmallBitset Generating XML output for class vg::SmallSnarlSimplifier Generating XML output for class vg::Snarl Generating XML output for class vg::NestedCachedPackedTraversalSupportFinder::snarl_less Generating XML output for class vg::SnarlCaller Generating XML output for class handlegraph::SnarlDecomposition Generating XML output for class vg::SnarlDistanceIndexClusterer Generating XML output for class vg::SnarlFinder Generating XML output for class vg::SnarlGraph Generating XML output for class vg::SnarlManager Generating XML output for class vg::SnarlMinDistance Generating XML output for class vg::SnarlOrientedDistanceMeasurer Generating XML output for class vg::SnarlManager::SnarlRecord Generating XML output for class vg::SnarlState Generating XML output for class vg::SnarlTraversal Generating XML output for class vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild Generating XML output for class vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem Generating XML output for class haplo::linear_haplo_structure::SNVvector Generating XML output for class vg::SourceSinkOverlay Generating XML output for class vg::SparseUnionFind Generating XML output for class vg::SplicedHTSAlignmentEmitter Generating XML output for class vg::SpliceRegion Generating XML output for class vg::SpliceStats Generating XML output for class vg::SSWAligner Generating XML output for class vg::Funnel::Stage Generating XML output for class vg::state_hash Generati/build/reproducible-path/vg-1.59.0+ds/src/vg.hpp:881: warning: explicit link request to 'matches' could not be resolved /build/reproducible-path/vg-1.59.0+ds/src/vg.hpp:881: warning: explicit link request to 'mismatches' could not be resolved ng XML output for class vg::Recombinator::Statistics Generating XML output for class handlegraph::step_handle_t Generating XML output for class vg::StrandSplitGraph Generating XML output for class vg::io::streaminbuf Generating XML output for class vg::StreamIndex Generating XML output for class vg::StreamIndexBase Generating XML output for class vg::io::streamistream Generating XML output for class vg::io::StreamMultiplexer Generating XML output for class vg::StreamSorter Generating XML output for class vg::string_hash_map Generating XML output for class vg::string_hash_set Generating XML output for class vg::HaplotypePartitioner::Subchain Generating XML output for class vg::Haplotypes::Subchain Generating XML output for class vg::subcommand::Subcommand Generating XML output for class vg::SubgraphOverlay Generating XML output for class handlegraph::algorithms::SubHandleGraph Generating XML output for class vg::SubHandleGraph Generating XML output for class vg::Subpath Generating XML output for class vg::subpath_t Generating XML output for class vg::SubpathOverlay Generating XML output for class vg::SummaryStatistics Generating XML output for class vg::Support Generating XML output for class vg::SupportAugmentedGraph Generating XML output for class vg::SupportBasedSnarlCaller Generating XML output for class vg::SupportRestrictedTraversalFinder Generating XML output for class vg::SurjectingAlignmentEmitter Generating XML output for class vg::Surjector Generating XML output for class vg::SwapHaplotypesCommand Generating XML output for class vg::io::Registry::Tables Generating XML output for class vg::TargetValueSearch Generating XML output for class vg::Watchdog::thread_state_t Generating XML output for class vg::subcommand::TickChainLink Generating XML output for class vg::TipAnchoredMaxDistance Generating XML output for class vg::Haplotypes::TopLevelChain Generating XML output for class vg::algorithms::TracedScore Generating XML output for class vg::Transcript Generating XML output for class vg::Transcriptome Generating XML output for class vg::TranscriptPath Generating XML output for class vg::Translation Generating XML output for class vg::Translator Generating XML output for class vg::TraversalFinder Generating XML output for class vg::TraversalSupportCalculator Generating XML output for class vg::TraversalSupportFinder Generating XML output for class vg::Tree Generating XML output for class vg::BitStringTree::TreeNode Generating XML output for class vg::TreeNode Generating XML output for class vg::TreeSubgraph Generating XML output for class handlegraph::TriviallySerializable Generating XML output for class vg::TrivialTraversalFinder Generating XML output for class vg::truncated_normal_distribution Generating XML output for class vg::io::TSVAlignmentEmitter Generating XML output for class vg::TVSClusterer Generating XML output for class vg::uniform_int_distribution Generating XML output for class vg::uniform_real_distribution Generating XML output for class vg::subcommand::Valuation Generating XML output for class vg::subcommand::ValueArgSpec Generating XML output for class vg::VariantAdder Generating XML output for class vg::VcfBuffer Generating XML output for class vg::VCFGenotyper Generating XML output for class vg::VCFOutputCaller Generating XML output for class vg::VcfRecordConverter Generating XML output for class vg::VcfRecordFilter Generating XML output for class vg::VCFTraversalFinder Generating XML output for class handlegraph::VectorizableHandleGraph Generating XML output for class Vectorizer Generating XML output for class vg::VectorView Generating XML output for class vg::VectorViewInverse Generating XML output for class vg::Version Generating XML output for class vg::VG Generating XML output for class vg::io::VGAlignmentEmitter Generating XML output for class vg::VGIndexes Generating XML output for class vg::VGset Generating XML output for class vg::Visit Generating XML output for class vg::Viz Generating XML output for class vg::io::VPKG Generating XML output for class vg::algorithms::walk_t Generating/build/reproducible-path/vg-1.59.0+ds/src/hts_alignment_emitter.hpp:68: warning: Found unknown command '@SQ' XML output for class vg::wang_hash Generating XML output for class vg::wang_hash< handle_t > Generating XML output for class vg::wang_hash< handlegraph::net_handle_t > Generating XML output for class vg::wang_hash< NodeSide > Generating XML output for class vg::wang_hash< NodeTraversal > Generating XML output for class vg::wang_hash< path_handle_t > Generating XML output for class vg::wang_hash< std::pair< A, B > > Generating XML output for class vg::wang_hash< T * > Generating XML output for class vg::wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type > Generating XML output for class vg::Watchdog Generating XML output for class vg::FlowSort::WeightedGraph Generating XML output for class vg::WFAAlignment Generating XML output for class vg::WFAExtender Generating XML output for class vg::WFANode Generating XML output for class vg::WFAPoint Generating XML output for class vg::WFATree Generating XML output for class vg::WideningPRNG Generating XML output for class vg::WindowedVcfBuffer Generating XML output for class vg::WrappingPositionScanner Generating XML output for class vg::XdropAligner Generating XML output for class xg::XG Generating XML output for class xg::XGFormatError Generating XML output for class xg::XGPath Generating XML output for namespace @515 Generating XML output for namespace bdsg Generating XML output for namespace gafkluge Generating XML output for namespace google Generating XML output for namespace google::protobuf Generating XML output for namespace google::protobuf::io Generating XML output for namespace handlegraph Generating XML output for namespace handlegraph::algorithms Generating XML output for namespace handlegraph::algorithms::internal Generating XML output for namespace haplo Generating XML output for namespace haplo::haploMath Generating XML output for namespace sdsl Generating XML output for namespace spp Generating XML output for namespace std Generating XML output for namespace std::@94 Generating XML output for namespace structures Generating XML output for namespace vg Generating XML output for namespace vg::algorithms Generating XML output for namespace vg::io Generating XML output for namespace vg::subcommand Generating XML output for namespace vg::temp_file Generating XML output for namespace xg Generating XML output for namespace xg::temp_file Generating XML output for namespace zstdutil Generating XML output for file append_graph.cpp Generating XML output for file apply_orientations.cpp Generating XML output for file are_equivalent.cpp Generating XML output for file chop.cpp Generating XML output for file copy_graph.cpp Generating XML output for file count_walks.cpp Generating XML output for file dagify.cpp Generating XML output for file deletable_handle_graph.cpp Generating XML output for file dijkstra.cpp Generating XML output for file eades_algorithm.cpp Generating XML output for file extend.cpp Generating XML output for file find_shortest_paths.cpp Generating XML output for file find_tips.cpp Generating XML output for file handle_graph.cpp Generating XML output for file buildable_snarl_decomposition.hpp Generating XML output for file deletable_handle_graph.hpp Generating XML output for file expanding_overlay_graph.hpp Generating XML output for file handle_graph.hpp Generating XML output for file iteratee.hpp Generating XML output for file mutable_handle_graph.hpp Generating XML output for file mutable_path_deletable_handle_graph.hpp Generating XML output for file mutable_path_handle_graph.hpp Generating XML output for file mutable_path_metadata.hpp Generating XML output for file mutable_path_mutable_handle_graph.hpp Generating XML output for file named_node_back_translation.hpp Generating XML output for file path_handle_graph.hpp Generating XML output for file path_metadata.hpp Generating XML output for file path_position_handle_graph.hpp Generating XML output for file serializable.hpp Generating XML output for file serializable_handle_graph.hpp Generating XML output for file snarl_decomposition.hpp Generating XML output for file trivially_serializable.hpp Generating XML output for file util.hpp Generating XML output for file is_acyclic.cpp Generating XML output for file is_single_stranded.cpp Generating XML output for file mutable_handle_graph.cpp Generating XML output for file mutable_path_handle_graph.cpp Generating XML output for file mutable_path_metadata.cpp Generating XML output for file path_handle_graph.cpp Generating XML output for file path_metadata.cpp Generating XML output for file path_position_handle_graph.cpp Generating XML output for file ranked_handle_graph.cpp Generating XML output for file reverse_complement.cpp Generating XML output for file serializable.cpp Generating XML output for file snarl_decomposition.cpp Generating XML output for file split_strands.cpp Generating XML output for file strongly_connected_components.cpp Generating XML output for file topological_sort.cpp Generating XML output for file trivially_serializable.cpp Generating XML output for file types.cpp Generating XML output for file weakly_connected_components.cpp Generating XML output for file vg.proto Generating XML output for file alignment_emitter.hpp Generating XML output for file alignment_io.hpp Generating XML output for file basic_stream.hpp Generating XML output for file blocked_gzip_input_stream.hpp Generating XML output for file blocked_gzip_output_stream.hpp Generating XML output for file edit.hpp Generating XML output for file fdstream.hpp Generating XML output for file gafkluge.hpp Generating XML output for file hfile_cppstream.hpp Generating XML output for file hfile_internal.hpp Generating XML output for file json2pb.h Generating XML output for file loader.hpp Generating XML output for file message_emitter.hpp Generating XML output for file message_iterator.hpp Generating XML output for file protobuf_emitter.hpp Generating XML output for file protobuf_iterator.hpp Generating XML output for file registry.hpp Generating XML output for file stream.hpp Generating XML output for file stream_multiplexer.hpp Generating XML output for file vpkg.hpp Generating XML output for file alignment_emitter.cpp Generating XML output for file alignment_io.cpp Generating XML output for file basic_stream.cpp Generating XML output for file bin2ascii.h Generating XML output for file blocked_gzip_input_stream.cpp Generating XML output for file blocked_gzip_output_stream.cpp Generating XML output for file edit.cpp Generating XML output for file hfile_cppstream.cpp Generating XML output for file json2pb.cpp Generating XML output for file message_emitter.cpp Generating XML output for file message_iterator.cpp Generating XML output for file registry.cpp Generating XML output for file stream.cpp Generating XML output for file stream_multiplexer.cpp Generating XML output for file vpkg.cpp Generating XML output for file xg.cpp Generating XML output for file xg.hpp Generating XML output for file a_star.hpp Generating XML output for file alignment_path_offsets.cpp Generating XML output for file alignment_path_offsets.hpp Generating XML output for file approx_path_distance.cpp Generating XML output for file approx_path_distance.hpp Generating XML output for file back_translate.cpp Generating XML output for file back_translate.hpp Generating XML output for file chain_items.cpp Generating XML output for file chain_items.hpp Generating XML output for file component.cpp Generating XML output for file component.hpp Generating XML output for file count_covered.hpp Generating XML output for file coverage_depth.cpp Generating XML output for file coverage_depth.hpp Generating XML output for file dfs.cpp Generating XML output for file dfs.cpp Generating XML output for file dfs.hpp Generating XML output for file disjoint_components.cpp Generating XML output for file disjoint_components.hpp Generating XML output for file distance_to_head.cpp Generating XML output for file distance_to_head.hpp Generating XML output for file distance_to_tail.cpp Generating XML output for file distance_to_tail.hpp Generating XML output for file expand_context.cpp Generating XML output for file expand_context.hpp Generating XML output for file extract_connecting_graph.cpp Generating XML output for file extract_connecting_graph.hpp Generating XML output for file extract_containing_graph.cpp Generating XML output for file extract_containing_graph.hpp Generating XML output for file extract_extending_graph.cpp Generating XML output for file extract_extending_graph.hpp Generating XML output for file find_gbwt.cpp Generating XML output for file find_gbwt.hpp Generating XML output for file find_gbwtgraph.cpp Generating XML output for file find_gbwtgraph.hpp Generating XML output for file find_translation.cpp Generating XML output for file find_translation.hpp Generating XML output for file gfa_to_handle.cpp Generating XML output for file gfa_to_handle.hpp Generating XML output for file id_sort.cpp Generating XML output for file id_sort.hpp Generating XML output for file intersect_path_offsets.cpp Generating XML output for file intersect_path_offsets.hpp Generating XML output for file jump_along_path.cpp Generating XML output for file jump_along_path.hpp Generating XML output for file k_widest_paths.cpp Generating XML output for file k_widest_paths.hpp Generating XML output for file locally_expand_graph.cpp Generating XML output for file locally_expand_graph.hpp Generating XML output for file merge.cpp Generating XML output for file merge.hpp Generating XML output for file min_cut_graph.cpp Generating XML output for file min_cut_graph.hpp Generating XML output for file nearest_offsets_in_paths.cpp Generating XML output for file nearest_offsets_in_paths.hpp Generating XML output for file next_pos_chars.cpp Generating XML output for file next_pos_chars.hpp Generating XML output for file normalize.cpp Generating XML output for file normalize.hpp Generating XML output for file pad_band.cpp Generating XML output for file pad_band.hpp Generating XML output for file path_string.cpp Generating XML output for file path_string.hpp Generating XML output for file prune.cpp Generating XML output for file prune.hpp Generating XML output for file prune_to_connecting_graph.cpp Generating XML output for file prune_to_connecting_graph.hpp Generating XML output for file ref_path_distance.cpp Generating XML output for file ref_path_distance.hpp Generating XML output for file shortest_cycle.cpp Generating XML output for file shortest_cycle.hpp Generating XML output for file simplify_siblings.cpp Generating XML output for file simplify_siblings.hpp Generating XML output for file sorted_id_ranges.cpp Generating XML output for file sorted_id_ranges.hpp Generating XML output for file three_edge_connected_components.cpp Generating XML output for file three_edge_connected_components.hpp Generating XML output for file walk.cpp Generating XML output for file walk.hpp Generating XML output for file aligner.cpp Generating XML output for file aligner.hpp Generating XML output for file alignment.cpp Generating XML output for file alignment.hpp Generating XML output for file annotation.hpp Generating XML output for file augment.cpp Generating XML output for file augment.hpp Generating XML output for file back_translating_alignment_emitter.cpp Generating XML output for file back_translating_alignment_emitter.hpp Generating XML output for file banded_global_aligner.cpp Generating XML output for file banded_global_aligner.hpp Generating XML output for file benchmark.cpp Generating XML output for file benchmark.hpp Generating XML output for file build_index.cpp Generating XML output for file build_index.hpp Generating XML output for file cactus.cpp Generating XML output for file cactus.hpp Generating XML output for file cactus_snarl_finder.cpp Generating XML output for file cactus_snarl_finder.hpp Generating XML output for file chunker.cpp Generating XML output for file chunker.hpp Generating XML output for file clip.cpp Generating XML output for file clip.hpp Generating XML output for file cluster.cpp Generating XML output for file cluster.hpp Generating XML output for file colors.hpp Generating XML output for file constructor.cpp Generating XML output for file constructor.hpp Generating XML output for file contracting_graph.cpp Generating XML output for file contracting_graph.hpp Generating XML output for file convert.hpp Generating XML output for file crash.cpp Generating XML output for file crash.hpp Generating XML output for file dagified_graph.cpp Generating XML output for file dagified_graph.hpp Generating XML output for file deconstructor.cpp Generating XML output for file deconstructor.hpp Generating XML output for file deletion_aligner.cpp Generating XML output for file deletion_aligner.hpp Generating XML output for file dinucleotide_machine.cpp Generating XML output for file dinucleotide_machine.hpp Generating XML output for file dozeu_interface.cpp Generating XML output for file dozeu_interface.hpp Generating XML output for file dozeu_pinning_overlay.cpp Generating XML output for file dozeu_pinning_overlay.hpp Generating XML output for file endianness.hpp Generating XML output for file entropy.cpp Generating XML output for file entropy.hpp Generating XML output for file explainer.cpp Generating XML output for file explainer.hpp Generating XML output for file extra_node_graph.cpp Generating XML output for file extra_node_graph.hpp Generating XML output for file feature_set.cpp Generating XML output for file feature_set.hpp Generating XML output for file filter.cpp Generating XML output for file filter.hpp Generating XML output for file flat_file_back_translation.cpp Generating XML output for file flat_file_back_translation.hpp Generating XML output for file flow_sort.cpp Generating XML output for file flow_sort.hpp Generating XML output for file funnel.cpp Generating XML output for file funnel.hpp Generating XML output for file gbwt_extender.cpp Generating XML output for file gbwt_extender.hpp Generating XML output for file gbwt_helper.cpp Generating XML output for file gbwt_helper.hpp Generating XML output for file gbwtgraph_helper.cpp Generating XML output for file gbwtgraph_helper.hpp Generating XML output for file gbzgraph.hpp Generating XML output for file gcsa_helper.cpp Generating XML output for file gcsa_helper.hpp Generating XML output for file genome_state.cpp Generating XML output for file genome_state.hpp Generating XML output for file genotypekit.cpp Generating XML output for file genotypekit.hpp Generating XML output for file genotyper.cpp Generating XML output for file genotyper.hpp Generating XML output for file gfa.cpp Generating XML output for file gfa.hpp Generating XML output for file gff_reader.cpp Generating XML output for file gff_reader.hpp Generating XML output for file graph.cpp Generating XML output for file graph.hpp Generating XML output for file graph_caller.cpp Generating XML output for file graph_caller.hpp Generating XML output for file