WARNING: (guile-user): imported module (guix build utils) overrides core binding `delete' starting phase `separate-from-pid1' build process now running as PID 10 phase `separate-from-pid1' succeeded after 0.0 seconds starting phase `set-SOURCE-DATE-EPOCH' phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds starting phase `set-paths' environment variable `PATH' set to `/gnu/store/9aiawd5b9jlh1cyhpdrh4dr79dm66y5h-meson-1.5.2/bin:/gnu/store/qawfmb8fcb981r53b3nj025rvp3w35gb-ninja-1.11.1/bin:/gnu/store/k3k7ilrr8jg3yj8h45a9m6wqi6b748f3-bash-tap-1.0.2/bin:/gnu/store/vihp73m28hc0kral08z61mhxd5bhf870-bc-1.07.1/bin:/gnu/store/zajmyhi888hf7d4d73ajyyrmicxvv7b8-grep-3.11/bin:/gnu/store/a34kfcidwii9xvv47i7gip7jzy4acfcw-parallel-20250122/bin:/gnu/store/v6bivyjbg6bj07s8iqfzdm6hpvypc0p1-perl-5.36.0/bin:/gnu/store/a3lsdsalcmg5wnk67869af7wljprkbam-pkg-config-0.29.2/bin:/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/bin:/gnu/store/a2hqpav82j3wgd61bg17xj2ihf7lil1g-samtools-1.19/bin:/gnu/store/ag8ln8wq4p3kff91dpl8h5jykrkhvmx5-fastahack-1.0.0/bin:/gnu/store/0kw802pzlgxnny41cv2x02vq11h8pbv8-htslib-1.19/bin:/gnu/store/37im95in2j8s9pwi39r6fg40sbhyj3f8-smithwaterman-0.0.0-2.2610e25/bin:/gnu/store/q5wfzn60s6pfm784zwi1fkfkmimc6kni-tabixpp-1.1.2/bin:/gnu/store/n3r6isih135c5l06x9gaiz028fs669zi-vcflib-1.0.9/bin:/gnu/store/j5zgzgsmbjgywr67r86h1n6s4qiabv5q-tar-1.34/bin:/gnu/store/0r2fx1lr1h2i3cl1x5fw4s4ly95qspya-gzip-1.13/bin:/gnu/store/56aq6sdx35f7rsxq8jq9ypafk0dhd3p3-bzip2-1.0.8/bin:/gnu/store/544ga5n6nq8y2961ihigra6n6a0r99nn-file-5.45/bin:/gnu/store/swmflx2bmqpf0drm167pxfpgyr7ckcam-diffutils-3.10/bin:/gnu/store/4jhlsg65s1zx90gnnfmaax52i8prnl45-patch-2.7.6/bin:/gnu/store/b5c62i99dsfa5j0j3f8g2j1xdi6fih22-findutils-4.9.0/bin:/gnu/store/vrl2r0ps24k1a6yap2chjylv5rhbndvr-gawk-5.3.0/bin:/gnu/store/3f0fjq25n2kwcmi0zyrf216wa6g8xpjw-zstd-1.5.2/bin:/gnu/store/3i4fr8riqw9azh1p4mqggl5vdz23kyr8-sed-4.8/bin:/gnu/store/7k8b93779dqpwcg2qjdvnf4nl43jv7hf-grep-3.11/bin:/gnu/store/fbaw0sb21gv02qq7gs9wg5y5wlpdgzih-xz-5.4.5/bin:/gnu/store/7h0mnlwalw23j9jmvz5n1i5mqkgb4d06-coreutils-9.1/bin:/gnu/store/lc6r1mh0jlcwixjziiw1zsx1my478rv1-make-4.4.1/bin:/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin:/gnu/store/3k6lyifyg024lk3gncsgf2gzjzvc70gv-ld-wrapper-0/bin:/gnu/store/ylgkrq9j1gyfig2y66srmgsbyh9w20d9-binutils-2.41/bin:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/bin:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/bin:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/sbin' environment variable `PERL5LIB' set to `/gnu/store/v6bivyjbg6bj07s8iqfzdm6hpvypc0p1-perl-5.36.0/lib/perl5/site_perl' environment variable `PKG_CONFIG_PATH' set to `/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/lib/pkgconfig:/gnu/store/2xgixnsks05aipwk2swl7vicx6mkr6z2-simde-0.8.2/lib/pkgconfig:/gnu/store/ag8ln8wq4p3kff91dpl8h5jykrkhvmx5-fastahack-1.0.0/lib/pkgconfig:/gnu/store/0kw802pzlgxnny41cv2x02vq11h8pbv8-htslib-1.19/lib/pkgconfig:/gnu/store/37im95in2j8s9pwi39r6fg40sbhyj3f8-smithwaterman-0.0.0-2.2610e25/lib/pkgconfig:/gnu/store/q5wfzn60s6pfm784zwi1fkfkmimc6kni-tabixpp-1.1.2/lib/pkgconfig:/gnu/store/n3r6isih135c5l06x9gaiz028fs669zi-vcflib-1.0.9/lib/pkgconfig:/gnu/store/544ga5n6nq8y2961ihigra6n6a0r99nn-file-5.45/lib/pkgconfig:/gnu/store/fbaw0sb21gv02qq7gs9wg5y5wlpdgzih-xz-5.4.5/lib/pkgconfig:/gnu/store/1prv14v6jfnzzg7szm57690b7fr6sx33-zlib-1.3/lib/pkgconfig:/gnu/store/w07x1nl7s7c6x3shz07hdqf286pqrh1c-wfa2-lib-2.3.3/lib/pkgconfig' environment variable `GUIX_PYTHONPATH' set to `/gnu/store/9aiawd5b9jlh1cyhpdrh4dr79dm66y5h-meson-1.5.2/lib/python3.10/site-packages:/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/lib/python3.10/site-packages' environment variable `PYTHONTZPATH' unset environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/include:/gnu/store/2xgixnsks05aipwk2swl7vicx6mkr6z2-simde-0.8.2/include:/gnu/store/ag8ln8wq4p3kff91dpl8h5jykrkhvmx5-fastahack-1.0.0/include:/gnu/store/0kw802pzlgxnny41cv2x02vq11h8pbv8-htslib-1.19/include:/gnu/store/37im95in2j8s9pwi39r6fg40sbhyj3f8-smithwaterman-0.0.0-2.2610e25/include:/gnu/store/q5wfzn60s6pfm784zwi1fkfkmimc6kni-tabixpp-1.1.2/include:/gnu/store/n3r6isih135c5l06x9gaiz028fs669zi-vcflib-1.0.9/include:/gnu/store/56aq6sdx35f7rsxq8jq9ypafk0dhd3p3-bzip2-1.0.8/include:/gnu/store/544ga5n6nq8y2961ihigra6n6a0r99nn-file-5.45/include:/gnu/store/vrl2r0ps24k1a6yap2chjylv5rhbndvr-gawk-5.3.0/include:/gnu/store/fbaw0sb21gv02qq7gs9wg5y5wlpdgzih-xz-5.4.5/include:/gnu/store/lc6r1mh0jlcwixjziiw1zsx1my478rv1-make-4.4.1/include:/gnu/store/ylgkrq9j1gyfig2y66srmgsbyh9w20d9-binutils-2.41/include:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/include:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/include:/gnu/store/1prv14v6jfnzzg7szm57690b7fr6sx33-zlib-1.3/include:/gnu/store/0hiskmlxbhmvh4qrxx4i6f6vwir1vlpn-htscodecs-1.6.0/include:/gnu/store/w07x1nl7s7c6x3shz07hdqf286pqrh1c-wfa2-lib-2.3.3/include:/gnu/store/svghsdn1x3fyili8ij791nn25zba9bpf-linux-libre-headers-5.15.49/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/include:/gnu/store/2xgixnsks05aipwk2swl7vicx6mkr6z2-simde-0.8.2/include:/gnu/store/ag8ln8wq4p3kff91dpl8h5jykrkhvmx5-fastahack-1.0.0/include:/gnu/store/0kw802pzlgxnny41cv2x02vq11h8pbv8-htslib-1.19/include:/gnu/store/37im95in2j8s9pwi39r6fg40sbhyj3f8-smithwaterman-0.0.0-2.2610e25/include:/gnu/store/q5wfzn60s6pfm784zwi1fkfkmimc6kni-tabixpp-1.1.2/include:/gnu/store/n3r6isih135c5l06x9gaiz028fs669zi-vcflib-1.0.9/include:/gnu/store/56aq6sdx35f7rsxq8jq9ypafk0dhd3p3-bzip2-1.0.8/include:/gnu/store/544ga5n6nq8y2961ihigra6n6a0r99nn-file-5.45/include:/gnu/store/vrl2r0ps24k1a6yap2chjylv5rhbndvr-gawk-5.3.0/include:/gnu/store/fbaw0sb21gv02qq7gs9wg5y5wlpdgzih-xz-5.4.5/include:/gnu/store/lc6r1mh0jlcwixjziiw1zsx1my478rv1-make-4.4.1/include:/gnu/store/ylgkrq9j1gyfig2y66srmgsbyh9w20d9-binutils-2.41/include:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/include/c++:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/include:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/include:/gnu/store/1prv14v6jfnzzg7szm57690b7fr6sx33-zlib-1.3/include:/gnu/store/0hiskmlxbhmvh4qrxx4i6f6vwir1vlpn-htscodecs-1.6.0/include:/gnu/store/w07x1nl7s7c6x3shz07hdqf286pqrh1c-wfa2-lib-2.3.3/include:/gnu/store/svghsdn1x3fyili8ij791nn25zba9bpf-linux-libre-headers-5.15.49/include' environment variable `OBJC_INCLUDE_PATH' set to `/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/include:/gnu/store/2xgixnsks05aipwk2swl7vicx6mkr6z2-simde-0.8.2/include:/gnu/store/ag8ln8wq4p3kff91dpl8h5jykrkhvmx5-fastahack-1.0.0/include:/gnu/store/0kw802pzlgxnny41cv2x02vq11h8pbv8-htslib-1.19/include:/gnu/store/37im95in2j8s9pwi39r6fg40sbhyj3f8-smithwaterman-0.0.0-2.2610e25/include:/gnu/store/q5wfzn60s6pfm784zwi1fkfkmimc6kni-tabixpp-1.1.2/include:/gnu/store/n3r6isih135c5l06x9gaiz028fs669zi-vcflib-1.0.9/include:/gnu/store/56aq6sdx35f7rsxq8jq9ypafk0dhd3p3-bzip2-1.0.8/include:/gnu/store/544ga5n6nq8y2961ihigra6n6a0r99nn-file-5.45/include:/gnu/store/vrl2r0ps24k1a6yap2chjylv5rhbndvr-gawk-5.3.0/include:/gnu/store/fbaw0sb21gv02qq7gs9wg5y5wlpdgzih-xz-5.4.5/include:/gnu/store/lc6r1mh0jlcwixjziiw1zsx1my478rv1-make-4.4.1/include:/gnu/store/ylgkrq9j1gyfig2y66srmgsbyh9w20d9-binutils-2.41/include:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/include:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/include:/gnu/store/1prv14v6jfnzzg7szm57690b7fr6sx33-zlib-1.3/include:/gnu/store/0hiskmlxbhmvh4qrxx4i6f6vwir1vlpn-htscodecs-1.6.0/include:/gnu/store/w07x1nl7s7c6x3shz07hdqf286pqrh1c-wfa2-lib-2.3.3/include:/gnu/store/svghsdn1x3fyili8ij791nn25zba9bpf-linux-libre-headers-5.15.49/include' environment variable `OBJCPLUS_INCLUDE_PATH' set to `/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/include:/gnu/store/2xgixnsks05aipwk2swl7vicx6mkr6z2-simde-0.8.2/include:/gnu/store/ag8ln8wq4p3kff91dpl8h5jykrkhvmx5-fastahack-1.0.0/include:/gnu/store/0kw802pzlgxnny41cv2x02vq11h8pbv8-htslib-1.19/include:/gnu/store/37im95in2j8s9pwi39r6fg40sbhyj3f8-smithwaterman-0.0.0-2.2610e25/include:/gnu/store/q5wfzn60s6pfm784zwi1fkfkmimc6kni-tabixpp-1.1.2/include:/gnu/store/n3r6isih135c5l06x9gaiz028fs669zi-vcflib-1.0.9/include:/gnu/store/56aq6sdx35f7rsxq8jq9ypafk0dhd3p3-bzip2-1.0.8/include:/gnu/store/544ga5n6nq8y2961ihigra6n6a0r99nn-file-5.45/include:/gnu/store/vrl2r0ps24k1a6yap2chjylv5rhbndvr-gawk-5.3.0/include:/gnu/store/fbaw0sb21gv02qq7gs9wg5y5wlpdgzih-xz-5.4.5/include:/gnu/store/lc6r1mh0jlcwixjziiw1zsx1my478rv1-make-4.4.1/include:/gnu/store/ylgkrq9j1gyfig2y66srmgsbyh9w20d9-binutils-2.41/include:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/include/c++:/gnu/store/86fc8bi3mciljxz7c79jx8zr4wsx7xw8-gcc-11.4.0/include:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/include:/gnu/store/1prv14v6jfnzzg7szm57690b7fr6sx33-zlib-1.3/include:/gnu/store/0hiskmlxbhmvh4qrxx4i6f6vwir1vlpn-htscodecs-1.6.0/include:/gnu/store/w07x1nl7s7c6x3shz07hdqf286pqrh1c-wfa2-lib-2.3.3/include:/gnu/store/svghsdn1x3fyili8ij791nn25zba9bpf-linux-libre-headers-5.15.49/include' environment variable `LIBRARY_PATH' set to `/gnu/store/9aiawd5b9jlh1cyhpdrh4dr79dm66y5h-meson-1.5.2/lib:/gnu/store/v6bivyjbg6bj07s8iqfzdm6hpvypc0p1-perl-5.36.0/lib:/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/lib:/gnu/store/2xgixnsks05aipwk2swl7vicx6mkr6z2-simde-0.8.2/lib:/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/lib:/gnu/store/ag8ln8wq4p3kff91dpl8h5jykrkhvmx5-fastahack-1.0.0/lib:/gnu/store/0kw802pzlgxnny41cv2x02vq11h8pbv8-htslib-1.19/lib:/gnu/store/37im95in2j8s9pwi39r6fg40sbhyj3f8-smithwaterman-0.0.0-2.2610e25/lib:/gnu/store/q5wfzn60s6pfm784zwi1fkfkmimc6kni-tabixpp-1.1.2/lib:/gnu/store/n3r6isih135c5l06x9gaiz028fs669zi-vcflib-1.0.9/lib:/gnu/store/56aq6sdx35f7rsxq8jq9ypafk0dhd3p3-bzip2-1.0.8/lib:/gnu/store/544ga5n6nq8y2961ihigra6n6a0r99nn-file-5.45/lib:/gnu/store/vrl2r0ps24k1a6yap2chjylv5rhbndvr-gawk-5.3.0/lib:/gnu/store/fbaw0sb21gv02qq7gs9wg5y5wlpdgzih-xz-5.4.5/lib:/gnu/store/ylgkrq9j1gyfig2y66srmgsbyh9w20d9-binutils-2.41/lib:/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/lib:/gnu/store/vqdiyyqbrv4akp68pfya4j6m3pdbnhca-glibc-2.39-static/lib:/gnu/store/1prv14v6jfnzzg7szm57690b7fr6sx33-zlib-1.3/lib:/gnu/store/0hiskmlxbhmvh4qrxx4i6f6vwir1vlpn-htscodecs-1.6.0/lib:/gnu/store/w07x1nl7s7c6x3shz07hdqf286pqrh1c-wfa2-lib-2.3.3/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/lib/locale' environment variable `TZDIR' unset phase `set-paths' succeeded after 0.4 seconds starting phase `install-locale' using 'C.UTF-8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/.travis.yml' -> `./.travis.yml' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/RELEASE-NOTES.md' -> `./RELEASE-NOTES.md' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/meson.build' -> `./meson.build' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/TODO.md' -> `./TODO.md' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/meson_options.txt' -> `./meson_options.txt' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/README.md' -> `./README.md' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/.gitignore' -> `./.gitignore' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/LICENSE' -> `./LICENSE' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/CMakeLists-do-not-use.txt' -> `./CMakeLists-do-not-use.txt' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/guix.scm' -> `./guix.scm' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/.gitmodules' -> `./.gitmodules' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/python/multiset.py' -> `./python/multiset.py' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/python/logsumexp.py' -> `./python/logsumexp.py' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/python/phred.py' -> `./python/phred.py' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/python/allelebayes.py' -> `./python/allelebayes.py' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/python/hwe.py' -> `./python/hwe.py' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/python/README' -> `./python/README' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/python/.gitignore' -> `./python/.gitignore' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/python/factorialln.py' -> `./python/factorialln.py' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/python/dirichlet.py' -> `./python/dirichlet.py' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/README.md' -> `./contrib/README.md' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/freebayes/dummy.cpp' -> `./contrib/freebayes/dummy.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/freebayes/levenshtein.cpp' -> `./contrib/freebayes/levenshtein.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/freebayes/alleles.cpp' -> `./contrib/freebayes/alleles.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/freebayes/GenotypePriors.h' -> `./contrib/freebayes/GenotypePriors.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/freebayes/bamfiltertech.cpp' -> `./contrib/freebayes/bamfiltertech.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/freebayes/GenotypePriors.cpp' -> `./contrib/freebayes/GenotypePriors.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/README.md' -> `./contrib/SeqLib/README.md' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/LICENSE' -> `./contrib/SeqLib/LICENSE' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/bwa/utils.h' -> `./contrib/SeqLib/bwa/utils.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/bwa/bwamem.h' -> `./contrib/SeqLib/bwa/bwamem.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/bwa/kseq.h' -> `./contrib/SeqLib/bwa/kseq.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/bwa/bntseq.h' -> `./contrib/SeqLib/bwa/bntseq.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/bwa/bwa.h' -> `./contrib/SeqLib/bwa/bwa.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/bwa/bwt.h' -> `./contrib/SeqLib/bwa/bwt.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/ThreadPool.h' -> `./contrib/SeqLib/SeqLib/ThreadPool.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/aho_corasick.hpp' -> `./contrib/SeqLib/SeqLib/aho_corasick.hpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/BamRecord.h' -> `./contrib/SeqLib/SeqLib/BamRecord.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp' -> `./contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/BamWalker.h' -> `./contrib/SeqLib/SeqLib/BamWalker.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/ReadFilter.h' -> `./contrib/SeqLib/SeqLib/ReadFilter.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/SeqLibCommon.h' -> `./contrib/SeqLib/SeqLib/SeqLibCommon.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/BamWriter.h' -> `./contrib/SeqLib/SeqLib/BamWriter.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/BamReader.h' -> `./contrib/SeqLib/SeqLib/BamReader.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/GenomicRegionCollection.h' -> `./contrib/SeqLib/SeqLib/GenomicRegionCollection.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/IntervalTree.h' -> `./contrib/SeqLib/SeqLib/IntervalTree.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/ssw.h' -> `./contrib/SeqLib/SeqLib/ssw.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/GenomicRegion.h' -> `./contrib/SeqLib/SeqLib/GenomicRegion.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/SeqLibUtils.h' -> `./contrib/SeqLib/SeqLib/SeqLibUtils.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/BamHeader.h' -> `./contrib/SeqLib/SeqLib/BamHeader.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/ssw_cpp.h' -> `./contrib/SeqLib/SeqLib/ssw_cpp.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/SeqLib/UnalignedSequence.h' -> `./contrib/SeqLib/SeqLib/UnalignedSequence.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/json/json-forwards.h' -> `./contrib/SeqLib/json/json-forwards.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/json/json.h' -> `./contrib/SeqLib/json/json.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/src/BamHeader.cpp' -> `./contrib/SeqLib/src/BamHeader.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/src/GenomicRegion.cpp' -> `./contrib/SeqLib/src/GenomicRegion.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/src/ssw.c' -> `./contrib/SeqLib/src/ssw.c' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/src/BamRecord.cpp' -> `./contrib/SeqLib/src/BamRecord.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/src/BamWriter.cpp' -> `./contrib/SeqLib/src/BamWriter.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/src/ssw_cpp.cpp' -> `./contrib/SeqLib/src/ssw_cpp.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/SeqLib/src/BamReader.cpp' -> `./contrib/SeqLib/src/BamReader.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmathint.h' -> `./contrib/ttmath/ttmathint.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmath.h' -> `./contrib/ttmath/ttmath.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmathobjects.h' -> `./contrib/ttmath/ttmathobjects.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmathdec.h' -> `./contrib/ttmath/ttmathdec.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmathuint.h' -> `./contrib/ttmath/ttmathuint.