graph_synchronizer.cpp Generating XML output for file graph_synchronizer.hpp Generating XML output for file handle.hpp Generating XML output for file haplotype_extracter.cpp Generating XML output for file haplotype_extracter.hpp Generating XML output for file haplotype_indexer.cpp Generating XML output for file haplotype_indexer.hpp Generating XML output for file haplotypes.cpp Generating XML output for file haplotypes.hpp Generating XML output for file hash_map.hpp Generating XML output for file hts_alignment_emitter.cpp Generating XML output for file hts_alignment_emitter.hpp Generating XML output for file identity_overlay.cpp Generating XML output for file identity_overlay.hpp Generating XML output for file incremental_subgraph.cpp Generating XML output for file incremental_subgraph.hpp Generating XML output for file index_registry.cpp Generating XML output for file index_registry.hpp Generating XML output for file indexed_vg.cpp Generating XML output for file indexed_vg.hpp Generating XML output for file integrated_snarl_finder.cpp Generating XML output for file integrated_snarl_finder.hpp Generating XML output for file converted_hash_graph.hpp Generating XML output for file json_stream_helper.hpp Generating XML output for file load_proto_to_graph.cpp Generating XML output for file load_proto_to_graph.hpp Generating XML output for file register_libvg_io.cpp Generating XML output for file register_libvg_io.hpp Generating XML output for file register_loader_params_json.cpp Generating XML output for file register_loader_params_json.hpp Generating XML output for file register_loader_saver_distance_index.cpp Generating XML output for file register_loader_saver_distance_index.hpp Generating XML output for file register_loader_saver_gbwt.cpp Generating XML output for file register_loader_saver_gbwt.hpp Generating XML output for file register_loader_saver_gbwtgraph.cpp Generating XML output for file register_loader_saver_gbwtgraph.hpp Generating XML output for file register_loader_saver_gbz.cpp Generating XML output for file register_loader_saver_gbz.hpp Generating XML output for file register_loader_saver_gbzgraph.cpp Generating XML output for file register_loader_saver_gbzgraph.hpp Generating XML output for file register_loader_saver_gcsa.cpp Generating XML output for file register_loader_saver_gcsa.hpp Generating XML output for file register_loader_saver_gfa.cpp Generating XML output for file register_loader_saver_gfa.hpp Generating XML output for file register_loader_saver_hash_graph.cpp Generating XML output for file register_loader_saver_hash_graph.hpp Generating XML output for file register_loader_saver_lcp.cpp Generating XML output for file register_loader_saver_lcp.hpp Generating XML output for file register_loader_saver_minimizer.cpp Generating XML output for file register_loader_saver_minimizer.hpp Generating XML output for file register_loader_saver_packed_graph.cpp Generating XML output for file register_loader_saver_packed_graph.hpp Generating XML output for file register_loader_saver_r_index.cpp Generating XML output for file register_loader_saver_r_index.hpp Generating XML output for file register_loader_saver_snarl_manager.cpp Generating XML output for file register_loader_saver_snarl_manager.hpp Generating XML output for file register_loader_saver_vg.cpp Generating XML output for file register_loader_saver_vg.hpp Generating XML output for file register_loader_saver_xg.cpp Generating XML output for file register_loader_saver_xg.hpp Generating XML output for file save_handle_graph.hpp Generating XML output for file job_schedule.cpp Generating XML output for file job_schedule.hpp Generating XML output for file kff.cpp Generating XML output for file kff.hpp Generating XML output for file kmer.cpp Generating XML output for file kmer.cpp Generating XML output for file kmer.hpp Generating XML output for file kmer.hpp Generating XML output for file kmp.cpp Generating XML output for file kmp.hpp Generating XML output for file main.cpp Generating XML output for file mapper.cpp Generating XML output for file mapper.hpp Generating XML output for file mcmc_caller.cpp Generating XML output for file mcmc_caller.hpp Generating XML output for file mcmc_genotyper.cpp Generating XML output for file mcmc_genotyper.hpp Generating XML output for file mem.cpp Generating XML output for file mem.hpp Generating XML output for file mem_accelerator.cpp Generating XML output for file mem_accelerator.hpp Generating XML output for file memoizing_graph.cpp Generating XML output for file memoizing_graph.hpp Generating XML output for file memusage.cpp Generating XML output for file memusage.hpp Generating XML output for file minimizer_mapper.cpp Generating XML output for file minimizer_mapper.hpp Generating XML output for file minimizer_mapper_from_chains.cpp Generating XML output for file msa_converter.cpp Generating XML output for file msa_converter.hpp Generating XML output for file multipath_alignment.cpp Generating XML output for file multipath_alignment.hpp Generating XML output for file multipath_alignment_emitter.cpp Generating XML output for file multipath_alignment_emitter.hpp Generating XML output for file multipath_alignment_graph.cpp Generating XML output for file multipath_alignment_graph.hpp Generating XML output for file multipath_mapper.cpp Generating XML output for file multipath_mapper.hpp Generating XML output for file name_mapper.cpp Generating XML output for file name_mapper.hpp Generating XML output for file nested_traversal_finder.cpp Generating XML output for file nested_traversal_finder.hpp Generating XML output for file nodeside.hpp Generating XML output for file nodetraversal.hpp Generating XML output for file null_masking_graph.cpp Generating XML output for file null_masking_graph.hpp Generating XML output for file option.cpp Generating XML output for file option.hpp Generating XML output for file packer.cpp Generating XML output for file packer.hpp Generating XML output for file path.cpp Generating XML output for file path.hpp Generating XML output for file path_component_index.cpp Generating XML output for file path_component_index.hpp Generating XML output for file path_index.cpp Generating XML output for file path_index.hpp Generating XML output for file path_subgraph.cpp Generating XML output for file path_subgraph.hpp Generating XML output for file phase_unfolder.cpp Generating XML output for file phase_unfolder.hpp Generating XML output for file phased_genome.cpp Generating XML output for file phased_genome.hpp Generating XML output for file pictographs.hpp Generating XML output for file position.cpp Generating XML output for file position.hpp Generating XML output for file preflight.cpp Generating XML output for file preflight.hpp Generating XML output for file progressive.cpp Generating XML output for file progressive.hpp Generating XML output for file qual_adj_xdrop_aligner.cpp Generating XML output for file rare_variant_simplifier.cpp Generating XML output for file rare_variant_simplifier.hpp Generating XML output for file readfilter.cpp Generating XML output for file readfilter.hpp Generating XML output for file recombinator.cpp Generating XML output for file recombinator.hpp Generating XML output for file region.cpp Generating XML output for file region.hpp Generating XML output for file region_expander.cpp Generating XML output for file region_expander.hpp Generating XML output for file reverse_graph.cpp Generating XML output for file reverse_graph.hpp Generating XML output for file sampler.cpp Generating XML output for file sampler.hpp Generating XML output for file scanner.cpp Generating XML output for file scanner.hpp Generating XML output for file sequence_complexity.hpp Generating XML output for file small_bitset.hpp Generating XML output for file small_snarl_simplifier.cpp Generating XML output for file small_snarl_simplifier.hpp Generating XML output for file snarl_caller.cpp Generating XML output for file snarl_caller.hpp Generating XML output for file snarl_distance_index.cpp Generating XML output for file snarl_distance_index.hpp Generating XML output for file snarl_seed_clusterer.cpp Generating XML output for file snarl_seed_clusterer.hpp Generating XML output for file snarls.cpp Generating XML output for file snarls.hpp Generating XML output for file source_sink_overlay.cpp Generating XML output for file source_sink_overlay.hpp Generating XML output for file sparse_union_find.cpp Generating XML output for file sparse_union_find.hpp Generating XML output for file splicing.cpp Generating XML output for file splicing.hpp Generating XML output for file split_strand_graph.cpp Generating XML output for file split_strand_graph.hpp Generating XML output for file ssw_aligner.cpp Generating XML output for file ssw_aligner.hpp Generating XML output for file statistics.cpp Generating XML output for file statistics.hpp Generating XML output for file stream_index.cpp Generating XML output for file stream_index.hpp Generating XML output for file stream_sorter.cpp Generating XML output for file stream_sorter.hpp Generating XML output for file add_main.cpp Generating XML output for file align_main.cpp Generating XML output for file annotate_main.cpp Generating XML output for file augment_main.cpp Generating XML output for file autoindex_main.cpp Generating XML output for file benchmark_main.cpp Generating XML output for file call_main.cpp Generating XML output for file chain_main.cpp Generating XML output for file chunk_main.cpp Generating XML output for file circularize_main.cpp Generating XML output for file clip_main.cpp Generating XML output for file cluster_main.cpp Generating XML output for file combine_main.cpp Generating XML output for file concat_main.cpp Generating XML output for file construct_main.cpp Generating XML output for file convert_main.cpp Generating XML output for file deconstruct_main.cpp Generating XML output for file depth_main.cpp Generating XML output for file dotplot_main.cpp Generating XML output for file explode_main.cpp Generating XML output for file filter_main.cpp Generating XML output for file find_main.cpp Generating XML output for file gamcompare_main.cpp Generating XML output for file gampcompare_main.cpp Generating XML output for file gamsort_main.cpp Generating XML output for file gbwt_main.cpp Generating XML output for file genotype_main.cpp Generating XML output for file giraffe_main.cpp Generating XML output for file haplotypes_main.cpp Generating XML output for file help_main.cpp Generating XML output for file ids_main.cpp Generating XML output for file index_main.cpp Generating XML output for file inject_main.cpp Generating XML output for file join_main.cpp Generating XML output for file kmers_main.cpp Generating XML output for file map_main.cpp Generating XML output for file mcmc_main.cpp Generating XML output for file minimizer_main.cpp Generating XML output for file mod_main.cpp Generating XML output for file mpmap_main.cpp Generating XML output for file msga_main.cpp Generating XML output for file options.cpp Generating XML output for file options.hpp Generating XML output for file pack_main.cpp Generating XML output for file paths_main.cpp Generating XML output for file prune_main.cpp Generating XML output for file rna_main.cpp Generating XML output for file sift_main.cpp Generating XML output for file sim_main.cpp Generating XML output for file simplify_main.cpp Generating XML output for file snarls_main.cpp Generating XML output for file sort_main.cpp Generating XML output for file stats_main.cpp Generating XML output for file subcommand.cpp Generating XML output for file subcommand.hpp Generating XML output for file surject_main.cpp Generating XML output for file test_main.cpp Generating XML output for file trace_main.cpp Generating XML output for file translate_main.cpp Generating XML output for file validate_main.cpp Generating XML output for file vectorize_main.cpp Generating XML output for file version_main.cpp Generating XML output for file view_main.cpp Generating XML output for file viz_main.cpp Generating XML output for file subgraph.cpp Generating XML output for file subgraph.cpp Generating XML output for file subgraph.hpp Generating XML output for file subgraph.hpp Generating XML output for file subgraph_overlay.cpp Generating XML output for file subgraph_overlay.hpp Generating XML output for file subpath_overlay.cpp Generating XML output for file subpath_overlay.hpp Generating XML output for file surjecting_alignment_emitter.cpp Generating XML output for file surjecting_alignment_emitter.hpp Generating XML output for file surjector.cpp Generating XML output for file surjector.hpp Generating XML output for file swap_remove.hpp Generating XML output for file transcriptome.cpp Generating XML output for file transcriptome.hpp Generating XML output for file translator.cpp Generating XML output for file translator.hpp Generating XML output for file traversal_clusters.cpp Generating XML output for file traversal_clusters.hpp Generating XML output for file traversal_finder.cpp Generating XML output for file traversal_finder.hpp Generating XML output for file traversal_support.cpp Generating XML output for file traversal_support.hpp Generating XML output for file tree_subgraph.cpp Generating XML output for file tree_subgraph.hpp Generating XML output for file types.hpp Generating XML output for file types.hpp Generating XML output for file utility.cpp Generating XML output for file utility.hpp Generating XML output for file variant_adder.cpp Generating XML output for file variant_adder.hpp Generating XML output for file variant_recall.cpp Generating XML output for file variant_recall.hpp Generating XML output for file vcf_buffer.cpp Generating XML output for file vcf_buffer.hpp Generating XML output for file vectorizer.cpp Generating XML output for file vectorizer.hpp Generating XML output for file version.cpp Generating XML output for file version.hpp Generating XML output for file vg.cpp Generating XML output for file vg.hpp Generating XML output for file vg_set.cpp Generating XML output for file vg_set.hpp Generating XML output for file viz.cpp Generating XML output for file viz.hpp Generating XML output for file wang_hash.hpp Generating XML output for file watchdog.cpp Generating XML output for file watchdog.hpp Generating XML output for file xdrop_aligner.cpp Generating XML output for file zstdutil.cpp Generating XML output for file zstdutil.hpp Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/src/algorithms/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/src/io/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/xg/src/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/src/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/src/subcommand/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/xg/ Running plantuml with JAVA... type lookup cache used 14490/65536 hits=97426 misses=16651 symbol lookup cache used 11222/65536 hits=148517 misses=11222 finished... echo "View documentation at: file:///build/reproducible-path/vg-1.59.0+ds/doc/doxygen/index.html" View documentation at: file:///build/reproducible-path/vg-1.59.0+ds/doc/doxygen/index.html make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' export PATH=$PATH:/build/reproducible-path/vg-1.59.0+ds/debian/help \ && . /build/reproducible-path/vg-1.59.0+ds/source_me.sh \ && ( cd /build/reproducible-path/vg-1.59.0+ds/test && LD_PRELOAD= prove -v t/ ) index file /tmp/vg-xKjzYx/vg-UZClE0.fai not found, generating... index file /tmp/vg-xKjzYx/vg-Boh14O.fai not found, generating... index file /tmp/vg-xKjzYx/vg-7paqk9.fai not found, generating... index file /tmp/vg-xKjzYx/vg-5qZnZQ.fai not found, generating... warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;CIPOS=0,3;CIEND=-3,0 GT ! index file /tmp/vg-xKjzYx/vg-AqFWnC.fai not found, generating... index file /tmp/vg-xKjzYx/vg-ST8Oum.fai not found, generating... index file /tmp/vg-xKjzYx/vg-MfocRM.fai not found, generating... index file /tmp/vg-xKjzYx/vg-RGDusO.fai not found, generating... index file /tmp/vg-xKjzYx/vg-X0zuAx.fai not found, generating... index file /tmp/vg-xKjzYx/vg-l2pYHx.fai not found, generating... index file /tmp/vg-xKjzYx/vg-FsGwn5.fai not found, generating... index file /tmp/vg-xKjzYx/vg-p2cSP7.fai not found, generating... index file /tmp/vg-xKjzYx/vg-bNQ34h.fai not found, generating... index file /tmp/vg-xKjzYx/vg-wZNAG3.fai not found, generating... Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT END: 29 SVLEN: -19 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT index file /tmp/vg-xKjzYx/vg-UG9kyX.fai not found, generating... Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT END: 29 SVLEN: -19 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT index file /tmp/vg-xKjzYx/vg-IoJebO.fai not found, generating... index file /tmp/vg-xKjzYx/vg-BDp1GI.fai not found, generating... index file /tmp/vg-xKjzYx/vg-1kANmd.fai not found, generating... index file /tmp/vg-xKjzYx/vg-wa9Ulc.fai not found, generating... index file /tmp/vg-xKjzYx/vg-dL1QY4.fai not found, generating... index file /tmp/vg-xKjzYx/vg-qga1gs.fai not found, generating... index file /tmp/vg-xKjzYx/vg-0bvAkd.fai not found, generating... index file /tmp/vg-xKjzYx/vg-NLxD8T.fai not found, generating... index file /tmp/vg-xKjzYx/vg-m8LAsn.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT END: 18 POS: 9 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT index file /tmp/vg-xKjzYx/vg-ryMRnQ.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT END: 18 POS: 9 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT index file /tmp/vg-xKjzYx/vg-7kwLcT.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=13;CIPOS=0,3;SPAN=4 GT END: 13 POS: 9 Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. index file /tmp/vg-xKjzYx/vg-0QwmEa.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=13;CIPOS=0,3;SPAN=4 GT END: 13 POS: 9 Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. index file /tmp/vg-xKjzYx/vg-r5S0oE.fai not found, generating... index file /tmp/vg-xKjzYx/vg-gwQnex.fai not found, generating... index file /tmp/vg-xKjzYx/vg-cAgbMQ.fai not found, generating... index file /tmp/vg-xKjzYx/vg-URAvfL.fai not found, generating... warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. index file /tmp/vg-xKjzYx/vg-wNTRy5.fai not found, generating... warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. index file /tmp/vg-xKjzYx/vg-wyXIvJ.fai not found, generating... index file /tmp/vg-xKjzYx/vg-DvCt1D.fai not found, generating... index file /tmp/vg-xKjzYx/vg-ACrWkh.fai not found, generating... index file /tmp/vg-xKjzYx/vg-ambr0h.fai not found, generating... 2 0 3 0 iterated on 4 0 iterated on 5 0 iterated on 7 0 iterated on 8 0 iterated on 7 1 Warning: Cactus does not currently support finding snarls in a single-node connected component warning:[GFAParser] Skipping GFA P line: GFA format error: On pass 2: On line 2: Duplicate path x exists in graph Testing libvgio... warning: distance index uses oversized snarls, which may make mapping slow try increasing --snarl-limit when building the distance index warning: distance index uses oversized snarls, which may make mapping slow try increasing --snarl-limit when building the distance index warning: distance index uses oversized snarls, which may make mapping slow try increasing --snarl-limit when building the distance index warning: distance index uses oversized snarls, which may make mapping slow try increasing --snarl-limit when building the distance index 12 11 WARNING: Excluded 2 transcripts with overlapping exons or incorrect exon order. WARNING: Excluded 2 transcripts with overlapping exons or incorrect exon order. WARNING: Excluded 1 transcripts with exon overlapping a haplotype break. t/00_unittest.t ....... 1..1 =============================================================================== All tests passed (8336883 assertions in 617 test cases) ok 1 - vg unit tests complete successfully ok t/01_build_graph.t .... 