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmathtypes.h' -> `./contrib/ttmath/ttmathtypes.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmaththreads.h' -> `./contrib/ttmath/ttmaththreads.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmathuint_noasm.h' -> `./contrib/ttmath/ttmathuint_noasm.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/COPYRIGHT' -> `./contrib/ttmath/COPYRIGHT' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmathuint_x86.h' -> `./contrib/ttmath/ttmathuint_x86.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmathuint_x86_64.h' -> `./contrib/ttmath/ttmathuint_x86_64.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmathuint_x86_64_msvc.asm' -> `./contrib/ttmath/ttmathuint_x86_64_msvc.asm' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmathmisc.h' -> `./contrib/ttmath/ttmathmisc.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmathparser.h' -> `./contrib/ttmath/ttmathparser.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/ttmath/ttmathbig.h' -> `./contrib/ttmath/ttmathbig.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/htslib_config/config.h' -> `./contrib/htslib_config/config.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/htslib_config/config_vars.h' -> `./contrib/htslib_config/config_vars.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/contrib/htslib_config/version.h' -> `./contrib/htslib_config/version.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/.github/ISSUE_TEMPLATE/bug_report.md' -> `./.github/ISSUE_TEMPLATE/bug_report.md' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/.github/workflows/ci_test.yml' -> `./.github/workflows/ci_test.yml' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/.github/workflows/main.yml' -> `./.github/workflows/main.yml' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/.github/workflows/support-tracker-bot.yaml' -> `./.github/workflows/support-tracker-bot.yaml' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/.github/workflows/issue-tracker-bot.yaml' -> `./.github/workflows/issue-tracker-bot.yaml' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/examples/freebayes-env.yaml' -> `./examples/freebayes-env.yaml' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/examples/pipeline.sh' -> `./examples/pipeline.sh' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/examples/snakemake-freebayes-parallel.smk' -> `./examples/snakemake-freebayes-parallel.smk' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/scripts/freebayes-parallel' -> `./scripts/freebayes-parallel' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/scripts/split_ref_by_bai_datasize.py' -> `./scripts/split_ref_by_bai_datasize.py' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/scripts/vcffirstheader' -> `./scripts/vcffirstheader' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/scripts/bgziptabix' -> `./scripts/bgziptabix' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/scripts/sam_add_rg.pl' -> `./scripts/sam_add_rg.pl' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/scripts/update_version.sh' -> `./scripts/update_version.sh' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/scripts/generate_freebayes_region_scripts.sh' -> `./scripts/generate_freebayes_region_scripts.sh' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/scripts/fasta_generate_regions.py' -> `./scripts/fasta_generate_regions.py' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/scripts/GenerateFreebayesRegions.R' -> `./scripts/GenerateFreebayesRegions.R' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/scripts/coverage_to_regions.py' -> `./scripts/coverage_to_regions.py' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/scripts/samples.cnv' -> `./scripts/samples.cnv' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/runner.sh' -> `./test/runner.sh' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/splice/1:883884-887618.fa' -> `./test/splice/1:883884-887618.fa' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/splice/1:883884-887618.fa.fai' -> `./test/splice/1:883884-887618.fa.fai' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/splice/1:883884-887618.bam' -> `./test/splice/1:883884-887618.bam' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/splice/1:883884-887618.bam.bai' -> `./test/splice/1:883884-887618.bam.bai' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/regression/NA12878.chr22.tiny.vcf' -> `./test/regression/NA12878.chr22.tiny.vcf' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/regression/README.md' -> `./test/regression/README.md' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/t/00_region_and_target_handling.t' -> `./test/t/00_region_and_target_handling.t' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/t/01b_call_variants.t' -> `./test/t/01b_call_variants.t' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/t/03_reference_bases.t' -> `./test/t/03_reference_bases.t' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/t/02_multi_bam.t' -> `./test/t/02_multi_bam.t' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/t/01_call_variants.t' -> `./test/t/01_call_variants.t' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/data/test.bam' -> `./test/data/test.bam' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/data/test.ref.fai' -> `./test/data/test.ref.fai' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/data/test.vcf' -> `./test/data/test.vcf' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/data/test.bed' -> `./test/data/test.bed' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/data/test.bam.bai' -> `./test/data/test.bam.bai' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/data/targets.bed' -> `./test/data/targets.bed' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/data/test.alt' -> `./test/data/test.alt' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/data/test.ref' -> `./test/data/test.ref' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/performance/benchmark.md' -> `./test/performance/benchmark.md' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/q.vcf.gz.tbi' -> `./test/tiny/q.vcf.gz.tbi' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/NA12878.chr22.tiny.cram' -> `./test/tiny/NA12878.chr22.tiny.cram' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/q_spiked.vcf.gz.tbi' -> `./test/tiny/q_spiked.vcf.gz.tbi' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/q