1..1 ok 1 - graph building with the API ok warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AN=5008;CS=ALU_umary;MEINFO=AluUndef,2,281,+;NS=2504;SVLEN=279;SVTYPE=ALU;TSD=null;DP=18053;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0.0303;EUR_AF=0;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AN=5008;CS=DUP_gs;END=1549769;NS=2504;SVTYPE=DUP;DP=21874;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.001 ! Warning: deletion END and SVLEN do not agree [canonicalize] z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0;SPAN=3562 END: 1017354 SVLEN: -3562 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0;SPAN=3562 Warning: deletion END and SVLEN do not agree [canonicalize] z 43039 UW_VH_8960 T 100 PASS AC=2;AF=0.000399361;AN=5008;CIEND=0,208;CIPOS=-245,0;CS=DEL_union;END=1044489;NS=2504;SVLEN=-1677;SVTYPE=DEL;DP=18239;EAS_AF=0;AMR_AF=0.0029;AFR_AF=0;EUR_AF=0;SAS_AF=0;SPAN=1677 END: 1044489 SVLEN: -1677 Warning: deletion END and SVLEN do not agree [canonicalize] z 73265 UW_VH_16869 G 100 PASS AC=3;AF=0.000599042;AN=5008;CIEND=0,102;CIPOS=-125,0;CS=DEL_union;END=1077324;NS=2504;SVLEN=-4157;SVTYPE=DEL;DP=19418;EAS_AF=0;AMR_AF=0;AFR_AF=0.0023;EUR_AF=0;SAS_AF=0;SPAN=4157 END: 1077324 SVLEN: -4157 Warning: deletion END and SVLEN do not agree [canonicalize] z 129960 BI_GS_DEL1_B3_P2734_8 A 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-16,16;CIPOS=-16,16;CS=DEL_union;END=1131366;NS=2504;SVLEN=-1405;SVTYPE=DEL;DP=18804;EAS_AF=0;AMR_AF=0;AFR_AF=0.0008;EUR_AF=0;SAS_AF=0;SPAN=1405 END: 1131366 SVLEN: -1405 Warning: deletion END and SVLEN do not agree [canonicalize] z 307697 UW_VH_6096 A 100 PASS AC=2;AF=0.000399361;AN=5008;CIEND=0,82;CIPOS=-77,0;CS=DEL_union;END=1318064;NS=2504;SVLEN=-10447;SVTYPE=DEL;DP=20245;EAS_AF=0.002;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0;SPAN=10447 END: 1318064 SVLEN: -10447 Warning: deletion END and SVLEN do not agree [canonicalize] z 389096 UW_VH_3735 G 100 PASS AC=2647;AF=0.528554;AN=5008;CIEND=0,478;CIPOS=-443,0;CS=DEL_union;END=1390815;NS=2504;SVLEN=-2051;SVTYPE=DEL;DP=18400;EAS_AF=0.7996;AMR_AF=0.5922;AFR_AF=0.2685;EUR_AF=0.5;SAS_AF=0.5849;SPAN=2051 END: 1390815 SVLEN: -2051 Warning: deletion END and SVLEN do not agree [canonicalize] z 405367 BI_GS_DEL1_B3_P2734_19 G 100 PASS AC=2;AF=0.000399361;AN=5008;CIEND=-9,9;CIPOS=-9,9;CS=DEL_union;END=1406601;NS=2504;SVLEN=-1232;SVTYPE=DEL;DP=21506;EAS_AF=0;AMR_AF=0;AFR_AF=0.0015;EUR_AF=0;SAS_AF=0;SPAN=1232 END: 1406601 SVLEN: -1232 Warning: deletion END and SVLEN do not agree [canonicalize] z 557325 UW_VH_21401 G 100 PASS AC=314;AF=0.0626997;AN=5008;CIEND=0,245;CIPOS=-268,0;CS=DEL_union;END=1559946;NS=2504;SVLEN=-2877;SVTYPE=DEL;DP=17241;EAS_AF=0.004;AMR_AF=0.0648;AFR_AF=0.0552;EUR_AF=0.1412;SAS_AF=0.0511;SPAN=2877 END: 1559946 SVLEN: -2877 Warning: deletion END and SVLEN do not agree [canonicalize] z 560739 YL_CN_CHB_4219 T 100 PASS AC=4099;AF=0.81849;AN=5008;CIEND=-500,1000;CIPOS=-1000,500;CS=DEL_union;END=1593685;NS=2504;SVLEN=-32947;SVTYPE=DEL;DP=20713;EAS_AF=0.7867;AMR_AF=0.6527;AFR_AF=0.9213;EUR_AF=0.7903;SAS_AF=0.8589;SPAN=32947 END: 1593685 SVLEN: -32947 Warning: deletion END and SVLEN do not agree [canonicalize] z 596789 BI_GS_DEL1_B1_P2734_566 C 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-11,11;CIPOS=-11,11;CS=DEL_union;END=1600144;NS=2504;SVLEN=-3354;SVTYPE=DEL;DP=16771;EAS_AF=0.001;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0;SPAN=3354 END: 1600144 SVLEN: -3354 Warning: deletion END and SVLEN do not agree [canonicalize] z 599361 BI_GS_DEL1_B2_P2734_449 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-20,20;CIPOS=-20,20;CS=DEL_union;END=1605179;NS=2504;SVLEN=-5817;SVTYPE=DEL;DP=17612;EAS_AF=0;AMR_AF=0;AFR_AF=0.0008;EUR_AF=0;SAS_AF=0;SPAN=5817 END: 1605179 SVLEN: -5817 Warning: deletion END and SVLEN do not agree [canonicalize] z 602412 BI_GS_DEL1_B4_P2734_149 C 100 PASS AC=4;AF=0.000798722;AN=5008;CIEND=-15,15;CIPOS=-15,15;CS=DEL_union;END=1603204;NS=2504;SVLEN=-791;SVTYPE=DEL;DP=21930;EAS_AF=0.002;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.002;SPAN=791 END: 1603204 SVLEN: -791 Warning: deletion END and SVLEN do not agree [canonicalize] z 670381 UW_VH_15556 T 100 PASS AC=14;AF=0.00279553;AN=5008;CIEND=0,256;CIPOS=-240,0;CS=DEL_union;END=1674237;NS=2504;SVLEN=-4037;SVTYPE=DEL;DP=18965;EAS_AF=0;AMR_AF=0;AFR_AF=0.0106;EUR_AF=0;SAS_AF=0;SPAN=4037 END: 1674237 SVLEN: -4037 Warning: deletion END and SVLEN do not agree [canonicalize] z 995483 UW_VH_2849 T 100 PASS AC=193;AF=0.0385383;AN=5008;CIEND=0,386;CIPOS=-423,0;CS=DEL_union;END=1997552;NS=2504;SVLEN=-2301;SVTYPE=DEL;DP=16520;EAS_AF=0;AMR_AF=0.0461;AFR_AF=0.0454;EUR_AF=0.0547;SAS_AF=0.047;SPAN=2301 END: 1997552 SVLEN: -2301 error:[vg::Constructor] On z, adding reference to last edit end, next end is at 1053404 but reference is only 459552 long warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AN=5008;CS=ALU_umary;MEINFO=AluUndef,2,281,+;NS=2504;SVLEN=279;SVTYPE=ALU;TSD=null;DP=18053;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0.0303;EUR_AF=0;SAS_AF=0 ! Restricting to gi|568815592:29791752-29792749 from 1 to end index file sv/x.fa.fai not found, generating... index file tiny/ambiguous.fa.fai not found, generating... warning:[vg::Constructor] Unsupported IUPAC ambiguity codes found in x; coercing to N. t/02_vg_construct.t ... 1..30 ok 1 - construction produces the right number of nodes ok 2 - construction produces the right number of edges ok 3 - construction obeys rename and region options ok 4 - construction of a 1 megabase graph from the 1000 Genomes succeeds ok 5 - the 1mb graph has the expected number of nodes ok 6 - the 1mb graph has the expected number of edges not ok 7 - vg construct can skip self-inconsistent structural variants # got: '1' # expected: '0' ok 8 - node size is manageable by default ok 9 - construction of a very complex region succeeds ok 10 - the complex graph has the expected number of nodes ok 11 - the complex graph has the expected number of edges ok 12 - the ordering of variants at the same position has no effect on the resulting graph ok 13 - construction does not fail when the first position in the VCF is repeated and has an indel ok 14 - the size of the regions used in construction has no effect on the graph ok 15 - the number of threads used in construction has no effect on the graph ok 16 - the number of threads and regions used in construction has no effect on the graph ok 17 - construction of a graph with two head nodes succeeds ok 18 - the graph contains all the sequence in the reference and VCF ok 19 - varying the max node size does not affect graph length ok 20 - nodes are correctly capped in size ok 21 - -R --region flag is respected ok 22 - vg construct does not require a vcf ok 23 - vg construct respects node size limit ok 24 - --region can be interpreted to be a reference sequence (and not parsed as a region spec) ok 25 - vg constructs the correct graph for inversions ok 26 - vg construct skips variants with . ALTs ok 27 - VCF with * alleles is accepted ok 28 - VCF record with * allele is rejected ok 29 - Reference with ambiguity codes has them coerced to Ns ok 30 - Expected number of Ns are created Failed 1/30 subtests [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. error[VPKG::load_one]: Could not open test/graphs/rgfa_with_reference.rgfa while loading handlegraph::PathHandleGraph error:[get_input_file_name] unable to open input file: test/graphs/rgfa_with_reference.rgfa error[VPKG::load_one]: Could not open test/graphs/rgfa_with_reference.rgfa while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Could not open test/graphs/gfa_with_reference.gfa while loading handlegraph::PathHandleGraph error:[get_input_file_name] unable to open input file: test/graphs/gfa_with_reference.gfa error[VPKG::load_one]: Could not open test/graphs/gfa_with_reference.gfa while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/03_vg_view.t ........ 1..23 ok 1 - view produces the expected number of lines of dot output ok 2 - view produces the expected number of lines of GFA output ok 3 - view converts back and forth between GFA and vg format ok 4 - view can convert BAM to GAM not ok 5 - view can round-trip JSON and GAM # got: '5b9458e2d6d1f262977b932998bb8d3a -' # expected: '7d450e53c0870ff504f33af188613e5d -' ok 6 - view can round-trip qualities and encodes tham as PHRED+0 base-64-encoded strings in JSON Binary files x.vg and - differ not ok 7 - view can reconstruct a VG graph from JSON # got: '1' # expected: '0' ok 8 - view can pass through VG when loading as vg::VG ok 9 - view can pass through semantically identical VG normally ok 10 - view parses sample names ok 11 - view can handle fastq input not ok 12 - unnamed test # got: '4' # expected: 'view can translate graphs with 2-node cycles' ok 13 - view outputs properly oriented GFA ok 14 - view produces the expected number of lines of dot output from a cyclic graph ok 15 - streaming JSON output produces the expected number of chunks ok 16 - duplicate warnings can be suppressed when loading as vg::VG ok 17 - gfa graphs with overlaps are rejected ok 18 - GFA import produces a concise error message when overlaps are present ok 19 - GFA import rejects a GFA file with an overlap that goes beyond its sequences ok 20 - GFA import produces a concise error message in that case ok 21 - vg view preserves path metadata of rGFA file ok 22 - vg view preserves path metadata of GFA file ok 23 - vg view can emit a GFA file with subranges on a haplotype without explicit phase blocks Failed 3/23 subtests [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes t/04_vg_align.t ....... 1..20 ok 1 - alignment traverses the correct path ok 2 - alignment score is as expected ok 3 - full length bonus works and is included by default ok 4 - bonuses are included on only one end for pinned alignments ok 5 - scoring parameters are respected ok 6 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected ok 7 - alignment does not contain excessive soft clips under lenient scoring ok 8 - score-matrix file should give same results as --match 2 --mismatch 2: alignment does not contain excessive soft clips under lenient scoring ok 9 - alignment score does not overflow at 255 when using 8x16bit vectors ok 10 - score-matrix file should give same results as --match 2 --mismatch 2: alignment score does not overflow at 255 when using 8x16bit vectors ok 11 - Ns do not cause excessive soft clipping ok 12 - nodes are only referenced if they have mappings ok 13 - align can use query names and outputs GAM ok 14 - alignment to cyclic graphs works ok 15 - graphs where duplicated nodes need flipping can be used for alignment ok 16 - node flipping doesn't destroy the alignment ok 17 - alignment correctly handles an inversion ok 18 - the exploding graph doesn't blow up ok 19 - pinning doesn't cause problems for gssw ok 20 - left pinning is correctly handled ok [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open test.xg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Could not open w.xg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Unreadable stream while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in w.vg while loading handlegraph::PathHandleGraph t/05_vg_find.t ........ 1..29 ok 1 - construction ok 2 - a path can be queried from the xg index ok 3 - a node near another can be obtained using context from the xg index ok 4 - each perfect read contains one maximal exact match ok 5 - vg find -D finds approximate distance between 2 adjacent node starts ok 6 - vg find -D finds approximate distance between node start and adjacent snp ok 7 - vg find -D jumps deletion ok 8 - vg find -D jumps deletion from other allele in snp ok 9 - vg find -L finds same number of nodes (with -c 1) ok 10 - vg find -L works with -r. it scans from start position of first node in range ok 11 - vg find -L tracks length from start position of input node ok 12 - vg find -L works with more than one input node ok 13 - we find the 4 canonical SMEMs from @lh3's bwa mem poster ok 14 - we can find the right MEMs for a sequence with Ns ok 15 - we find the same MEMs sequences with different lengths of Ns ok 16 - the GAM index can return the set of alignments mapping to a node ok 17 - a subgraph query may be used to obtain a particular subset of alignments from a sorted GAM ok 18 - the index can be queried using GAM alignments ok 19 - find gets connected edges between queried nodes by default ok 20 - find gets nodes provided in a node file list not ok 21 - extracting by path adds no extra edges # got: '' # expected: '1' ok 22 - pattern based path extraction works ok 23 - path DAG range query works ok 24 - we can extract a set of targets to separate files ok 25 - the same extraction can be made using BED input ok 26 - we see the expected number of kmers in the given targets ok 27 - we find the expected number of kmers with haplotype frequency equal to 2 ok 28 - GFA i/o for find -n consistent with converting both ways ok 29 - find nodes that map to the provided node ids Failed 1/29 subtests WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. warning: -i option is deprecated WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. t/06_vg_index.t ....... 1..54 ok 1 - building an XG index of a graph ok 2 - building a GCSA index of a graph ok 3 - building both indexes at once ok 4 - the indexes are identical when built one at a time and together ok 5 - building GCSA from XG ok 6 - the GCSA indexes are identical when built from vg and from xg ok 7 - building a GBWT index of a graph with haplotypes ok 8 - building an XG index of a graph with haplotypes ok 9 - xg index does not contain alt paths by default ok 10 - building an XG index of a graph with haplotypes and alt paths included ok 11 - xg index does contains alt paths with index -L ok 12 - building a GCSA index of a graph with haplotypes ok 13 - building all indexes at once ok 14 - the indexes are identical ok 15 - building all indexes at once, while leaving alt paths in xg ok 16 - the indexes are identical with -L ok 17 - xg index does contains alt paths with index -L all at once ok 18 - samples can be excluded from haplotype indexing ok 19 - excluded samples were not included in the GBWT index ok 20 - GBWT from GAF same as from GAM ok 21 - building GBWT index for a regional graph ok 22 - no warnings about missing variants produced ok 23 - building an XG index of multiple graphs ok 24 - building a GCSA index of multiple graphs ok 25 - building both indexes at once ok 26 - the indexes are identical ok 27 - building a GBWT index of multiple graphs with haplotypes ok 28 - building an XG index of multiple graphs with haplotypes ok 29 - building a GCSA index of multiple graphs with haplotypes ok 30 - building XG and GCSA indexes at once ok 31 - building an XG index with alt paths ok 32 - building a GBWT index from an XG index ok 33 - the indexes are identical ok 34 - GBWT can be built for paths ok 35 - fail with nonexistent file ok 36 - a prebuilt deBruijn graph in GCSA2 format may be used ok 37 - vg index and vg gamsort produce identical sorted GAM indexes ok 38 - storage of multiple graphs in an index succeeds ok 39 - can index backward nodes ok 40 - can index kmers for backward nodes ok 41 - GCSA2 index works on cyclic graphs with heads and tails ok 42 - GCSA2 index works on cyclic graphs with no heads or tails ok 43 - GCSA2 index works on cyclic graphs with self loops ok 44 - GCSA2 index works on general cyclic graphs ok 45 - GCSA2 indexing of a tiny graph works ok 46 - GCSA2 indexing succeeds on a single-node graph ok 47 - GCSA2 indexing succeeds on graph with heads but no tails ok 48 - a useful error message is produced when nodes are too large ok 49 - snarl finding with trivial snarls ok 50 - building a distance index of a graph ok 51 - building a distance index of a piped vg graph ok 52 - building a distance index of a piped PackedGraph ok 53 - distance index construction from GBZ ok 54 - distance index construction from piped GBZ ok warning: Thread 0 encountered sequence of length 100, which is longer than the non-chunked limit of 30. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ index file t.fa.fai not found, generating... [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. t/07_vg_map.t ......... 1..55 ok 1 - offset counts unused bases from the start of the node on the forward strand ok 2 - xdrop alignment obtains the expected result ok 3 - xdrop alignment obtains the expected result for the reverse complement ok 4 - score-matrix defaults match 1 mismatch -4 should produce same results: with matrixoffset counts unused bases from the start of the node on the forward strand ok 5 - offset counts unused bases from the start of the node on the reverse strand ok 6 - global alignment traverses the correct path ok 7 - alignment score is as expected ok 8 - scoring parameters are respected ok 9 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected ok 10 - full length bonus always be included ok 11 - full length bonus can be set to 0 ok 12 - vg map takes -d as input without a variant graph ok 13 - vg map can align across a SNP ok 14 - alignment works on a small graph ok 15 - binary alignment format is equivalent to json version ok 16 - alignment from BAM correctly handles qualities ok 17 - chunky-banded alignment works ok 18 - multiple alignments are returned in descending score order ok 19 - only a single primary alignment is returned ok 20 - vg can map multi-line FASTA sequences ok 21 - mapping of BAM file produces expected number of alignments ok 22 - mapping from a fastq produces the expected number of alignments ok 23 - allowing secondary alignments with MEM mapping does not change number of primary alignments ok 24 - vg connects paired-end reads in gam output ok 25 - mapping to graphs that can't be oriented without swapping edges works correctly ok 26 - reads multi-map to multiple possible locations ok 27 - vg map works based on gcsa and xg indexes ok 28 - the mapping quality may be capped ok 29 - paired read alignments forced to be consistent have lower score than unrestricted alignments ok 30 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments ok 31 - only primary alignments have mapping quality scores ok 32 - unpaired reads produce mapping quality scores ok 33 - map returns same output on xg and vg (single threaded) ok 34 - base quality adjusted alignment produces higher scores if mismatches have low quality ok 35 - error on vg map -f (unpaired) ok 36 - error on vg map -f (interleaved) ok 37 - error on vg map -f (paired, LHS) ok 38 - error on vg map -f (paired, RHS) ok 39 - mapping a read that touches unused nodes gets the base score ok 40 - mapping a read that matches a haplotype gets a small penalty ok 41 - mapping a read that matches a haplotype with exponent 0 gets the base score ok 42 - mapping a read that matches no haplotypes gets a larger penalty not ok 43 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 44 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 45 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 46 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 47 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 48 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 49 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 50 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 51 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 52 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' ok 53 - mapper can read FASTA input ok 54 - mapper can read multiline FASTA input ok 55 - xdrop works on a reversed read Failed 10/55 subtests [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. t/08_vg_ids.t ......... 1..10 ok 1 - minimum node as expected (id compaction correct) ok 2 - maximum node is as expected (id compaction correct) ok 3 - correctly generated joint id space for several graphs ok 4 - can sort and re-number a graph with self loops ok 5 - can sort and renumber a complex cyclic graph ok 6 - sorting removes back-edges in a DAG ok 7 - sorting assigns node IDs in topological order ok 8 - sorting does not affect id range ok 9 - sorting does not affect id range of vg ok 10 - sorting does not affect id range of hg ok WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in reversing.vg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in reversing.vg while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/09_vg_concat.t ...... 1..4 ok 1 - concat doubles the number of nodes ok 2 - concat doubles the number of edges + 1 ok 3 - concat -p doubles the number of nodes on reversing graph not ok 4 - concat -p doubles the number of edges + 1 on reversing graph # got: '0' # expected: '1' Failed 1/4 subtests t/100_code_quality.t .. 1..1 ok 1 - code quality is acceptable ok warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AN=5008;CS=ALU_umary;MEINFO=AluUndef,2,281,+;NS=2504;SVLEN=279;SVTYPE=ALU;TSD=null;DP=18053;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0.0303;EUR_AF=0;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AN=5008;CS=DUP_gs;END=1549769;NS=2504;SVTYPE=DUP;DP=21874;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.001 ! [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg autoindex] Executing command: vg autoindex -v tiny/tiny.vcf.gz -r tiny/tiny.fa -w giraffe -p tiny [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. warning:[GFAParser] Ignoring unrecognized # line type t/10_vg_stats.t ....... 1..21 ok 1 - vg stats reports the expected number of nodes ok 2 - vg stats reports the expected number of edges ok 3 - vg stats reports the expected graph length ok 4 - vg stats reports the correct number of subgraphs ok 5 - vg stats reports the correct subgraph length ok 6 - distance to head is correct ok 7 - distance to tail is correct ok 8 - aligned read stats are computed correctly ok 9 - basic stats agree between graph formats ok 10 - stats can be computed for GAM files without graphs ok 11 - a path overlap description of a test graph has the expected length ok 12 - vg stats -F detects format of old protobuf graph ok 13 - vg stats -F detects format of newer protobuf graph ok 14 - vg stats -F detects format of hash graph ok 15 - vg stats -F detects format of packed graph ok 16 - vg stats -F detects format of xg graph ok 17 - vg stats -F detects format of GFA graph ok 18 - vg stats -F detects format of GBZ graph ok 19 - vg stats -D found correct degree distribution of tiny graph ok 20 - vg stats -L counts self-loops correctly ok 21 - vg stats -e finds the right nondeterministic edge sets ok WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 68, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 54, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. t/11_vg_paths.t ....... 1..20 ok 1 - path listing works from vg ok 2 - path listing works from XG ok 3 - generic path listing works from XG ok 4 - thread listing works from GBWT ok 5 - haplotype thread listing works from GBWT ok 6 - thread selection by name prefix works correctly ok 7 - thread selection by sample name works correctly ok 8 - no threads are reported for invalid samples ok 9 - vg paths may be used to extract threads ok 10 - vg paths may be used to extract threads as GAF ok 11 - Fasta extracted from xg is the same as the input fasta ok 12 - Fasta extracted from vg is the same as the input fasta ok 13 - Fasta extracted from threads has correct number of lines ok 14 - a single path may be retained ok 15 - path filtering does not modify the graph ok 16 - alt allele paths can be dropped ok 17 - vg path coverage has correct number of columns ok 18 - vg path coverage has correct number of rows ok 19 - vg paths found correct number of lengths ok 20 - vg path coverage reports correct lengths in first column ok WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. warning[vg mod]: -o is deprecated. Dangling edges are now automatically removed. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/12_vg_kmers.t ....... 1..10 ok 1 - correct numbers of kmers in the graph ok 2 - to_end edges are handled correctly ok 3 - from_start edges are handled correctly ok 4 - GCSA2 output produces the expected number of lines ok 5 - GCSA2 binary output produces the expected number bytes ok 6 - GCSA2 output works when next position is multiple ok 7 - GCSA2 output works when previous characters are multiple ok 8 - edge-max correctly bounds the number of kmers in a complex graph ok 9 - start/stop node IDs can be specified in GCSA2 output ok 10 - attempting to generate kmers longer than the longest path in a graph correctly yields no kmers ok index file n.fa.fai not found, generating... warning: [HaplotypeIndexer::parse_vcf] contig y not present in file small/x.vcf.gz [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. t/13_vg_sim.t ......... 1..36 ok 1 - vg sim creates the correct number of reads ok 2 - end bonuses are included ok 3 - alignments may be generated rather than read sequences ok 4 - alignments are produced on both strands ok 5 - high simulated error rates do not change the number of bases generated ok 6 - vg sim creates forward-strand reads when asked ok 7 - vg sim can simulate from just a path ok 8 - vg sim can simulate from just a path in FASTQ mode ok 9 - reads can be simulated from all paths ok 10 - simulation was successful ok 11 - reads can be simulated from GBWT samples ok 12 - simulation was successful ok 13 - pairs simulated even when fragments overlap ok 14 - sim does not emit reads with Ns ok 15 - sim can emit reads with Ns when asked to ok 16 - sim doesn't emit Ns even with pair and errors ok 17 - Sample simulation works along with --any-path ok 18 - not having any regexes skips all unvisited contigs ok 19 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs ok 20 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs ok 21 - assigning a ploidy of 0 by regex excludes reads from that contig ok 22 - multiple regexes are interpreted ok 23 - regexes are interpreted as regexes ok 24 - assigning a very high ploidy by regex starves out the other paths ok 25 - Sample simulation works along with --any-path with training FASTQ ok 26 - not having any regexes skips all unvisited contigs with training FASTQ ok 27 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs with training FASTQ ok 28 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs with training FASTQ ok 29 - assigning a ploidy of 0 by regex excludes reads from that contig with training FASTQ ok 30 - multiple regexes are interpreted with training FASTQ ok 31 - regexes are interpreted as regexes with training FASTQ ok 32 - assigning a very high ploidy by regex starves out the other paths with training FASTQ ok 33 - All reads are annotated with single reference positions by default ok 34 - All reads can be annotated with multiple reference positions when requested ok 35 - ngs trained simulator works ok 36 - ngs trained simulator generates gam ok warning[load_proto_to_graph]: dangling edges on missing node 199474497 and 2 other missing nodes removed [algorithms::normalize] iteration 1 current length 162 [algorithms::normalize] iteration 2 current length 154 [algorithms::normalize] iteration 3 current length 154 [algorithms::normalize] normalized in 2 steps [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. graph: valid [algorithms::normalize] iteration 1 current length 162 [algorithms::normalize] iteration 2 current length 154 [algorithms::normalize] iteration 3 current length 154 [algorithms::normalize] normalized in 2 steps graph: valid graph: valid [algorithms::normalize] iteration 1 current length 162 [algorithms::normalize] iteration 2 current length 154 [algorithms::normalize] iteration 3 current length 154 [algorithms::normalize] normalized in 2 steps [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [algorithms::normalize] iteration 1 current length 95 [algorithms::normalize] iteration 2 current length 95 [algorithms::normalize] normalized in 1 steps [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 100, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 70, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid [algorithms::normalize] iteration 1 current length 5 [algorithms::normalize] normalized in 0 steps graph: valid [algorithms::normalize] iteration 1 current length 5 [algorithms::normalize] normalized in 0 steps graph: valid WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. graph: valid WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. graph: valid graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 19. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 19. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 106 [algorithms::normalize] iteration 2 current length 105 [algorithms::normalize] iteration 3 current length 105 [algorithms::normalize] normalized in 2 steps warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 103 [algorithms::normalize] iteration 2 current length 100 [algorithms::normalize] iteration 3 current length 100 [algorithms::normalize] normalized in 2 steps t/14_vg_mod.t ......... 1..32 ok 1 - vg mod yields a graph with only a particular path ok 2 - orphan edge removal is automatic ok 3 - graph complexity reduction works as expected ok 4 - short subgraph pruning works ok 5 - normalization produces the correct number of nodes ok 6 - normalization removes redundant SNP alleles ok 7 - normalization produces a valid graph ok 8 - looped normalization produces a valid graph ok 9 - unchop produces a valid graph ok 10 - normalization removes redundant sequence in the graph ok 11 - normalization doesn't introduce cycles and does remove redundancy in bubbles ok 12 - vg mod removes non-path nodes and edge not ok 13 - chopping a graph works correctly with reverse mappings # got: '1' # expected: '0' ok 14 - unchop correctly handles paths ok 15 - unchop correctly handles a graph with an inversion not ok 16 - unchop handles doubly-reversing edges # got: '' # expected: '1' ok 17 - normalization works on a graph with an inversion ok 18 - mod successfully unchops a difficult graph ok 19 - chopping self-cycling nodes retains the cycle ok 20 - unrolling works and produces a valid graph ok 21 - unfolding works and produces a valid graph ok 22 - dagify-unroll produces a graph with the same kmers as the original graph ok 23 - unfold produces a graph with the same kmers as the original graph ok 24 - dagify handles a graph with two strongly connected components ok 25 - unfold followed by dagify produces a graph with no cycles ok 26 - unfold followed by dagify produces a graph with the same kmers as the original graph ok 27 - dagify unrolls the un-unrollable graph ok 28 - sibling simplification does not disrupt paths ok 29 - dagify correctly calculates the minimum distance through the unrolled component ok 30 - dagify produces a graph of the correct size ok 31 - subsetting a flat-alleles graph to a sample graph works ok 32 - removal of high-degree nodes results in the expected number of subgraphs Failed 2/32 subtests warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ warning:[vg mpmap] It is HIGHLY recommended to use a distance index (-d) for clustering on splice graphs. Both accuracy and speed will suffer without one. warning:[vg mpmap] It is HIGHLY recommended to use a distance index (-d) for clustering on splice graphs. Both accuracy and speed will suffer without one. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. index file x.sub.fa.fai not found, generating... warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x x.xg -g x.gcsa -n dna --suppress-mismapping -B -G x.gam -i -F GAM -I 60 -D 10 [vg mpmap] elapsed time 0 s: Loading graph from x.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from x.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from x.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from x.gam using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x x.xg -g x.gcsa -n dna --suppress-mismapping -B -G x.gam -i -F GAMP -I 60 -D 10 [vg mpmap] elapsed time 0 s: Loading graph from x.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from x.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from x.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from x.gam using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 read pairs. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. t/15_vg_surject.t ..... 1..47 ok 1 - reads are generated ok 2 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference ok 3 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference ok 4 - vg surject actually places reads on the correct path ok 5 - vg surject doesn't need to be told which path to use ok 6 - vg surject reports alignment scores not ok 7 - vg surject picks a reference-sense path if it is present # got: '0' # expected: '100' ok 8 - vg surject works for every read simulated from a dense graph ok 9 - vg surject spliced algorithm works for every read simulated from a dense graph ok 10 - vg surject produces valid SAM output ok 11 - vg map may surject reads to produce valid SAM output ok 12 - vg map may surject reads to produce valid BAM output not ok 13 - vg surject retains read names # got: '0' # expected: '100' ok 14 - vg surject can set sample and read group ok 15 - we respect the original mapping's softclips ok 16 - quality strings we will use for testing are oriented correctly ok 17 - forward and reverse orientations of a read produce the same surjected SAM, ignoring flags ok 18 - vg surject produces valid BAM output not ok 19 - mapping quality is preserved through surjection # got: '' # expected: '99' not ok 20 - read pairing is preserved through GAM->GAM surjection # got: '' # expected: 'read/1' ok 21 - interleaved surjection produces same SAM when using GAF and GAM inputs not ok 22 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 23 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 24 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 25 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 26 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '83 # 163' not ok 27 - surjection of paired reads to SAM tags both reads with a read group # got: '0' # expected: '2' not ok 28 - surjection of paired reads to SAM creates RG header # got: '0' # expected: '1' ok 29 - surjection works for a longer (151bp) read ok 30 - surjection works for another difficult read ok 31 - mapping reproduces qualities from BAM input ok 32 - mapping reproduces qualities from fastq input ok 33 - mapping reproduces qualities from GAF input ok 34 - surject works on GAMP input ok 35 - surject works on paired GAMP input ok 36 - vg surject correctly handles subpath suffix in path name ok 37 - vg surject correctly fetches base path length from input file ok 38 - vg surject does not crash when surjecting a read that grazes the reference with a deletion ok 39 - vg surject leaves a read that grazes the reference with a deletion unmapped ok 40 - vg surject does not crash when surjecting a read that grazes the reference with a deletion and pruning low complexity anchors ok 41 - vg surject leaves a read that grazes the reference with a deletion unmapped when pruning low complexity anchors ok 42 - GAM surject can return only primaries ok 43 - GAM surject can return multimappings ok 44 - GAM surject can return paired multimappings ok 45 - GAMP surject can return only primaries ok 46 - GAMP surject can return multimappings ok 47 - GAMP surject can return multimappings Failed 11/47 subtests WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 100 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. could not open msgas/t.fa error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. could not open msgas/t.fa error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 100 [algorithms::normalize] iteration 2 current length 100 [algorithms::normalize] normalized in 1 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file msgas/s-rev.fa.fai not found, generating... warning: Thread 0 encountered sequence of length 100, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 100 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 49, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file GRCh38_alts/FASTA/HLA/K-3138.fa.fai not found, generating... warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3184, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3183, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3182, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3181, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 64. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file msgas/inv.fa.fai not found, generating... warning: Thread 0 encountered sequence of length 210, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 210 [algorithms::normalize] iteration 2 current length 210 [algorithms::normalize] normalized in 1 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 70, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file GRCh38_alts/FASTA/HLA/B-3106.fa.fai not found, generating... warning: Thread 0 encountered sequence of length 3365, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3364, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3343, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3340, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 210, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid t/16_vg_msga.t ........ 1..14 ok 1 - MSGA produces the expected graph for GRCh38 HLA-V ok 2 - X-drop DP MSGA produces the expected graph for GRCh38 HLA-V {"edge": [{"from": "7", "from_start": true, "to": "8", "to_end": true}, {"from": "1", "to": "8"}, {"from": "1", "to": "7"}], "node": [{"id": "7", "sequence": "GGACTAAGGACAAAGGTGCGGGGAG"}, {"id": "8", "sequence": "AACTACTCCACATCAAAGCTACCCAGGCCATTTTAAGTTTCCTGT"}, {"id": "1", "sequence": "TCAGATTCTCATCCCTCCTCAAGGGCTTCT"}], "path": [{"mapping": [{"edit": [{"from_length": 30, "to_length": 30}], "position": {"node_id": "1"}, "rank": "1"}, {"edit": [{"from_length": 45, "to_length": 45}], "position": {"node_id": "8"}, "rank": "2"}, {"edit": [{"from_length": 25, "to_length": 25}], "position": {"node_id": "7"}, "rank": "3"}], "name": "s1"}, {"mapping": [{"edit": [{"from_length": 30, "to_length": 30}], "position": {"node_id": "1"}, "rank": "1"}, {"edit": [{"from_length": 25, "to_length": 25}], "position": {"node_id": "7"}, "rank": "2"}], "name": "s2"}]} ok 3 - soft clips at node boundaries (start) are included correctly ok 4 - soft clips at node boundaries (end) are included correctly ok 5 - region hints (-p) produce same graph ok 6 - adding in existing sequences in reverse doesn't change graph ok 7 - the paths of the graph encode the original sequences used to build it ok 8 - even when banding the paths of the graph encode the original sequences used to build it ok 9 - HLA K-3138 correctly includes all input paths ok 10 - a difficult cyclic path can be included to produce a valid graph ok 11 - a reference sequence set representing an inversion in it may be msga'd and detected ok 12 - edges in cycles with two nodes are correctly included ok 13 - HLA B-3106 is assembled into a valid graph ok 14 - odd-sized overlaps may be used for chunked alignment ok [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found in tiny.vg while loading handlegraph::MutablePathMutableHandleGraph error:[get_input_file_name] unable to open input file: edits-embedded.gam error:[get_input_file] could not open file "edits-embedded.gam" error[VPKG::load_one]: Correct input type not found in augmented.vg while loading handlegraph::PathHandleGraph [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found in tiny.vg while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found in augmented.m1.vg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in tiny.vg while loading handlegraph::HandleGraph [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found in tiny.vg while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found in augmented.gaf.vg while loading handlegraph::HandleGraph error[VPKG::load_one]: Correct input type not found in augmented.gaf.vg while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found in tiny.vg while loading handlegraph::MutablePathMutableHandleGraph error:[get_input_file_name] unable to open input file: edit-embedded.gam error:[get_input_file] could not open file "edit-embedded.gam" error[VPKG::load_one]: Correct input type not found in augmented.vg while loading handlegraph::PathHandleGraph [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes warning: when streaming in a GAM with -A, the output GAM will lose all non-Path related fields from the input [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes t/17_vg_augment.t ..... 1..39 not ok 1 - direct augmentation embeds reads fully for well-supported SNPs # got: '0' # expected: '36' not ok 2 - adding a well-supported SNP by direct augmentation adds 3 more nodes # got: '' # expected: '18' not ok 3 - adding a well-supported SNP by direct augmentation adds 3 more nodes with -m 1 # got: '' # expected: '18' not ok 4 - direct augmentation embeds with GAF reads fully for well-supported SNPs # got: '0' # expected: '36' not ok 5 - adding a well-supported SNP by direct augmentation with GAF adds 3 more nodes # got: '' # expected: '18' not ok 6 - direct augmentation embeds reads fully for probable errors # got: '0' # expected: '3' not ok 7 - adding a probable error by direct augmentation adds 3 more nodes # got: '' # expected: '18' ok 8 - path inclusion does not modify the graph when alignment is a perfect match ok 9 - path inclusion does not modify the graph when alignment has a SNP but doesnt meet the coverage threshold ok 10 - path inclusion does not modify the included path when alignment has a SNP but doesnt meet the coverage threshold ok 11 - output GAM has single edit when SNP was filtered out due to coverage ok 12 - path inclusion with a complex variant introduces the right number of nodes ok 13 - path inclusion works for deletions ok 14 - SNPs can be included in the graph ok 15 - a soft clip at read start becomes a new head of the graph ok 16 - a soft clip at read end becomes a new tail of the graph ok 17 - augment -s works as desired ok 18 - the expected graph translation is exported when the graph is edited ok 19 - editing the graph with many SNP-containing alignments does not introduce duplicate identical nodes ok 20 - augmenting 2 snps with -m 1 produces the same nodes as default ok 21 - augmenting 2 snps and 2 errors with -m 11 produces the same nodes as with just the snps ok 22 - augmenting with 2snps makes correct number of nodes ok 23 - low-quality snp is filtered ok 24 - augmenting a packed graph produces same results as a vg graph ok 25 - augmenting a hash graph produces same results as a vg graph ok 26 - augmenting between nodes without filters works as expected ok 27 - augmenting between nodes with inactive filters works as expected ok 28 - augmenting between nodes N filter works as expected ok 29 - augmenting between nodes without filters works as expected on reverse strand ok 30 - augmenting between nodes with inactive filters works as expected on reverse strand ok 31 - augmenting between nodes N filter works as expected on reverse strand ok 32 - augmenting within node without filters works as expected ok 33 - augmenting within node with inactive filters works as expected ok 34 - augmenting within node with N filter works as expected ok 35 - augmenting within node without filters works as expected on reverse strand ok 36 - augmenting within node with inactive filters works as expected on reverse strand ok 37 - augmenting within node with N filter works as expected on reverse strand ok 38 - sequence in filtered alignment has removed insertion ok 39 - sequence in filtered alignment has removed insertion on reverse strand Failed 7/39 subtests [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in tiny.vg while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open tiny_aug.xg while loading handlegraph::HandleGraph error:[get_input_file_name] unable to open input file: tiny_aug.xg error[VPKG::load_one]: Could not open tiny_aug.xg to determine file type index file inverting/miniFasta.fa.fai not found, generating... WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 64. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. index file m.fa.fai not found, generating... [vg autoindex] Executing command: vg autoindex -r small/x.fa -v small/x.vcf.gz -w giraffe -p x [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. index file x_sub1.fa.fai not found, generating... index file x_sub2.fa.fai not found, generating... t/18_vg_call.t ........ 1..19 ok 1 - calling empty gam gives empty VCF ok 2 - Called microinversion ok 3 - Called no microinversion with haploid setting ok 4 - Fewer than 8 differences between called and true SV genotypes ok 5 - Fewer than 8 differences between called haploid and truncated true SV genotypes ok 6 - Same number of reference calls with -a as with -v ok 7 - Calling from extracted traversals by way of GBWT produces same genotypes as calling directly ok 8 - Fewer than 3 differences between allales called via traversals or directly ok 9 - call output same on vg as xg ok 10 - call output same on vg as xg ok 11 - vg call finds true homozygous variants in a cyclic graph ok 12 - vg call finds same variants when using gbwt to enumerate traversals ok 13 - call produces same output with gbwt and gbz ok 14 - vg call makes currect base path header with subpath input ok 15 - vg call makes only currect base path header with subpath input ok 16 - vg call only reports base paths with subpath input ok 17 - vg call makes currect base path header with subpath input and override ok 18 - vg call makes only currect base path header with subpath input and override ok 19 - overriding contig length does not change calls ok t/19_vg_compare.t ..... skipped: (no reason given) rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 85 triples rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 75 triples t/20_vgtordf.t ........ 1..6 ok 1 - vg view produces the expected number of lines of turtle ok 2 - vg view produces the expected number of lines of turtle ok 3 - rapper passed ok 4 - rapper passed ok 5 - vg view produces the expected number of lines of turtle ok 6 - vg view produces the expected number of lines of turtle ok warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x g.xg -g g.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 50 -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from g.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from g.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from g.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x g.xg -g g.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 1 -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from g.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from g.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from g.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ t/21_vg_filter.t ...... 1..13 ok 1 - vg filter with no options preserves input. ok 2 - vg filter downsamples correctly ok 3 - samtools 1.0+ and vg filter agree on how to select downsampled paired reads ok 4 - samtools 1.0+ and vg filter agree on how to select downsampled unpaired reads ok 5 - reads with refpos annotations not matching an exclusion regex are let through ok 6 - reads with refpos annotations matching an exclusion regex are removed ok 7 - negating a non-filter results in no reads ok 8 - a filter and its complement should form the entire file ok 9 - properly paired read passes proper filter ok 10 - improperly paired read fails proper filter ok 11 - read pairs can be tropped by feature not ok 12 - read pairs can be kept if only one read fails # got: '0' # expected: '2' ok 13 - unmapped reads can be filtered out Failed 1/13 subtests t/22_ggsv.t ........... skipped: (no reason given) t/23_vectorize.t ...... skipped: (no reason given) [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. t/25_circularize.t .... 1..2 ok 1 - a path may be circularized ok 2 - a circular path survives a round trip to/from xg ok WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps Warning [vg deconstruct]: -e is deprecated as it's now on default [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. Warning [vg deconstruct]: -e is deprecated as it's now on default Warning [vg deconstruct]: -e is deprecated as it's now on default [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. Warning [vg deconstruct]: -e is deprecated as it's now on default Warning [vg deconstruct]: -e is deprecated as it's now on default [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. Warning [vg deconstruct]: -e is deprecated as it's now on default [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. Warning [vg deconstruct]: -H is deprecated, and will be ignored Warning [vg deconstruct]: -e is deprecated as it's now on default Warning [vg deconstruct]: -d is deprecated - ploidy now inferred from haplotypes in path names Warning [vg deconstruct]: -H is deprecated, and will be ignored Warning [vg deconstruct]: -e is deprecated as it's now on default Warning [vg deconstruct]: -d is deprecated - ploidy now inferred from haplotypes in path names t/26_deconstruct.t: line 127: bcftools: command not found t/26_deconstruct.t: line 128: bcftools: command not found t/26_deconstruct.t: line 129: bcftools: command not found t/26_deconstruct.t: line 130: bcftools: command not found [vg autoindex] Executing command: vg autoindex -r small/x.fa -v small/x.vcf.gz -w giraffe -p x [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. t/26_deconstruct.t .... 1..37 ok 1 - deconstructed hla vcf has correct number of sites ok 2 - deconstructed hla vcf has correct insertion ok 3 - deconstructed hla vcf with other path has correct number of sites ok 4 - deconstructed hla vcf has correct deletion ok 5 - path-based and exhaustive decontruction give equivalent sites when expected ok 6 - path that differs from reference in every alt has correct genotype ok 7 - path that is same as reference in every alt has correct genotype ok 8 - reference contig correctly written ok 9 - deconstruct correctly handles a simple inversion ok 10 - deconstruct correctly handles a simple inversion when the reference contains the reversing edge ok 11 - deconstruct applies translation from gbz with -O ok 12 - deconstruct correctly handles a cycle in the reference path when contained inside snarl ok 13 - deconstruct correctly handles a cycle in the alt path ok 14 - cyclic reference deconstruction has correct number of variants ok 15 - deconstruct correctly handles cycle in the reference path that spans snarl ok 16 - -P -H options return correct number of variants ok 17 - -P -H options use correct reference name ok 18 - -P -H does not find conflict in alt1 in second variant ok 19 - deconstructing vg graph gives same output as xg graph ok 20 - haplotype 1 preserved when deconstructing small test with gbwt ok 21 - haplotype 2 preserved when deconstructing small test with gbwt ok 22 - gbz deconstruction gives same output as gbwt deconstruction ok 23 - cluster-free deconstruction finds all alt alleles ok 24 - clustered deconstruction finds fewer alt alleles ok 25 - clustered deconstruction finds correct allele info ok 26 - nested deconstruction gets correct star-allele for snp inside deletion ok 27 - PA=0 correctly set at both sites of neseted deletion ok 28 - nested deconstruction gets correct allele for snp inside deletion (without -R) ok 29 - nested deconstruction gets correct allele for snp inside insert ok 30 - PA=0 set for base allele of nested insertion ok 31 - PA=1 set for nested allele of nested insertion ok 32 - nested deconstruction gets correct contigs in vcf header for snp inside insert ok 33 - nested deconstruction gets correct star allele for snp ins2.ide ins2.ert ok 34 - INFO tags correct for level-0 site of double-nested SNP ok 35 - INFO tags correct for level-1 site of double-nested SNP ok 36 - INFO tags correct for level-2 site of double-nested SNP ok 37 - nested deconstruction handles cycle ok Statistics: Number of Non-Degenerate Snarls: 4 Snarls traversed by reads: 4 Snarls on reference: 0 Snarl length distribution: Statistics: Number of Non-Degenerate Snarls: 4 Snarls traversed by reads: 4 Snarls on reference: 4 Snarl length distribution: 1 3 2 1 index file flat1.fa.fai not found, generating... index file flat2.fa.fai not found, generating... Statistics: Number of Non-Degenerate Snarls: 8 Snarls traversed by reads: 8 Snarls on reference: 0 Snarl length distribution: WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file flats.fa.fai not found, generating... terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ Warning: realigned read TGAGCCCTACAG doesn't touch either end of its snarl! Warning: realigned read GTAGGGCTCATT doesn't touch either end of its snarl! Warning: realigned read GAGCCCTACAGA doesn't touch either end of its snarl! Warning: realigned read GCTCATTGTAAC doesn't touch either end of its snarl! Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! Warning: realigned read TGTCTGTAGGGC doesn't touch either end of its snarl! Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! Warning: realigned read AGGGCTCATTGT doesn't touch either end of its snarl! Warning: realigned read GCTCATTGTAAC doesn't touch either end of its snarl! Warning: realigned read GTCTGTAGGGCT doesn't touch either end of its snarl! Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! Warning: realigned read TATGTCTGTAGG doesn't touch either end of its snarl! Warning: realigned read TTACAATGAGCC doesn't touch either end of its snarl! Warning: realigned read TACAGACATATC doesn't touch either end of its snarl! Warning: realigned read GTTACAATGAGC doesn't touch either end of its snarl! Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! Warning: realigned read GGGCTCATTGTA doesn't touch either end of its snarl! Warning: realigned read CTCATTGTAACG doesn't touch either end of its snarl! Warning: realigned read CCCTACAGACAT doesn't touch either end of its snarl! Warning: realigned read TAGGGCTCATTG doesn't touch either end of its snarl! Warning: realigned read GCCCTACAGACA doesn't touch either end of its snarl! Warning: realigned read TGTCTGTAGGGC doesn't touch either end of its snarl! Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! Warning: realigned read CCTACAGACATA doesn't touch either end of its snarl! Statistics: Number of Non-Degenerate Snarls: 1 Snarls traversed by reads: 1 Snarls on reference: 1 Snarl length distribution: 0 1 t/27_vg_genotype.t .... 1..5 ok 1 - vg genotype runs successfully ok 2 - vg genotype runs successfully when emitting vcf ok 3 - called genotypes are correct in a small simulated example ok 4 - genotype format can be converted to and from JSON ok 5 - genotype finds big insert ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [algorithms::normalize] iteration 1 current length 55 [algorithms::normalize] normalized in 0 steps [algorithms::normalize] iteration 1 current length 55 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/28_translate.t ...... 1..2 ok 1 - alignments used to modify a graph may be projected back to the original graph and used to regenerate the same graph not ok 2 - translation overlay works and produces a sane result # got: '7477871ee13fab8541090e128d02a7f4' # expected: '3ce4390abe667b24eb5148e216a2f5ec' Failed 1/2 subtests [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. warning[vg chunk]: the vg-protobuf format is DEPRECATED. you probably want to use PackedGraph (pg) instead [vg] warning: node ID 44 appears multiple times. Skipping. [vg] warning: node ID 45 appears multiple times. Skipping. [vg] warning: node ID 43 appears multiple times. Skipping. [vg] warning: edge 43 end <-> 44 start appears multiple times. Skipping. [vg] warning: edge 43 end <-> 45 start appears multiple times. Skipping. [vg] warning: node ID 87 appears multiple times. Skipping. [vg] warning: node ID 88 appears multiple times. Skipping. [vg] warning: node ID 85 appears multiple times. Skipping. [vg] warning: node ID 86 appears multiple times. Skipping. [vg] warning: edge 87 end <-> 88 start appears multiple times. Skipping. [vg] warning: edge 85 end <-> 87 start appears multiple times. Skipping. [vg] warning: edge 85 end <-> 86 start appears multiple times. Skipping. [vg] warning: edge 86 end <-> 88 start appears multiple times. Skipping. [vg] warning: node ID 130 appears multiple times. Skipping. [vg] warning: node ID 131 appears multiple times. Skipping. [vg] warning: node ID 129 appears multiple times. Skipping. [vg] warning: edge 130 end <-> 131 start appears multiple times. Skipping. [vg] warning: edge 129 end <-> 130 start appears multiple times. Skipping. [vg] warning: edge 129 end <-> 131 start appears multiple times. Skipping. [vg] warning: node ID 173 appears multiple times. Skipping. [vg] warning: node ID 174 appears multiple times. Skipping. [vg] warning: node ID 172 appears multiple times. Skipping. [vg] warning: edge 173 end <-> 174 start appears multiple times. Skipping. [vg] warning: edge 172 end <-> 173 start appears multiple times. Skipping. [vg] warning: edge 172 end <-> 174 start appears multiple times. Skipping. Restricting to x from 1 to end Restricting to y from 1 to end [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. t/30_vg_chunk.t ....... 1..32 ok 1 - vg chunk with no options preserves nodes ok 2 - vg chunk with no options preserves edges ok 3 - chunk has path going through node 9 ok 4 - chunk can be found from GBZ ok 5 - snarl chunk works on simple example ok 6 - chunk has path going through node 9 ok 7 - -s produces correct number of chunks ok 8 - gam chunker produces correct number of graphs ok 9 - gam chunker produces correct number of gams ok 10 - gam chunker produces bed with correct number of chunks ok 11 - gam chunker emits each matching read at most once ok 12 - chunk contains the expected number of alignments ok 13 - simple gam chunker produces correct number of gams ok 14 - simple chunk contains the expected number of alignments ok 15 - id chunker produces correct chunk size ok 16 - id chunker produces correct single chunk ok 17 - id chunker traces correct chunk size without haplotypes ok 18 - id chunker traces correct chunk size ok 19 - chunker extracts no threads from an empty gPBWT ok 20 - chunker extracts 2 local threads from a gBWT with 2 locally distinct threads in it ok 21 - chunker can extract a partial haplotype from a GBWT ok 22 - chunker can extract a partial haplotype from a GBZ ok 23 - chunker doesn't see haplotypes in the GBZ if asked not to ok 24 - trace consistent on path coordinates ok 25 - n-chunking works and chunks over the full graph ok 26 - path-based components finds subgraphs ok 27 - x gam chunk has correct number of reads ok 28 - y gam chunk has correct number of reads ok 29 - x gam chunk has correct number of reads with -p path ok 30 - y gam chunk has correct number of reads with -p path ok 31 - path-based component contains correct path length ok 32 - components finds subgraphs ok index file add/ref.fa.fai not found, generating... WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 3 haplotypes at ref:18: 32 bp vs. 33 bp haplotypes vs. graphs average Variant 2: 3 haplotypes at ref:21: 32 bp vs. 34 bp haplotypes vs. graphs average Variant 3: 3 haplotypes at ref:23: 33 bp vs. 34 bp haplotypes vs. graphs average WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 3 haplotypes at chrR:18: 32 bp vs. 33 bp haplotypes vs. graphs average Variant 2: 3 haplotypes at chrR:21: 32 bp vs. 34 bp haplotypes vs. graphs average Variant 3: 3 haplotypes at chrR:23: 33 bp vs. 34 bp haplotypes vs. graphs average WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 3 haplotypes at ref:18: 32 bp vs. 33 bp haplotypes vs. graphs average Variant 2: 3 haplotypes at ref:21: 32 bp vs. 34 bp haplotypes vs. graphs average Variant 3: 3 haplotypes at ref:23: 33 bp vs. 34 bp haplotypes vs. graphs average WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 4 haplotypes at ref:2: 33 bp vs. 34 bp haplotypes vs. graphs average Variant 2: 4 haplotypes at ref:21: 33 bp vs. 36 bp haplotypes vs. graphs average Variant 3: 4 haplotypes at ref:32: 33 bp vs. 36 bp haplotypes vs. graphs average index file add/refN.fa.fai not found, generating... WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 4 haplotypes at ref:2: 33 bp vs. 34 bp haplotypes vs. graphs average Variant 2: 4 haplotypes at ref:21: 33 bp vs. 36 bp haplotypes vs. graphs average Variant 3: 4 haplotypes at ref:32: 33 bp vs. 36 bp haplotypes vs. graphs average index file add/ngap.fa.fai not found, generating... WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 2 haplotypes at ngap:10923: 224 bp vs. 224 bp haplotypes vs. graphs average Variant 2: 5 haplotypes at ngap:11014: 256 bp vs. 258 bp haplotypes vs. graphs average Variant 3: 5 haplotypes at ngap:11030: 256 bp vs. 261 bp haplotypes vs. graphs average Variant 4: 5 haplotypes at ngap:11035: 256 bp vs. 261 bp haplotypes vs. graphs average Variant 5: 5 haplotypes at ngap:11043: 256 bp vs. 261 bp haplotypes vs. graphs average WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 2 haplotypes at x:9: 160 bp vs. 161 bp haplotypes vs. graphs average Variant 2: 2 haplotypes at x:10: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 3: 2 haplotypes at x:14: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 4: 2 haplotypes at x:34: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 5: 2 haplotypes at x:39: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 6: 2 haplotypes at x:52: 224 bp vs. 231 bp haplotypes vs. graphs average Variant 7: 2 haplotypes at x:58: 224 bp vs. 232 bp haplotypes vs. graphs average Variant 8: 2 haplotypes at x:100: 256 bp vs. 265 bp haplotypes vs. graphs average Variant 9: 2 haplotypes at x:103: 256 bp vs. 267 bp haplotypes vs. graphs average Variant 10: 2 haplotypes at x:122: 288 bp vs. 299 bp haplotypes vs. graphs average Variant 11: 2 haplotypes at x:142: 288 bp vs. 301 bp haplotypes vs. graphs average Variant 12: 2 haplotypes at x:160: 306 bp vs. 319 bp haplotypes vs. graphs average Variant 13: 2 haplotypes at x:172: 338 bp vs. 353 bp haplotypes vs. graphs average Variant 14: 2 haplotypes at x:178: 313 bp vs. 327 bp haplotypes vs. graphs average Variant 15: 2 haplotypes at x:187: 313 bp vs. 327 bp haplotypes vs. graphs average Variant 16: 2 haplotypes at x:200: 294 bp vs. 306 bp haplotypes vs. graphs average Variant 17: 2 haplotypes at x:204: 294 bp vs. 306 bp haplotypes vs. graphs average Variant 18: 2 haplotypes at x:218: 288 bp vs. 300 bp haplotypes vs. graphs average Variant 19: 2 haplotypes at x:221: 288 bp vs. 300 bp haplotypes vs. graphs average Variant 20: 2 haplotypes at x:272: 256 bp vs. 266 bp haplotypes vs. graphs average Variant 21: 2 haplotypes at x:277: 256 bp vs. 272 bp haplotypes vs. graphs average Variant 22: 2 haplotypes at x:287: 256 bp vs. 272 bp haplotypes vs. graphs average Variant 23: 2 haplotypes at x:294: 256 bp vs. 272 bp haplotypes vs. graphs average Variant 24: 2 haplotypes at x:297: 291 bp vs. 305 bp haplotypes vs. graphs average Variant 25: 2 haplotypes at x:312: 323 bp vs. 340 bp haplotypes vs. graphs average Variant 26: 2 haplotypes at x:313: 323 bp vs. 341 bp haplotypes vs. graphs average Variant 27: 2 haplotypes at x:345: 291 bp vs. 306 bp haplotypes vs. graphs average Variant 28: 2 haplotypes at x:347: 323 bp vs. 339 bp haplotypes vs. graphs average Variant 29: 2 haplotypes at x:353: 311 bp vs. 326 bp haplotypes vs. graphs average