with spaces.regions' -> `./test/tiny/q with spaces.regions' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/NA12878.chr22.tiny.hla.bam.bai' -> `./test/tiny/NA12878.chr22.tiny.hla.bam.bai' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/q.regions' -> `./test/tiny/q.regions' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/1read.bam.bai' -> `./test/tiny/1read.bam.bai' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/q with spaces.fa.fai' -> `./test/tiny/q with spaces.fa.fai' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/hla.vcf.gz' -> `./test/tiny/hla.vcf.gz' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/q_spiked.vcf.gz' -> `./test/tiny/q_spiked.vcf.gz' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/q.fa.fai' -> `./test/tiny/q.fa.fai' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/hla.vcf.gz.tbi' -> `./test/tiny/hla.vcf.gz.tbi' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/NA12878.chr22.tiny.bam.bai' -> `./test/tiny/NA12878.chr22.tiny.bam.bai' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/hla.fa' -> `./test/tiny/hla.fa' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/q.fa' -> `./test/tiny/q.fa' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/1read.bam' -> `./test/tiny/1read.bam' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/NA12878.chr22.tiny.giab.vcf' -> `./test/tiny/NA12878.chr22.tiny.giab.vcf' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/NA12878.chr22.tiny.hla.bam' -> `./test/tiny/NA12878.chr22.tiny.hla.bam' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/q with spaces.fa' -> `./test/tiny/q with spaces.fa' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/hla.fa.fai' -> `./test/tiny/hla.fa.fai' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/q.vcf.gz' -> `./test/tiny/q.vcf.gz' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/test/tiny/NA12878.chr22.tiny.bam' -> `./test/tiny/NA12878.chr22.tiny.bam' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/LeftAlign.cpp' -> `./src/LeftAlign.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Sample.h' -> `./src/Sample.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/freebayes.cpp' -> `./src/freebayes.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Contamination.h' -> `./src/Contamination.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Parameters.cpp' -> `./src/Parameters.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Allele.h' -> `./src/Allele.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Result.h' -> `./src/Result.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/AlleleParser.h' -> `./src/AlleleParser.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Logging.h' -> `./src/Logging.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/CNV.cpp' -> `./src/CNV.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/SegfaultHandler.cpp' -> `./src/SegfaultHandler.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Marginals.cpp' -> `./src/Marginals.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/bamleftalign.cpp' -> `./src/bamleftalign.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/version_git.h' -> `./src/version_git.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/FBFasta.cpp' -> `./src/FBFasta.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/ResultData.h' -> `./src/ResultData.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Contamination.cpp' -> `./src/Contamination.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Parameters.h' -> `./src/Parameters.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Utility.h' -> `./src/Utility.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/CNV.h' -> `./src/CNV.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Bias.cpp' -> `./src/Bias.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/BedReader.cpp' -> `./src/BedReader.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/IndelAllele.cpp' -> `./src/IndelAllele.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Multinomial.cpp' -> `./src/Multinomial.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Marginals.h' -> `./src/Marginals.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Result.cpp' -> `./src/Result.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Ewens.h' -> `./src/Ewens.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Multinomial.h' -> `./src/Multinomial.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Product.h' -> `./src/Product.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Dirichlet.h' -> `./src/Dirichlet.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/DataLikelihood.cpp' -> `./src/DataLikelihood.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/.gitignore' -> `./src/.gitignore' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Sum.h' -> `./src/Sum.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/NonCall.cpp' -> `./src/NonCall.