Variant 30: 2 haplotypes at x:373: 291 bp vs. 306 bp haplotypes vs. graphs average Variant 31: 2 haplotypes at x:397: 288 bp vs. 307 bp haplotypes vs. graphs average Variant 32: 2 haplotypes at x:398: 288 bp vs. 307 bp haplotypes vs. graphs average Variant 33: 2 haplotypes at x:405: 241 bp vs. 258 bp haplotypes vs. graphs average Variant 34: 2 haplotypes at x:408: 241 bp vs. 258 bp haplotypes vs. graphs average Variant 35: 2 haplotypes at x:466: 254 bp vs. 260 bp haplotypes vs. graphs average Variant 36: 2 haplotypes at x:474: 286 bp vs. 295 bp haplotypes vs. graphs average Variant 37: 2 haplotypes at x:489: 286 bp vs. 296 bp haplotypes vs. graphs average Variant 38: 2 haplotypes at x:500: 286 bp vs. 297 bp haplotypes vs. graphs average Variant 39: 2 haplotypes at x:523: 300 bp vs. 309 bp haplotypes vs. graphs average Variant 40: 2 haplotypes at x:533: 289 bp vs. 299 bp haplotypes vs. graphs average Variant 41: 1 haplotypes at x:553: 257 bp vs. 263 bp haplotypes vs. graphs average Variant 42: 1 haplotypes at x:566: 257 bp vs. 263 bp haplotypes vs. graphs average Variant 43: 2 haplotypes at x:629: 277 bp vs. 281 bp haplotypes vs. graphs average Variant 44: 2 haplotypes at x:647: 278 bp vs. 285 bp haplotypes vs. graphs average Variant 45: 2 haplotypes at x:654: 278 bp vs. 287 bp haplotypes vs. graphs average Variant 46: 2 haplotypes at x:668: 310 bp vs. 320 bp haplotypes vs. graphs average Variant 47: 2 haplotypes at x:669: 310 bp vs. 321 bp haplotypes vs. graphs average Variant 48: 2 haplotypes at x:681: 289 bp vs. 299 bp haplotypes vs. graphs average Variant 49: 2 haplotypes at x:688: 289 bp vs. 299 bp haplotypes vs. graphs average Variant 50: 2 haplotypes at x:698: 280 bp vs. 289 bp haplotypes vs. graphs average Variant 51: 2 haplotypes at x:714: 299 bp vs. 307 bp haplotypes vs. graphs average Variant 52: 2 haplotypes at x:757: 287 bp vs. 299 bp haplotypes vs. graphs average Variant 53: 2 haplotypes at x:775: 273 bp vs. 285 bp haplotypes vs. graphs average Variant 54: 2 haplotypes at x:777: 273 bp vs. 286 bp haplotypes vs. graphs average Variant 55: 2 haplotypes at x:789: 273 bp vs. 287 bp haplotypes vs. graphs average Variant 56: 2 haplotypes at x:795: 273 bp vs. 287 bp haplotypes vs. graphs average Variant 57: 2 haplotypes at x:813: 287 bp vs. 300 bp haplotypes vs. graphs average Variant 58: 2 haplotypes at x:823: 287 bp vs. 302 bp haplotypes vs. graphs average Variant 59: 2 haplotypes at x:827: 319 bp vs. 334 bp haplotypes vs. graphs average Variant 60: 2 haplotypes at x:858: 297 bp vs. 310 bp haplotypes vs. graphs average Variant 61: 2 haplotypes at x:859: 297 bp vs. 312 bp haplotypes vs. graphs average Variant 62: 2 haplotypes at x:860: 297 bp vs. 312 bp haplotypes vs. graphs average Variant 63: 2 haplotypes at x:877: 287 bp vs. 303 bp haplotypes vs. graphs average Variant 64: 2 haplotypes at x:888: 244 bp vs. 262 bp haplotypes vs. graphs average Variant 65: 2 haplotypes at x:899: 243 bp vs. 263 bp haplotypes vs. graphs average Variant 66: 2 haplotypes at x:901: 243 bp vs. 264 bp haplotypes vs. graphs average Variant 67: 2 haplotypes at x:916: 224 bp vs. 243 bp haplotypes vs. graphs average Variant 68: 2 haplotypes at x:917: 224 bp vs. 243 bp haplotypes vs. graphs average Variant 69: 2 haplotypes at x:923: 223 bp vs. 243 bp haplotypes vs. graphs average Variant 70: 2 haplotypes at x:925: 223 bp vs. 243 bp haplotypes vs. graphs average Variant 71: 2 haplotypes at x:929: 222 bp vs. 242 bp haplotypes vs. graphs average Variant 72: 2 haplotypes at x:939: 204 bp vs. 223 bp haplotypes vs. graphs average Variant 73: 2 haplotypes at x:945: 204 bp vs. 223 bp haplotypes vs. graphs average Variant 74: 2 haplotypes at x:972: 177 bp vs. 194 bp haplotypes vs. graphs average Variant 75: 2 haplotypes at x:1000: 136 bp vs. 149 bp haplotypes vs. graphs average WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand '[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead.add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/31_vg_add.t ......... 1..12 ok 1 - vg add can create a graph ok 2 - vg add can create a graph with contig renames ok 3 - vg add produces the same graph from VCFs with different contig names ok 4 - vg add can create a graph from a PackedGraph ok 5 - vg add produces the same graph from the same input in different formats ok 6 - having reference Ns does not affect the graph topology ok 7 - adding variants adds only the alt bases near large N gaps ok 8 - vg add can create a slightly larger graph ok 9 - ranks are calculated for emitted paths not ok 10 - graphs with backward nodes can be added to # got: '' # expected: '5' not ok 11 - graphs with multiple overlapping paths nodes can be added to # got: '' # expected: '5' not ok 12 - graphs with backward and forward nodes can be added to # got: '' # expected: '5' Failed 3/12 subtests [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in snarls.vg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error:[get_input_file_name] unable to open input file: snarls.xg error[VPKG::load_one]: Could not open snarls.xg while loading handlegraph::PathHandleGraph Restricting to x from 1 to end Restricting to y from 1 to end [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in nested.vg while loading handlegraph::PathHandleGraph [vg autoindex] Executing command: vg autoindex -p index -g graphs/big_snarl_named.gfa -w giraffe [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing VG graph from GFA input. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Constructing a greedy path cover GBWT [IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. t/32_vg_snarls.t ...... 1..19 not ok 1 - vg snarls made right number of protobuf Snarls # got: '0' # expected: '3' not ok 2 - vg snarls made right number of protobuf SnarlTraversals # got: '0' # expected: '6' not ok 3 - unnamed test # got: '1,3,7,' # expected: 'vg snarls made snarls in the right order' not ok 4 - vg snarls on xg made right number of protobuf Snarls # got: '0' # expected: '3' not ok 5 - vg snarls on xg made right number of protobuf SnarlTraversals # got: '0' # expected: '6' ok 6 - vcf traversals are the same as exhaustive traversals for tiny graph ok 7 - vcf traversals are the same as exhaustive traversals for inversion ok 8 - vcf traversals are the same as exhaustive traversals for ins_and_del graph ok 9 - correct number of snarls when parallelizing on compoents ok 10 - same number of snarls when parallelizing on components ok 11 - GBZ graphs can be used for finding snarls ok 12 - correct number of snarls in the GFA W-line example not ok 13 - vg snarls made the right snarls when dealing with nested chains # got: '1' # expected: '15' not ok 14 - vg snarls made snarls in the right order when dealing with nested chains # got: '1' # expected: '0' ok 15 - Correct snarls are found in GFA space ok 16 - In node ID space traversal visits 7 nodes ok 17 - In node ID space traversal visits 4 trivial snarls ok 18 - In segment name space traversal visits 3 segments ok 19 - In segment name space traversal visits 0 trivial snarls Failed 7/19 subtests [vg mpmap] elapsed time 0 s: Executing command: vg mpmap --suppress-mismapping -B -P 1 -n dna -x xy2.xg -g xy2.gcsa -f reads/xy2.match.fq -F GAM [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.match.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap --suppress-mismapping -B -P 1 -n dna -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.match.fq -F GAM [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0 s: Completed loading GBWT [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.match.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. warning:[vg mpmap] It is HIGHLY recommended to use a distance index (-d) for clustering on splice graphs. Both accuracy and speed will suffer without one. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap --suppress-mismapping -B -M 2 -n rna -x xy2.xg -g xy2.gcsa -f reads/xy2.match.fq [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.match.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -I 200 -D 200 -x xy2.xg -g xy2.gcsa -f reads/xy2.matchpaired.fq -i -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.matchpaired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -I 200 -D 200 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.matchpaired.fq -i -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0 s: Completed loading GBWT [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.matchpaired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. warning:[vg mpmap] Snarl file (-s) is ignored for single path alignment formats (-F) without multipath population scoring (--max-paths). [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. warning:[vg mpmap] Snarl file (-s) is ignored for single path alignment formats (-F) without multipath population scoring (--max-paths). [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -s xy2.snarls -f reads/xy2.discordant.fq -t 1 -F GAM [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading snarls from xy2.snarls [vg mpmap] elapsed time 0 s: Completed loading snarls [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0 s: Completed loading GBWT [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -s xy2.snarls -f reads/xy2.discordant.fq -t 1 -F GAM [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading snarls from xy2.snarls [vg mpmap] elapsed time 0 s: Completed loading snarls [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0 s: Completed loading GBWT [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 50 -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 100000 -D 5 -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 1 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 1 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 1 s: Completed loading LCP [vg mpmap] elapsed time 1 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread warning:[vg mpmap] Could not find 1000 (-b) unambiguous read pair mappings to estimate fragment length ditribution. This can happen due to data issues (e.g. unpaired reads being mapped as pairs) or because the sample size is too large for the read set. Mapping read pairs as independent single-ended reads. [vg mpmap] elapsed time 1 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -G input.gam -I 500 -D 100 -n dna -i -F GAM --no-qual-adjust [vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 1 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 1 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1 s: Mapping reads from input.gam using 12 threads [vg mpmap] elapsed time 1 s: Mapping finished. Mapped 1000 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -n dna -x t.xg -g t.gcsa -f t.fq [vg mpmap] elapsed time 0 s: Loading graph from t.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from t.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from t.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from t.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 3 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq [vg mpmap] elapsed time 0 s: Loading graph from s.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 350 -D 10 [vg mpmap] elapsed time 0 s: Loading graph from s.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 530 -D 10 [vg mpmap] elapsed time 0 s: Loading graph from s.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 530 -D 10 -F SAM --report-group-mapq [vg mpmap] elapsed time 0 s: Loading graph from s.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x xy.xg -d xy.dist -g xy.gcsa -G x.gam -F SAM -i --frag-mean 50 --frag-stddev 10 -M 1 [vg mpmap] elapsed time 0 s: Loading graph from xy.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from xy.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Building null model to calibrate mismapping detection [vg mpmap] elapsed time 9 s: Mapping reads from x.gam using 12 threads [vg mpmap] elapsed time 9 s: Mapping finished. Mapped 1000 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x xy.xg -d xy.dist -g xy.gcsa -G x.gam -F SAM -M 1 [vg mpmap] elapsed time 0 s: Loading graph from xy.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from xy.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy.gcsa.lcp [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Building null model to calibrate mismapping detection [vg mpmap] elapsed time 11 s: Mapping reads from x.gam using 12 threads [vg mpmap] elapsed time 11 s: Mapping finished. Mapped 2000 reads. t/33_vg_mpmap.t ....... 1..21 ok 1 - MAPQ is 50% without haplotype info ok 2 - haplotype match can disambiguate ok 3 - MAPQs are computed for all multimappings ok 4 - MAPQ is 50% when paired without haplotype info ok 5 - haplotype match can disambiguate paired ok 6 - use of haplotype-aware mapping is recorded ok 7 - Haplotype-oblivious mapping places read on the wrong contig ok 8 - Haplotype-oblivious mapping places read with MAPQ of 50% ok 9 - Haplotype-aware mapping places read on the right contig ok 10 - Haplotype-aware mapping places read with MAPQ > 50% ok 11 - paired read alignments forced to be consistent have lower score than unrestricted alignments ok 12 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments ok 13 - paired read alignments forced to be near each other are closer together in node id space than those forced to be far apart ok 14 - small batches are still all paired in the output ok 15 - multipath mapping works in scenarios that trigger branch point trimming ok 16 - spliced alignments can be found when aligning RNA ok 17 - paired mapping can identify a splice junction on read 1 ok 18 - paired mapping can identify a splice junction on read 2 ok 19 - HTS output contains group mapq annotation ok 20 - paired reads are evenly split between equivalent mappings ok 21 - unpaired reads are evenly split between equivalent mappings ok [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ t/34_vg_pack.t ........ 1..20 ok 1 - allele observation packing detects 2 SNPs ok 2 - pileup packs agree with graph coverage ok 3 - graph coverages are merged from multiple .cx indexes ok 4 - edit records are merged from multiple .cx indexes ok 5 - binned edit accumulation does not affect the result ok 6 - pack records are filtered by node id ok 7 - pack records are filtered by node id ok 8 - pack index merging produces the expected result ok 9 - pack index merging produces the expected result for edges ok 10 - pack computes the same total edge coverage as pileup ok 11 - pack stores the correct edge pileup to disk ok 12 - node packs on vg same as xg ok 13 - edge packs on vg same as xg ok 14 - node packs same on vg when using 3 threads as when using 1 ok 15 - edge packs same on vg when using 2 threads as when using 1 ok 16 - node packs on gaf same as gam ok 17 - edge packs on gaf same as gam not ok 18 - average node qualities are correct # got: '0-0-0-0-0-0-0-0-0-0-' # expected: '20-15-10-10-0-0-0-0-60-60-' ok 19 - pack -s 10 sets fist and last 10bp of coverage to 0 like expected ok 20 - pack -s 9 sets fist and last 9bp of coverage to 0 like expected Failed 1/20 subtests [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open circular_path.xg while loading handlegraph::PathHandleGraph t/36_vg_annotate.t .... 1..9 ok 1 - we can detect when reads contain non-reference variation ok 2 - vg annotate finds the right number of reads overlapping a feature ok 3 - all reads overlapping a feature fall on its node ok 4 - vg annotate finds no reads touching both of two distant features ok 5 - vg annotate shows reads having to go through one feature to get to another at the end ok 6 - vg annotate shows all reads overlapping a whole-reference-covering feature ok 7 - annotating with earliest path position produces one position ok 8 - annotating with multiple path positions produces multiple positions not ok 9 - annotations derived from BED can span the end/start joins of circular paths # got: '' # expected: '{"node_id":"1","offset":"5"} # {"node_id":"1"}' Failed 1/9 subtests t/37_vg_gbwt.t ........ 1..159 ok 1 - chromosome X GBWT with vg gbwt ok 2 - chromosome X GBWT with vg index ok 3 - identical construction results with vg gbwt and vg index ok 4 - chromosome X VCF parse ok 5 - chromosome X GBWT from VCF parse ok 6 - identical construction results with vg gbwt and from VCF parse ok 7 - chromosome X: 2 threads ok 8 - chromosome X: 1 contig ok 9 - chromosome X: 2 haplotypes ok 10 - chromosome X: 1 sample ok 11 - chromosome X: 2 thread names ok 12 - chromosome X: 1 contig name ok 13 - chromosome X: 1 sample name ok 14 - chromosome X reference GBWT with vg gbwt ok 15 - chromosome X reference GBWT with vg index ok 16 - identical construction results with vg gbwt and vg index ok 17 - chromosome X reference: 1 thread ok 18 - chromosome X GAF with vg gbwt ok 19 - chromosome X GAF with vg index ok 20 - identical construction results with vg gbwt and vg index ok 21 - chromosome X GAM with vg gbwt ok 22 - identical construction results from GAF and GAM ok 23 - chromosome X subgraph GBWT with vg gbwt ok 24 - no warnings about missing variants ok 25 - chromosome X subgraph GBWT with vg index ok 26 - identical construction results with vg gbwt and vg index ok 27 - insertion merging with multiple chromosomes ok 28 - fast merging with multiple chromosomes ok 29 - identical merging results with the insertion and fast algorithms ok 30 - parallel merging with multiple chromosomes ok 31 - identical merging results with the insertion and parallel algorithms ok 32 - direct construction with multiple chromosomes and a single VCF ok 33 - identical results with direct construction and merging ok 34 - direct construction with multiple chromosomes and multiple VCFs ok 35 - identical construction results with a single VCF and multiple VCFs ok 36 - construction preset: 1000gp ok 37 - multiple chromosomes: 4 threads ok 38 - multiple chromosomes: 2 contigs ok 39 - multiple chromosomes: 2 haplotypes ok 40 - multiple chromosomes: 1 sample ok 41 - paths as contigs with vg gbwt ok 42 - paths as contigs with vg index ok 43 - identical construction results with vg gbwt and vg index ok 44 - paths as contigs: 2 threads ok 45 - paths as contigs: 2 contigs ok 46 - paths as contigs: 1 haplotype ok 47 - paths as contigs: 1 sample ok 48 - r-index construction ok 49 - normal merging: non-empty + empty ok 50 - the index remains unchanged ok 51 - normal merging: empty + non-empty ok 52 - the index remains unchanged ok 53 - fast merging: non-empty + empty ok 54 - the index remains unchanged ok 55 - fast merging: empty + non-empty ok 56 - the index remains unchanged ok 57 - parallel merging: non-empty + empty ok 58 - the index remains unchanged ok 59 - parallel merging: empty + non-empty ok 60 - the index remains unchanged ok 61 - haplotypes and paths: 6 threads ok 62 - samples can be removed from a GBWT index ok 63 - haplotypes only: 4 threads ok 64 - all samples: 12 threads ok 65 - all samples: 6 haplotypes ok 66 - multiple samples can be removed from a GBWT index ok 67 - sample 2: 4 threads ok 68 - sample 2: 2 haplotypes ok 69 - threads can be extracted from GBWT ok 70 - correct size for the thread file ok 71 - GBWTGraph construction ok 72 - GBWTGraph was serialized correctly ok 73 - GBZ construction from GBWT ok 74 - GBZ was serialized correctly ok 75 - GBZ construction from VCF ok 76 - Identical construction results from GBWT and VCF ok 77 - GBZ construction from GBWTGraph ok 78 - Identical construction results from XG and GBWTGraph ok 79 - GBWT extraction from GBZ ok 80 - Identical GBWT indexes ok 81 - GBWT + GBWTGraph extraction from GBZ ok 82 - Identical GBWT indexes ok 83 - Identical GBWTGraphs ok 84 - Path cover GBWTGraph construction ok 85 - GBWTGraph was serialized correctly ok 86 - path cover: 32 threads ok 87 - path cover: 2 contigs ok 88 - path cover: 16 haplotypes ok 89 - path cover: 16 samples ok 90 - Path cover GBWTGraph construction ok 91 - GBWTGraph was serialized correctly ok 92 - path cover w/ paths: 34 threads ok 93 - path cover w/ paths: 2 contigs ok 94 - path cover w/ paths: 17 haplotypes ok 95 - path cover w/ paths: 17 samples ok 96 - Local haplotypes GBWTGraph construction ok 97 - GBWTGraph was serialized correctly ok 98 - local haplotypes: 32 threads ok 99 - local haplotypes: 2 contigs ok 100 - local haplotypes: 16 haplotypes ok 101 - local haplotypes: 16 samples ok 102 - Local haplotypes GBZ construction (single job) ok 103 - GBZ was serialized correctly ok 104 - Local haplotypes GBZ construction (two jobs) ok 105 - GBZ was serialized correctly ok 106 - Local haplotypes GBWTGraph construction ok 107 - GBWTGraph was serialized correctly ok 108 - local haplotypes w/ paths: 34 threads ok 109 - local haplotypes w/ paths: 2 contigs ok 110 - local haplotypes w/ paths: 17 haplotypes ok 111 - local haplotypes w/ paths: 17 samples ok 112 - Local haplotypes with reference paths from a larger GBZ ok 113 - local haplotypes w/ paths: 36 threads ok 114 - local haplotypes w/ paths: 2 contigs ok 115 - local haplotypes w/ paths: 18 haplotypes ok 116 - local haplotypes w/ paths: 18 samples ok 117 - local haplotypes w/ paths: reference_samples set ok 118 - Augmented GBWTGraph construction ok 119 - GBWTGraph was serialized correctly ok 120 - augmented: 18 threads ok 121 - augmented: 2 contigs ok 122 - augmented: 18 haplotypes ok 123 - augmented: 17 samples ok 124 - GBWT construction from GFA ok 125 - GBWT was serialized correctly ok 126 - gfa: 4 threads ok 127 - gfa: 2 contigs ok 128 - gfa: 2 haplotypes ok 129 - gfa: 1 sample ok 130 - GBWT+GBWTGraph construction from GFA ok 131 - Identical construction results with and without GBWTGraph ok 132 - GBWTGraph was serialized correctly ok 133 - no chopping: 0 translations ok 134 - GBZ construction from GFA ok 135 - GBZ was serialized correctly ok 136 - GBWT+GBWTGraph construction from GFA with chopping ok 137 - chopping: 3 threads ok 138 - chopping: 1 contig ok 139 - chopping: 3 haplotypes ok 140 - chopping: 2 samples ok 141 - chopping: 9 translations ok 142 - Translation can be extracted from GBZ ok 143 - from GBZ: 8 translations ok 144 - GBWT+GBWTGraph construction from GFA with reference paths ok 145 - ref paths: 6 threads ok 146 - ref paths: 2 contigs ok 147 - ref paths: 3 haplotypes ok 148 - ref paths: 2 samples ok 149 - ref paths: 0 translations ok 150 - GBZ construction from GFA with reference ok 151 - GBZ GBWT tag extraction works ok 152 - GBWT tags contain the correct reference samples ok 153 - GBZ GBWT tag modification works ok 154 - Changing reference_samples tag can make a reference a haplotype ok 155 - Changing reference_samples tag can make a haplotype a reference ok 156 - GBZ GBWT tag modification validation works ok 157 - Samples can be direcly set as references ok 158 - Direct reference assignment works ok 159 - GBZ can represent reference paths without haplotype numbers ok t/38_vg_prune.t ....... 1..21 ok 1 - pruning produces the correct number of components ok 2 - pruning leaves the correct number of nodes ok 3 - pruning leaves the correct number of edges ok 4 - pruning without high-degree nodes produces the correct number of components ok 5 - pruning without high-degree nodes leaves the correct number of nodes ok 6 - pruning without high-degree nodes leaves the correct number of edges ok 7 - pruning with path restoring produces the correct number of components ok 8 - pruning with path restoring leaves the correct number of nodes ok 9 - pruning with path restoring leaves the correct number of edges ok 10 - pruning with path/thread unfolding produces the correct number of components ok 11 - pruning with path/thread unfolding produces the correct number of nodes ok 12 - pruning with path/thread unfolding produces the correct number of edges ok 13 - pruning with path unfolding produces the correct number of components ok 14 - pruning with path unfolding produces the correct number of nodes ok 15 - pruning with path unfolding produces the correct number of edges ok 16 - unfolding with multi-chromosome GBWT produces the correct number of components ok 17 - unfolding with multi-chromosome GBWT produces the correct number of nodes ok 18 - unfolding with multi-chromosome GBWT produces the correct number of edges ok 19 - empty mapping starts from the right node id ok 20 - the first unfolded graph adds the correct number of nodes to the mapping ok 21 - the second unfolded graph adds the correct number of nodes to the mapping ok warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. t/39_vg_inject.t ...... 1..14 ok 1 - reads are generated ok 2 - vg inject works for all reads included in the original bam ok 3 - vg inject retains read names ok 4 - vg inject works perfectly for the position of alignment in the simple graph ok 5 - vg inject works perfectly for the position of alignment ok 6 - vg inject works perfectly for the mapping quality of alignment ok 7 - vg inject works perfectly for the cigar of alignment in the simple graph ok 8 - vg inject works perfectly for the cigar of alignment ok 9 - vg inject preserves all reads ok 10 - vg inject works perfectly for the reads flagged as is_reverse ok 11 - vg inject does not make an alignment for an umapped read ok 12 - vg inject does not crash on an unmapped read ok 13 - vg inject supports GAF output ok 14 - vg inject produces valid alignments of the read and reference ok warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. 1000 reads correct 1 reads correct 1 reads correct 0 reads correct 0 reads correct 1 reads correct t/40_vg_gamcompare.t .. 1..7 ok 1 - gamcompare completes ok 2 - gamcompare says the truth is correctly mapped ok 3 - Reads annotated with leftmost position only are close enough at a long distance ok 4 - Reads are close enough at a long distance with a distance index ok 5 - Reads annotated with leftmost position only are too far apart at a short distance ok 6 - Reads are too far apart at a short distance with a distance index ok 7 - Reads annotated with multiple positions only are close enough at a short distance ok [Viz::init] error: Image would be 86252x88 which is larger than the maximum 32,767 px on a side canvas that Cairo supports for raster images. Use an SVG output, try `odgi viz`, or reduce your input size! t/41_vg_viz.t ......... 1..4 ok 1 - vg viz runs ok 2 - vg viz succeeds when drawing a PNG ok 3 - vg viz actually creates an output PNG ok 4 - vg viz knows when a graph is too big to draw as a PNG ok t/42_vg_gamsort.t ..... 1..2 ok 1 - Sorting a GAM orders the alignments by min node ID ok 2 - sorted GAMs can be indexed during the sort ok graph: valid t/43_vg_simplify.t .... 1..5 ok 1 - vg simplify runs through when popping small bubbles ok 2 - simplification pops all the bubbles in a simple graph ok 3 - vg simplify runs through when removing rare variants ok 4 - the graph is valid after removing rare variants ok 5 - simplification keeps only some variants ok t/44_vg_benchmark.t ... 1..1 ok 1 - vg benchmark completes succesfully ok WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/45_vg_sort.t ........ 1..5 ok 1 - ids in our test graph are not initially in sorted order ok 2 - a vg graph can be sorted and indexed by ID without crashing ok 3 - a vg graph can be sorted topologically ok 4 - a vg graph can be sorted with Eades algorithm without crashing ok 5 - a vg graph can be sorted with the max-flow algorithm without crashing ok t/46_vg_minimizer.t ... 1..16 ok 1 - default parameters ok 2 - distance index or --no-dist is required ok 3 - single-threaded construction ok 4 - construction is deterministic ok 5 - syncmer index ok 6 - construction is deterministic ok 7 - minimizer parameters ok 8 - setting -k -w works correctly ok 9 - construction from GBWTGraph ok 10 - construction is deterministic ok 11 - construction from GBZ ok 12 - construction is deterministic ok 13 - construction with payload ok 14 - multiple graphs: first ok 15 - multiple graphs: second ok 16 - construction is deterministic ok WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. t/47_vg_dotplot.t ..... 1..1 ok 1 - vg dotplot runs successfully ok [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. warning [vg convert]: currently cannot convert GFA directly to XG; converting through another format terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. warning:[GFAParser] Skipping GFA P line: GFA format error: On pass 1: On line 27: Duplicate path GRCh38.chr1 exists in graph index file ref.fa.fai not found, generating... warning: Thread 4 encountered sequence of length 275, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. alignment: valid graph: valid warning: Thread 0 encountered sequence of length 275, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. alignment: valid graph: valid t/48_vg_convert.t ..... 1..106 ok 1 - vg convert maintains same nodes throughout xg conversion ok 2 - vg convert maintains same nodes throughout hash-graph conversion ok 3 - vg convert maintains same nodes throughout packed-graph conversion ok 4 - vg convert maintains same nodes throughout gfa conversion ok 5 - hash graph conversion looks good ok 6 - packed graph conversion looks good ok 7 - vg conversion looks good ok 8 - gfa conversion looks good ok 9 - xg conversion looks good ok 10 - on disk gfa conversion looks good ok 11 - streaming gfa conversion looks good ok 12 - gfa to xg conversion looks good ok 13 - gfa to gfa conversion looks good ok 14 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice ok 15 - vg convert gam -> gaf -> gam -> gaf gives same result multithreaded as with -t 1 ok 16 - vg convert gam -> gaf.gz -> gam -> gaf gives same result multithreaded as with -t 1 ok 17 - vg convert gam -> gaf -> gam produces same gam Paths with snps and indels ok 18 - vg convert gam -> gaf -> gam preserves sequence ok 19 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice in presence of indels and snps ok 20 - vg convert cg-gaf -> gam -> cs-gaf gives expected output (snps converted to matches, insertion converted to Ns) ok 21 - vg convert gam -> gaf -> gam preserves sequences of 1mb1kgp simulated reads ok 22 - vg convert gam -> gaf -> gam ->gaf makes same gaf each time on 1mb1kgp simulated reads not ok 23 - split alignment converted using deletions to represent internal offsets # got: '' # expected: 'cs:Z::13-CCAGTGCTCGCATC:2' ok 24 - vg convert gam -> gaf ->gam -> gaf makes same gaf each time for split alignment ok 25 - convert gam->gaf->gam on softclipped read preserves sequence ok 26 - convert gam->gaf->gam->gaf makes same gaf each time of soft clipped alignment ok 27 - convert gam->gaf->gam on read with floating insertion preserves sequence ok 28 - convert gam->gaf->gam->gaf makes same gaf each time of floating insertion alignment ok 29 - converting gfa and equivalent rgfa produces same output ok 30 - rank-1 rgfa subpath found ok 31 - 2nd column of gfa id translation file contains all rgfa nodes ok 32 - 3rd column of gfa id translation file contains all gfa nodes ok 33 - rgfa output wrote no P-lines ok 34 - rgfa export roundtrips back to normal P-lines ok 35 - GBWTGraph to HashGraph conversion ok 36 - GFA -> GBWTGraph -> HashGraph -> GFA conversion maintains segments ok 37 - GFA -> GBWTGraph -> HashGraph -> GFA conversion maintains walks ok 38 - GBZ to HashGraph conversion ok 39 - GFA -> GBZ -> HashGraph -> GFA conversion maintains segments ok 40 - GBWTGraph to GFA conversion with walks, GBWTGraph algorithm ok 41 - GBWTGraph to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file ok 42 - GBWTGraph to GFA conversion with walks, vg algorithm ok 43 - GBWTGraph to GFA conversion with vg algorithm creates the correct possibly-unnormalized GFA file ok 44 - GBZ to GFA conversion with walks, GBWTGraph algorithm ok 45 - GBZ to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file ok 46 - GFA to HashGraph conversion ok 47 - GFA -> HashGraph -> GFA conversion maintains segments, links, walks, and paths ok 48 - GBWTGraph to HashGraph conversion with generic paths ok 49 - GBWTGraph to HashGraph conversion creates the correct generic paths ok 50 - GBWTGraph to HashGraph conversion creates the correct haplotype paths ok 51 - GBZ to HashGraph conversion with generic paths ok 52 - GBZ to HashGraph conversion creates the correct generic paths ok 53 - GBZ to HashGraph conversion creates the correct haplotype paths ok 54 - GBWTGraph to XG conversion with generic paths ok 55 - GBWTGraph to XG conversion creates the correct generic paths ok 56 - GBWTGraph to XG conversion creates the correct haplotype paths ok 57 - GBZ to XG conversion with generic paths ok 58 - GBZ to XG conversion creates the correct generic paths ok 59 - GBZ to XG conversion creates the correct haplotype paths ok 60 - GBZ to XG conversion while dropping haplotypes ok 61 - No haplotypes in the converted graph ok 62 - GBZ to HashGraph conversion while dropping haplotypes ok 63 - No haplotypes in the converted graph ok 64 - GBWTGraph to GFA conversion with paths and walks, GBWTGraph algorithm ok 65 - GBWTGraph to GFA conversion with GBWTGraph algorithm creates the expected normalized GFA file ok 66 - GBWTGraph to GFA conversion with paths and walks, vg algorithm ok 67 - GBWTGraph to GFA conversion with vg algorithm creates the correct possibly-unnormalized GFA file ok 68 - GBWTGraph to HashGraph conversion with paths and walks ok 69 - HashGraph to GFA conversion with paths and walks ok 70 - GBWTGraph to HashGraph to GFA conversion creates the correct possibly-unnormalized GFA file ok 71 - HashGraph to GFA conversion writing walks as paths ok 72 - HashGraph to GFA conversion writing walks as paths produces no walks ok 73 - HashGraph to GFA conversion writing walks as paths produces all expected paths ok 74 - GBZ to GFA conversion with paths and walks, GBWTGraph algorithm ok 75 - GBZ to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file ok 76 - GBZ to GFA conversion works with multiple threads ok 77 - GBZ to GFA with translation ok 78 - 8 segments ok 79 - GBZ to GFA without translation ok 80 - 9 segments ok 81 - GFA -> GBZ conversion preserves path metadata ok 82 - GFA -> GBZ -> GFA conversion preserves path metadata ok 83 - GFA -> HashGraph conversion preserves path metadata ok 84 - GFA -> HashGraph -> GFA conversion preserves path metadata ok 85 - rGFA -> HashGraph -> GBZ conversion preserves path metadata ok 86 - rGFA -> HashGraph -> GBZ -> GFA conversion preserves path metadata ok 87 - GFA -> HashGraph conversion works with redundant paths ok 88 - GFA -> HashGraph conversion with redundant paths keeps one copy of the redundant path ok 89 - GFA -> HashGraph conversion works with two-part reference path names ok 90 - GFA -> HashGraph conversion with with two-part reference path names gets the right paths ok 91 - No difference roundtripping a GFA if it's loaded as a GFA or HandleGraph warning:[GFAParser] Streaming GFA file references node 6 before it is defined. GFA lines will be buffered in a temporary file. ok 92 - Streaming an unsorted GFA gives same output as sorted ok 93 - Warning given when falling back to temp GFA buffer file ok 94 - Streaming an sorted GFA gives same output as reading from file ok 95 - No warnings given when streamed GFA is sorted ok 96 - Modding GFA directly produces same output as going through convert ok 97 - Modding sorted GFA stream produces same output as going through convert warning:[GFAParser] Streaming GFA file references node 6 before it is defined. GFA lines will be buffered in a temporary file. ok 98 - Modding unsorted GFA stream produces same output as going through convert ok 99 - Warning given when falling back to temp GFA buffer file in mod ok 100 - Modding unsorted GFA file produces same output as going through convert ok 101 - No warnings given when input GFA file is unsorted ok 102 - rGFA handled consistently when streaming as when loaded from file ok 103 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output (GAF check) ok 104 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output (GAM check) ok 105 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output for long node (GAF check) ok 106 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output for long node (GAM check) Failed 1/106 subtests [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. t/49_vg_depth.t ....... 1..6 ok 1 - vg depth gets correct depth from gam ok 2 - vg depth gets correct depth from pack ok 3 - vg depth gets correct number of bins ok 4 - vg depth gets correct depth from gaf ok 5 - vg depth of paths reports all paths ok 6 - vg depth of paths reports just path with selected prefix ok [IndexRegistry]: Constructing GBZ. Guessing that x.gbwt is Giraffe GBWT Guessing that x.xg is XG Guessing that x.xg is XG [IndexRegistry]: Combining Giraffe GBWT and GBWTGraph into GBZ. Guessing that x.gbwt is Giraffe GBWT Guessing that x.xg is XG Guessing that x.gg is GBWTGraph [IndexRegistry]: Constructing minimizer index. Guessing that x.dist is Giraffe Distance Index Guessing that x.gbwt is Giraffe GBWT Guessing that x.min is Minimizers Guessing that x.xg is XG Guessing that x.gg is GBWTGraph Guessing that x.dist is Giraffe Distance Index Guessing that x.gbwt is Giraffe GBWT Guessing that x.min is Minimizers Guessing that x.xg is XG Guessing that x.gg is GBWTGraph Guessing that x.dist is Giraffe Distance Index Guessing that x.gbwt is Giraffe GBWT Guessing that x.min is Minimizers Guessing that x.xg is XG Guessing that x.gg is GBWTGraph Guessing that x.dist is Giraffe Distance Index Guessing that x.gbwt is Giraffe GBWT Guessing that x.min is Minimizers Guessing that x.xg is XG Guessing that x.gg is GBWTGraph [vg minimizer] warning: --bounded-syncmers is deprecated, use --closed-syncmers instead Guessing that x.gg is GBWTGraph Guessing that x.giraffe.gbz is Giraffe GBZ Guessing that x.gg is GBWTGraph Guessing that x.giraffe.gbz is Giraffe GBZ Guessing that x.gg is GBWTGraph Guessing that x.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. index file x.fa.fai not found, generating... [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [IndexRegistry]: Checking for phasing in VCF(s). Guessing that x.dist is Giraffe Distance Index Guessing that x.min is Minimizers Guessing that x.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that x.dist is Giraffe Distance Index Guessing that x.min is Minimizers Guessing that x.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that x.dist is Giraffe Distance Index Guessing that x.min is Minimizers Guessing that x.giraffe.gbz is Giraffe GBZ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning[vg::giraffe]: Finalizing fragment length distribution before reaching maximum sample size mapped 0 reads single ended with 0 pairs of reads left unmapped mean: 0, stdev: 1 [IndexRegistry]: Checking for phasing in VCF(s). Guessing that x.dist is Giraffe Distance Index Guessing that x.min is Minimizers Guessing that x.giraffe.gbz is Giraffe GBZ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. index file xy.fa.fai not found, generating... [IndexRegistry]: Chunking FASTA(s). [IndexRegistry]: Chunking VCF(s). [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg autoindex] Executing command: vg autoindex -p brca -w giraffe -g graphs/cactus-BRCA2.gfa [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing VG graph from GFA input. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Constructing a greedy path cover GBWT [IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [W::bgzf_read_block] EOF marker is absent. The input may be truncated terminate called after throwing an instance of 'std::runtime_error' what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 79256662206 group 79256662202 ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [vg autoindex] Executing command: vg autoindex -p 1mb1kgp -w giraffe -P VG w/ Variant Paths:1mb1kgp.vg -P Giraffe Distance Index:1mb1kgp.dist -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Stripping allele paths from VG. [W::bgzf_read_block] EOF marker is absent. The input may be truncated terminate called after throwing an instance of 'std::runtime_error' what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 79256662206 group 79256662202 ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error:[vg giraffe] Couldn't open GBZ file 1mb1kgp.giraffe.gbz t/50_vg_giraffe.t ..... 1..50 ok 1 - a read can be mapped with xg + gbwt + min + dist specified without crashing ok 2 - a read can be mapped with gbz + min + dist specified without crashing ok 3 - a read can be mapped with gg + gbwt + min + dist specified without crashing ok 4 - a read can be mapped with the minimizer index being regenerated ok 5 - a read can be mapped with the indexes being inferred by name ok 6 - Mapping logs runtime per read ok 7 - Mapping produces the correct score ok 8 - a read can be mapped with the fast preset ok 9 - a read can be mapped with the default preset ok 10 - Mapping without a full length bonus produces the correct score ok 11 - a read can be mapped with syncmer indexes without crashing ok 12 - a read can be mapped when the distance index is not writable ok 13 - a read which softclips does not appear to loop ok 14 - a read can be mapped with just FASTA and VCF without crashing ok 15 - mapping with just a FASTA and a VCF produced JSON-able alignments ok 16 - mapping to manually-generated indexes and automatically-generated indexes is the same ok 17 - mapping with syncmers produces the same alignment as mapping with minimizers ok 18 - unpaired reads lack cross-references ok 19 - paired reads have cross-references not ok 20 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 21 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 22 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 23 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 24 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 25 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 26 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 27 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 28 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 29 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' ok 30 - surjecting with a sequence dictionary in non-sorted order produces headers in non-sorted order ok 31 - surjecting with a sequence dictionary in sorted order produces headers in sorted order ok 32 - paired reads are evenly split between equivalent mappings ok 33 - unpaired reads are evenly split between equivalent mappings ok 34 - provenance tracking succeeds for unpaired reads ok 35 - correctness tracking succeeds for unpaired reads ok 36 - unpaired reads are annotated with minimizer coverage ok 37 - provenance tracking succeeds for paired reads ok 38 - correctness tracking succeeds for paired reads ok 39 - paired reads are annotated with minimizer coverage ok 40 - paired reads all have nonzero correct minimizer coverage ok 41 - vg giraffe can map to BAM using a GBZ alone ok 42 - GBZ-based BAM contains the expected number of reads ok 43 - Mapping reads to named coordinates on a nontrivial graph without walks succeeds ok 44 - Reads are all mapped ok 45 - GFA segment names are all set ok 46 - Mapping reads as GAF to named coordinates on a nontrivial graph without walks succeeds ok 47 - Mapping reads as named GAF uses the same names as named GAM not ok 48 - A long read can be correctly aligned # got: '' # expected: '7999' not ok 49 - A long read has the correct edits found # got: '0' # expected: '2' not ok 50 - Long read minimizer set is correctly restricted # got: '0' # expected: '1' Failed 13/50 subtests [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. t/51_vg_combine.t ..... 1..10 ok 1 - combined graph as correct total nodes ok 2 - combined graph as correct total edges ok 3 - combined graph has same input path ok 4 - combined handle graph as correct total nodes ok 5 - combined handle graph as correct total edges ok 6 - combined handle graph has same input path ok 7 - path combined graph as correct total nodes ok 8 - path combined path graph as correct total edges ok 9 - path combined graph as correct number of paths ok 10 - combined path has correct size ok rm: cannot remove 'auto.*': No such file or directory [vg autoindex] Executing command: vg autoindex -p auto -w map -r tiny/tiny.fa -v tiny/tiny.vcf.gz --force-unphased [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Pruning complex regions of VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w map -r small/x.fa -v small/x.vcf.gz -r small/y.fa -v small/y.vcf.gz [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. index file small/y.fa.fai not found, generating... [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Pruning complex regions of VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w map -r small/xy.fa -v small/xy2.vcf.gz [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Chunking FASTA(s). [IndexRegistry]: Chunking VCF(s). [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Pruning complex regions of VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r tiny/tiny.fa -v tiny/tiny.vcf.gz -x tiny/tiny.gtf [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from spliced VG. [IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -r tiny/tiny.fa -v tiny/tiny.vcf.gz -x tiny/tiny.gtf --force-unphased [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Finishing spliced VG. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -r tiny/tiny.fa -x tiny/tiny.gtf [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA input. [IndexRegistry]: Finishing spliced VG. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/x.gtf -x small/y.gtf [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from spliced VG. [IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/x.gtf -x small/y.gtf --force-unphased [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Finishing spliced VG. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 1 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Chunking FASTA(s). [IndexRegistry]: Chunking VCF(s). [IndexRegistry]: Chunking GTF/GFF(s). [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from spliced VG. [IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r small/xy.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Chunking FASTA(s). [IndexRegistry]: Chunking VCF(s). [IndexRegistry]: Chunking GTF/GFF(s). [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from spliced VG. [IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Adding splice junctions to GBZ-format graph. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf -H graphs/gfa_with_w_lines_haplo.gtf [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Adding splice junctions to GBZ-format graph. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w rpvg -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Constructing haplotype-transcript GBWT and spliced graph from GBZ-format graph. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w rpvg -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf -H graphs/gfa_with_w_lines_haplo.gtf [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Constructing haplotype-transcript GBWT and spliced graph from GBZ-format graph. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w giraffe -r tiny/tiny.fa -v tiny/tiny.vcf.gz [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [vg autoindex] Executing command: vg autoindex -p auto -w giraffe -g graphs/gfa_with_w_lines.gfa [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. warning [vg convert]: currently cannot convert GFA directly to XG; converting through another format [vg autoindex] Executing command: vg autoindex -p auto -w giraffe -g graphs/named_with_walk.gfa [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [vg autoindex] Executing command: vg autoindex -p auto -w giraffe -g graphs/named.gfa [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing VG graph from GFA input. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Constructing a greedy path cover GBWT [IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. t/52_vg_autoindex.t ... 1..49 ok 1 - autoindexing successfully completes indexing for vg map with basic input ok 2 - autoindexing makes 3 outputs for vg map ok 3 - autoindexing makes an XG for vg map ok 4 - autoindexing makes a GCSA2/LCP pair for vg map ok 5 - basic autoindexing results can be used by vg map ok 6 - autoindexing successfully completes indexing for vg map with chunked input ok 7 - chunked autoindexing results can be used by vg map ok 8 - autoindexing successfully completes indexing for vg map with phased input ok 9 - phased autoindexing results can be used by vg map ok 10 - autoindexing successfully completes indexing for vg mpmap with unchunked input ok 11 - autoindexing creates 6 files for mpmap/rpvg ok 12 - basic autoindexing results can be used by vg mpmap ok 13 - haplotype transcript GBWT made by autoindex is valid ok 14 - transcript origin table has expected number of rows ok 15 - autoindexing successfully completes indexing for vg mpmap with unchunked, unphased input ok 16 - autoindexing creates 4 files for mpmap/rpvg ok 17 - basic unphased autoindexing results can be used by vg mpmap ok 18 - autoindexing successfully completes indexing for vg mpmap without variants ok 19 - autoindexing creates 4 files for mpmap without variants ok 20 - autoindexing results with no variants can be used by vg mpmap ok 21 - autoindexing successfully completes indexing for vg mpmap with chunked input ok 22 - autoindexing creates 6 files for mpmap/rpvg with chunked input ok 23 - autoindexing successfully completes indexing for vg mpmap with unphased chunked input ok 24 - autoindexing creates 4 files for mpmap/rpvg with chunked input ok 25 - autoindexing results with chunked unphased input can be used by vg mpmap ok 26 - autoindexing successfully completes indexing for vg mpmap with partially chunked input ok 27 - autoindexing successfully completes indexing for vg mpmap with another partially chunked input ok 28 - autoindexing successfully completes indexing for vg mpmap with GFA input ok 29 - autoindexing results with GFA input can be used by vg mpmap ok 30 - autoindexing successfully completes indexing for vg mpmap with GFA input and a haplotype GTF ok 31 - autoindexing results with GFA input and a haplotype GTF can be used by vg mpmap ok 32 - autoindexing successfully completes indexing for vg mpmap and rpvg with GFA input ok 33 - autoindexing successfully completes indexing for vg mpmap and rpvg with GFA input and a haplotype GTF ok 34 - autoindexing successfully completes indexing for vg giraffe with unchunked input ok 35 - autoindexing creates 3 inputs for vg giraffe ok 36 - basic autoindexing results can be used by vg giraffe ok 37 - autoindexing successfully completes indexing for vg giraffe with GFA input with W-lines ok 38 - autoindexing creates 3 inputs for vg giraffe from GFA input ok 39 - GFA autoindexing results can be used by vg giraffe ok 40 - autoindexing successfully completes on a GFA with named segments and W-lines ok 41 - GFA segment names are available in output GAM when a walk exists ok 42 - autoindexing successfully completes on a GFA with named segments and no W-lines ok 43 - GFA segment names are available in output GAM when no walks exist ok 44 - Running out of room during k-mer enumeration triggers a rewind ok 45 - Indexing is successful after rewinding from k-mer generation ok 46 - Running out of room during GCSA2 indexing triggers a rewind ok 47 - Indexing is successful after rewinding from GCSA2 indexing ok 48 - Running out of memory during GCSA2 indexing triggers a rewind ok 49 - Indexing is successful after rewinding from GCSA2 indexing ok WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps graph: valid graph: valid graph: valid graph: valid graph: valid graph: valid t/53_clip.t ........... 1..17 ok 1 - clipped graph is valid ok 2 - every step in clipped graph belongs to reference path ok 3 - clipped graph has same length as ref path ok 4 - clipped graph is valid ok 5 - Just one node filtered ok 6 - clipped graph is valid ok 7 - Just one edge filtered ok 8 - clipped graph is valid ok 9 - Just one node filtered ok 10 - clipped graph is valid ok 11 - clipping bad region changes nothing ok 12 - clipped graph is valid ok 13 - Just one node filtered ok 14 - stub clipping removed all stubs ok 15 - region clipping filtered out only 2 / 4 stub nodes ok 16 - Correct head after path stubbification ok 17 - Correct tail after path stubbification ok t/54_vg_haplotypes.t .. 1..21 ok 1 - generating haplotype information ok 2 - sampling from existing haplotype information ok 3 - 1 generated + 2 reference samples ok 4 - 2 contigs ok 5 - 4 generated + 2 reference haplotypes ok 6 - sampling the haplotypes directly ok 7 - the outputs are identical ok 8 - sampling without adding reference ok 9 - 1 sample ok 10 - 2 contigs ok 11 - 4 haplotypes ok 12 - diploid sampling ok 13 - 1 generated + 2 reference samples ok 14 - 2 contigs ok 15 - 2 generated + 2 reference haplotypes ok 16 - diploid sampling using a preset ok 17 - the outputs are identical ok 18 - Giraffe integration with a guessed output name ok 19 - the sampled graph is identical to a manually sampled one ok 20 - Giraffe integration with a specified output name ok 21 - the sampled graphs are identical ok Test Summary Report ------------------- t/02_vg_construct.t (Wstat: 0 Tests: 30 Failed: 1) Failed test: 7 t/03_vg_view.t (Wstat: 0 Tests: 23 Failed: 3) Failed tests: 5, 7, 12 t/05_vg_find.t (Wstat: 0 Tests: 29 Failed: 1) Failed test: 21 t/07_vg_map.t (Wstat: 0 Tests: 55 Failed: 10) Failed tests: 43-52 t/09_vg_concat.t (Wstat: 0 Tests: 4 Failed: 1) Failed test: 4 t/14_vg_mod.t (Wstat: 0 Tests: 32 Failed: 2) Failed tests: 13, 16 t/15_vg_surject.t (Wstat: 0 Tests: 47 Failed: 11) Failed tests: 7, 13, 19-20, 22-28 t/17_vg_augment.t (Wstat: 0 Tests: 39 Failed: 7) Failed tests: 1-7 t/21_vg_filter.t (Wstat: 0 Tests: 13 Failed: 1) Failed test: 12 t/28_translate.t (Wstat: 0 Tests: 2 Failed: 1) Failed test: 2 t/31_vg_add.t (Wstat: 0 Tests: 12 Failed: 3) Failed tests: 10-12 t/32_vg_snarls.t (Wstat: 0 Tests: 19 Failed: 7) Failed tests: 1-5, 13-14 t/34_vg_pack.t (Wstat: 0 Tests: 20 Failed: 1) Failed test: 18 t/36_vg_annotate.t (Wstat: 0 Tests: 9 Failed: 1) Failed test: 9 t/48_vg_convert.t (Wstat: 0 Tests: 106 Failed: 1) Failed test: 23 t/50_vg_giraffe.t (Wstat: 0 Tests: 50 Failed: 13) Failed tests: 20-29, 48-50 Files=53, Tests=1138, 493 wallclock secs ( 0.52 usr 0.21 sys + 718.89 cusr 221.05 csys = 940.67 CPU) Result: FAIL make[1]: [debian/rules:93: override_dh_auto_test-arch] Error 1 (ignored) make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' echo No arch independent tests No arch independent tests make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' dh_install bin/vg usr/bin/ make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_installdocs dh_installchangelogs dh_installman 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: cannot find library libhandlegraph.so needed by debian/vg/usr/bin/vg (ELF format: 'elf64-littleaarch64' abi: 'ELF:64:l:arm64:0'; RPATH: '') dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-2), " make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_md5sums dh_builddeb dpkg-deb: building package 'vg-dbgsym' in '../vg-dbgsym_1.59.0+ds-0.1_arm64.deb'. dpkg-deb: building package 'vg-docs' in '../vg-docs_1.59.0+ds-0.1_all.deb'. dpkg-deb: building package 'vg' in '../vg_1.59.0+ds-0.1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../vg_1.59.0+ds-0.1_arm64.buildinfo dpkg-genchanges --build=binary -O../vg_1.59.0+ds-0.1_arm64.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: including full 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/2636781 and its subdirectories I: Current time: Sat Jan 17 23:37:28 -12 2026 I: pbuilder-time-stamp: 1768736248 Mon Dec 16 05:14:36 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Mon Dec 16 05:14:36 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Mon Dec 16 05:39:56 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Mon Dec 16 05:39:57 UTC 2024 I: vg_1.59.0+ds-0.1_arm64.changes: Format: 1.8 Date: Thu, 21 Nov 2024 00:12:52 +0000 Source: vg Binary: vg vg-dbgsym vg-docs Architecture: arm64 all Version: 1.59.0+ds-0.1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Bastian Germann Description: vg - tools for working with genome variation graphs vg-docs - tools for working with genome variation graphs -- docs Closes: 1013061 1043312 1084554 Changes: vg (1.59.0+ds-0.1) unstable; urgency=medium . * Non-maintainer upload . [ Andreas Tille ] * Update lintian override info to new format: + debian/source/lintian-overrides: line 2 + debian/vg.lintian-overrides: line 5, 8-12 * Remove constraints unnecessary since buster (oldstable): + Build-Depends: Replace dependency on transitional package libncurses5-dev with replacement libtinfo6, libncurses-dev. . [ Pierre Gruet ] * Using tags and filenamemangle in d/watch . [ Michael R. Crusoe ] * New upstream version. Closes: #1013061, #1084554 * Added patch to deal with bashim. * debian/rules: unset LD_PRELOAD for qemu build + testing * debian/rules: if the SIMD level is supported by the build CPU as reported by lscpu, then require the tests for that version of the vg binary to pass. * debian/copyright: freshen * Freshen patches * update clean list * Standards-Version: 4.6.2 (routine-update) * Keep vendored copy of libssw until vg updates to a regular release * Refreshed patches, moved some of the crossbuild fixes into earlier patches to reduce churn. * d/patches/series: skip the ssw patches to use the code copy for now. * d/control: new build-dep: libzstd-dev * Force the use of the system package for SIMDe. * Added patch to fix gcc 12+ issues. * d/copyright: exclude the unused benchmarks.js from the vendored copies of atomic_queue * d/control: update names of obsolete packages to their replacements. Closes: #1043312 * Ignore test failures Checksums-Sha1: 7c5a3794bc07a4fc437bcb43a1f20c3f00bbb531 171097072 vg-dbgsym_1.59.0+ds-0.1_arm64.deb 10e7c0f96d3b7238bd4d2cbe5eebbc7de89638ab 2098644 vg-docs_1.59.0+ds-0.1_all.deb d50d222bb61db2bbf4e07ff5869c1432a8a8f6ef 16458 vg_1.59.0+ds-0.1_arm64.buildinfo 64c24bbc123a18e73814b69c8be08399be095940 8047820 vg_1.59.0+ds-0.1_arm64.deb Checksums-Sha256: d15597bb76043000b7172ac602330619a6670ea955f87675f750355e81d46eb9 171097072 vg-dbgsym_1.59.0+ds-0.1_arm64.deb 76b06860af84c3a826e14eb484651f4cf94c2035099beea9f3c594641a95421c 2098644 vg-docs_1.59.0+ds-0.1_all.deb efbebba88d5d8cf6cbb1a2456cc3c308b51c4974402a1283bd0aef02fc3f035d 16458 vg_1.59.0+ds-0.1_arm64.buildinfo 1ca7bb47f30a7d7698cc63b53ac97da708f628c23c3b06f55b5a07bd0eae5946 8047820 vg_1.59.0+ds-0.1_arm64.deb Files: ccf57f17ea9a47d92e80a2cb9c32efdd 171097072 debug optional vg-dbgsym_1.59.0+ds-0.1_arm64.deb 0a9df9f576e24c3759d9db71c3b55190 2098644 doc optional vg-docs_1.59.0+ds-0.1_all.deb a4b1293f603d9999b33767957ca26846 16458 science optional vg_1.59.0+ds-0.1_arm64.buildinfo 39805330fa5786633336d232c415a7ec 8047820 science optional vg_1.59.0+ds-0.1_arm64.deb Mon Dec 16 05:39:58 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_15-75276.service 2024-12-16 08:09:58 W: diffoscope.main: Received TERM signal; cleaning up temp files... # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.13mrvSh8/vg_1.59.0+ds-0.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.13mrvSh8/vg_1.59.0+ds-0.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.13mrvSh8/vg_1.59.0+ds-0.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.13mrvSh8/b1/vg_1.59.0+ds-0.1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.13mrvSh8/b2/vg_1.59.0+ds-0.1_arm64.changes ## close_archive (total time: 0.001s) 0.001s 10 calls diffoscope.comparators.xz.XzContainer 0.000s 9 calls diffoscope.comparators.tar.TarContainer 0.000s 4 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 5098.151s) 2486.873s 669 calls readelf 2068.390s 78 calls diff 519.919s 88 calls objdump 16.259s 2 calls objcopy 4.974s 20 calls xz 1.723s 11 calls strings 0.005s 1 call cmp 0.005s 1 call cmp (external) 0.002s 19 calls cmp (internal) ## compare_files (cumulative) (total time: 31565.540s) 6322.515s 3 calls abc.XzFile 6322.341s 1 call abc.DebFile 6321.217s 1 call abc.DebDataTarFile 6321.003s 1 call abc.ElfFile 6263.670s 4 calls diffoscope.comparators.elf.ElfCodeSection 14.495s 17 calls diffoscope.comparators.elf.ElfSection 0.263s 2 calls abc.TarFile 0.015s 1 call abc.TextFile 0.011s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection 0.010s 2 calls abc.Md5sumsFile ## container_extract (total time: 8.385s) 4.976s 20 calls diffoscope.comparators.xz.XzContainer 1.944s 14 calls diffoscope.comparators.deb.DebTarContainer 1.456s 24 calls diffoscope.comparators.deb.DebContainer 0.010s 18 calls diffoscope.comparators.tar.TarContainer ## has_same_content_as (total time: 0.009s) 0.006s 3 calls abc.DebFile 0.001s 4 calls abc.TextFile 0.000s 4 calls abc.Md5sumsFile 0.000s 4 calls abc.XzFile 0.000s 2 calls abc.DebDataTarFile 0.000s 2 calls abc.ElfFile 0.000s 2 calls abc.TarFile 0.000s 1 call abc.DotChangesFile 0.000s 17 calls diffoscope.comparators.elf.ElfSection 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 4 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## open_archive (total time: 0.000s) 0.000s 20 calls diffoscope.comparators.xz.XzContainer 0.000s 14 calls diffoscope.comparators.tar.TarContainer 0.000s 10 calls diffoscope.comparators.deb.DebContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## recognizes (total time: 5.793s) 2.190s 900 calls diffoscope.comparators.utils.archive.ArchiveMember 1.905s 1808 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 1.556s 12 calls diffoscope.comparators.binary.FilesystemFile 0.142s 324 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.278s) 0.278s 45 calls specialize 2024-12-16 08:09:58 W: diffoscope.main: Exiting... Finished with result: success Main processes terminated with: code=exited/status=124 Service runtime: 2h 30min 631ms CPU time consumed: 2h 33min 4.813s Mon Dec 16 08:09:59 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Mon Dec 16 08:09:59 UTC 2024 I: vg from unstable built successfully and reproducibly on arm64. Mon Dec 16 08:10:00 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Dec 16 08:10:00 UTC 2024 I: Submitting 20K b1/vg_1.59.0+ds-0.1_arm64.buildinfo.asc Mon Dec 16 08:10:01 UTC 2024 I: Submitting 20K b2/vg_1.59.0+ds-0.1_arm64.buildinfo.asc Mon Dec 16 08:10:02 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Dec 16 08:10:02 UTC 2024 I: Done submitting .buildinfo files. Mon Dec 16 08:10:02 UTC 2024 I: Removing signed vg_1.59.0+ds-0.1_arm64.buildinfo.asc files: removed './b1/vg_1.59.0+ds-0.1_arm64.buildinfo.asc' removed './b2/vg_1.59.0+ds-0.1_arm64.buildinfo.asc'