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/ResultData.cpp' -> `./src/ResultData.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Dirichlet.cpp' -> `./src/Dirichlet.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Genotype.h' -> `./src/Genotype.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/TryCatch.h' -> `./src/TryCatch.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/LeftAlign.h' -> `./src/LeftAlign.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/DataLikelihood.h' -> `./src/DataLikelihood.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Genotype.cpp' -> `./src/Genotype.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Sample.cpp' -> `./src/Sample.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/AlleleParser.cpp' -> `./src/AlleleParser.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/LargeFileSupport.h' -> `./src/LargeFileSupport.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Utility.cpp' -> `./src/Utility.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/SegfaultHandler.h' -> `./src/SegfaultHandler.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Bias.h' -> `./src/Bias.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/NonCall.h' -> `./src/NonCall.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Ewens.cpp' -> `./src/Ewens.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/Allele.cpp' -> `./src/Allele.cpp' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/IndelAllele.h' -> `./src/IndelAllele.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/FBFasta.h' -> `./src/FBFasta.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/src/BedReader.h' -> `./src/BedReader.h' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/paper/low_frequency_sensitivity.png' -> `./paper/low_frequency_sensitivity.png' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/paper/omni_errors.png' -> `./paper/omni_errors.png' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/paper/1000G_performance_comparison.png' -> `./paper/1000G_performance_comparison.png' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/paper/haplotype_calling.png' -> `./paper/haplotype_calling.png' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/paper/miseq.png' -> `./paper/miseq.png' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/paper/indel_error.png' -> `./paper/indel_error.png' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/paper/genome_research.bst' -> `./paper/genome_research.bst' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/paper/main.tex' -> `./paper/main.tex' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/paper/.gitignore' -> `./paper/.gitignore' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/paper/Makefile' -> `./paper/Makefile' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/paper/references.bib' -> `./paper/references.bib' `/gnu/store/l708j4n681qxnqi3fng6vgyag4d8mipv-freebayes-1.3.7-checkout/paper/100samples10x_0_25_both.png' -> `./paper/100samples10x_0_25_both.png' phase `unpack' succeeded after 0.1 seconds starting phase `unpack-submodule-sources' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/license' -> `test/test-simple-bash/license' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/package.yaml' -> `test/test-simple-bash/package.yaml' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/readme.asc' -> `test/test-simple-bash/readme.asc' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/change' -> `test/test-simple-bash/change' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/Makefile' -> `test/test-simple-bash/Makefile' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/note/todo' -> `test/test-simple-bash/note/todo' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/doc/manpage-base.xsl' -> `test/test-simple-bash/doc/manpage-base.xsl' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/doc/asciidoc.conf' -> `test/test-simple-bash/doc/asciidoc.conf' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/doc/test-simple.bash.1' -> `test/test-simple-bash/doc/test-simple.bash.1' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/doc/manpage-normal.xsl' -> `test/test-simple-bash/doc/manpage-normal.xsl' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/doc/test-simple.bash.asc' -> `test/test-simple-bash/doc/test-simple.bash.asc' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/test/no-label.t' -> `test/test-simple-bash/test/no-label.t' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/test/basics.t' -> `test/test-simple-bash/test/basics.t' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/test/doc.t' -> `test/test-simple-bash/test/doc.t' `/gnu/store/g3yr6jyx8biiwfl8yh8rj24c84kz4cy5-test-simple-bash-src-checkout/lib/test-simple.bash' -> `test/test-simple-bash/lib/test-simple.bash' phase `unpack-submodule-sources' succeeded after 0.0 seconds starting phase `patch-source' phase `patch-source' succeeded after 0.1 seconds starting phase `generate-gdk-pixbuf-loaders-cache-file' phase `generate-gdk-pixbuf-loaders-cache-file' succeeded after 0.0 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.0 seconds starting phase `patch-source-shebangs' patch-shebang: ./examples/pipeline.sh: changing `/bin/bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./python/allelebayes.py: changing `/usr/bin/env python3' to `/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/bin/python3' patch-shebang: ./python/dirichlet.py: changing `/usr/bin/env python3' to `/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/bin/python3' patch-shebang: ./python/hwe.py: changing `/usr/bin/env python3' to `/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/bin/python3' patch-shebang: ./python/multiset.py: changing `/usr/bin/env python3' to `/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/bin/python3' patch-shebang: ./scripts/bgziptabix: changing `/usr/bin/env bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./scripts/coverage_to_regions.py: changing `/usr/bin/env python3' to `/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/bin/python3' patch-shebang: ./scripts/fasta_generate_regions.py: changing `/usr/bin/env python3' to `/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/bin/python3' patch-shebang: ./scripts/freebayes-parallel: changing `/usr/bin/env bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./scripts/generate_freebayes_region_scripts.sh: changing `/bin/bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./scripts/sam_add_rg.pl: changing `/usr/bin/env perl' to `/gnu/store/v6bivyjbg6bj07s8iqfzdm6hpvypc0p1-perl-5.36.0/bin/perl' patch-shebang: ./scripts/split_ref_by_bai_datasize.py: changing `/usr/bin/env python3' to `/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/bin/python3' patch-shebang: ./scripts/update_version.sh: changing `/bin/sh' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/sh' patch-shebang: ./scripts/vcffirstheader: changing `/usr/bin/env python3' to `/gnu/store/kayi1a27qjbizw1870vgpwd6mzcdggql-python-3.10.7/bin/python3' patch-shebang: ./test/runner.sh: changing `/bin/sh' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/sh' patch-shebang: ./test/t/00_region_and_target_handling.t: changing `/usr/bin/env bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./test/t/01_call_variants.t: changing `/usr/bin/env bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./test/t/01b_call_variants.t: changing `/usr/bin/env bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./test/t/02_multi_bam.t: changing `/usr/bin/env bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./test/t/03_reference_bases.t: changing `/usr/bin/env bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./test/test-simple-bash/test/basics.t: changing `/bin/bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./test/test-simple-bash/test/doc.t: changing `/bin/bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./test/test-simple-bash/test/no-label.t: changing `/bin/bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash' phase `patch-source-shebangs' succeeded after 0.1 seconds starting phase `configure' The Meson build system Version: 1.5.2 Source dir: /tmp/guix-build-freebayes-1.3.7.drv-0/source Build dir: /tmp/guix-build-freebayes-1.3.7.drv-0/build Build type: native build Project name: freebayes Project version: 1.3.6 C compiler for the host machine: gcc (gcc 11.4.0 "gcc (GCC) 11.4.0") C linker for the host machine: gcc ld.bfd 2.41 C++ compiler for the host machine: c++ (gcc 11.4.0 "c++ (GCC) 11.4.0") C++ linker for the host machine: c++ ld.bfd 2.41 Host machine cpu family: x86_64 Host machine cpu: x86_64 Found pkg-config: YES (/gnu/store/a3lsdsalcmg5wnk67869af7wljprkbam-pkg-config-0.29.2/bin/pkg-config) 0.29.2 Run-time dependency zlib found: YES 1.3 Run-time dependency liblzma found: YES 5.4.5 Run-time dependency threads found: YES Library tabixpp found: YES Run-time dependency htslib found: YES 1.19 Library tabixpp found: YES Run-time dependency vcflib found: YES 1.0.9 Did not find CMake 'cmake' Found CMake: NO Run-time dependency libseqlib found: NO (tried pkgconfig and cmake) Compiler for C++ supports arguments -fpermissive: YES Compiler for C++ supports arguments -Wno-reorder: YES Compiler for C++ supports arguments -Wno-sign-compare: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES Program prove found: YES (/gnu/store/v6bivyjbg6bj07s8iqfzdm6hpvypc0p1-perl-5.36.0/bin/prove) Build targets in project: 4 freebayes 1.3.6 User defined options buildtype : debugoptimized prefix : /gnu/store/v8dppfka52c7yvkvmmfyv6idrj48d6ly-freebayes-1.3.7 c_link_args : -Wl,-rpath=/gnu/store/v8dppfka52c7yvkvmmfyv6idrj48d6ly-freebayes-1.3.7/lib cpp_link_args: -Wl,-rpath=/gnu/store/v8dppfka52c7yvkvmmfyv6idrj48d6ly-freebayes-1.3.7/lib Found ninja-1.11.1 at /gnu/store/qawfmb8fcb981r53b3nj025rvp3w35gb-ninja-1.11.1/bin/ninja phase `configure' succeeded after 3.3 seconds starting phase `patch-generated-file-shebangs' phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `build' [1/35] Compiling C object libcustom_seqlib.a.p/contrib_SeqLib_src_ssw.c.o [2/35] Compiling C++ object libcustom_seqlib.a.p/contrib_SeqLib_src_ssw_cpp.cpp.o [3/35] Compiling C++ object libcustom_seqlib.a.p/contrib_SeqLib_src_BamWriter.cpp.o [4/35] Compiling C++ object libcustom_seqlib.a.p/contrib_SeqLib_src_BamHeader.cpp.o [5/35] Compiling C++ object libfreebayes_common.a.p/src_Bias.cpp.o [6/35] Compiling C++ object libfreebayes_common.a.p/src_CNV.cpp.o [7/35] Compiling C++ object libcustom_seqlib.a.p/contrib_SeqLib_src_BamRecord.cpp.o [8/35] Compiling C++ object libfreebayes_common.a.p/src_BedReader.cpp.o [9/35] Compiling C++ object libfreebayes_common.a.p/src_Contamination.cpp.o [10/35] Compiling C++ object libcustom_seqlib.a.p/contrib_SeqLib_src_BamReader.cpp.o [11/35] Compiling C++ object libfreebayes_common.a.p/src_Dirichlet.cpp.o [12/35] Compiling C++ object libfreebayes_common.a.p/src_IndelAllele.cpp.o [13/35] Compiling C++ object libfreebayes_common.a.p/src_Allele.cpp.o [14/35] Compiling C++ object libfreebayes_common.a.p/src_Ewens.cpp.o [15/35] Compiling C++ object libfreebayes_common.a.p/src_Multinomial.cpp.o [16/35] Compiling C++ object libfreebayes_common.a.p/src_FBFasta.cpp.o [17/35] Compiling C++ object libcustom_seqlib.a.p/contrib_SeqLib_src_GenomicRegion.cpp.o [18/35] Linking static target libcustom_seqlib.a [19/35] Compiling C++ object libfreebayes_common.a.p/src_NonCall.cpp.o [20/35] Compiling C++ object libfreebayes_common.a.p/src_LeftAlign.cpp.o [21/35] Compiling C++ object libfreebayes_common.a.p/src_DataLikelihood.cpp.o [22/35] Compiling C++ object libfreebayes_common.a.p/src_SegfaultHandler.cpp.o [23/35] Compiling C++ object libfreebayes_common.a.p/src_Marginals.cpp.o [24/35] Compiling C++ object libfreebayes_common.a.p/src_Result.cpp.o [25/35] Compiling C++ object libfreebayes_common.a.p/src_Parameters.cpp.o [26/35] Compiling C++ object libfreebayes_common.a.p/src_Sample.cpp.o [27/35] Compiling C++ object libfreebayes_common.a.p/src_Utility.cpp.o In file included from ../source/contrib/ttmath/ttmathint.h:48, from ../source/contrib/ttmath/ttmathbig.h:46, from ../source/contrib/ttmath/ttmath.h:58, from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with long unsigned int value_size = 1]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<4, 1>]’ at ../source/contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../source/src/Utility.cpp:58:44: ../source/contrib/ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<4, 1>::mantissa.ttmath::UInt<1>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ In file included from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: ../source/contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../source/contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In file included from ../source/contrib/ttmath/ttmathbig.h:46, from ../source/contrib/ttmath/ttmath.h:58, from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: In member function ‘ttmath::uint ttmath::Int::FromUIntOrInt(const ttmath::UInt&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’, inlined from ‘ttmath::uint ttmath::Int::FromInt(const ttmath::Int&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:698:23, inlined from ‘ttmath::Int& ttmath::Int::operator=(const ttmath::Int&) [with long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:772:10, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3647:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<4, 1>]’ at ../source/contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../source/src/Utility.cpp:58:44: ../source/contrib/ttmath/ttmathint.h:652:61: warning: ‘result.ttmath::Big<4, 1>::exponent.ttmath::Int<4>::.ttmath::UInt<4>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ In file included from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: ../source/contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../source/contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In file included from ../source/contrib/ttmath/ttmathbig.h:46, from ../source/contrib/ttmath/ttmath.h:58, from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: In member function ‘ttmath::uint ttmath::Int::FromUIntOrInt(const ttmath::UInt&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’, inlined from ‘ttmath::uint ttmath::Int::FromInt(const ttmath::Int&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:698:23, inlined from ‘ttmath::Int& ttmath::Int::operator=(const ttmath::Int&) [with long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:772:10, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3647:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<4, 1>]’ at ../source/contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../source/src/Utility.cpp:58:44: ../source/contrib/ttmath/ttmathint.h:652:61: warning: ‘result.ttmath::Big<4, 1>::exponent.ttmath::Int<4>::.ttmath::UInt<4>::table[3]’ may be used uninitialized [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ In file included from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: ../source/contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../source/contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In file included from ../source/contrib/ttmath/ttmathbig.h:46, from ../source/contrib/ttmath/ttmath.h:58, from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: In member function ‘ttmath::uint ttmath::Int::FromUIntOrInt(const ttmath::UInt&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’, inlined from ‘ttmath::uint ttmath::Int::FromInt(const ttmath::Int&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:698:23, inlined from ‘ttmath::Int& ttmath::Int::operator=(const ttmath::Int&) [with long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:772:10, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3647:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<4, 1>]’ at ../source/contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../source/src/Utility.cpp:58:44: ../source/contrib/ttmath/ttmathint.h:652:61: warning: ‘result.ttmath::Big<4, 1>::exponent.ttmath::Int<4>::.ttmath::UInt<4>::table[2]’ may be used uninitialized [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ In file included from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: ../source/contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../source/contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In file included from ../source/contrib/ttmath/ttmathbig.h:46, from ../source/contrib/ttmath/ttmath.h:58, from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: In member function ‘ttmath::uint ttmath::Int::FromUIntOrInt(const ttmath::UInt&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’, inlined from ‘ttmath::uint ttmath::Int::FromInt(const ttmath::Int&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:698:23, inlined from ‘ttmath::Int& ttmath::Int::operator=(const ttmath::Int&) [with long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:772:10, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3647:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<4, 1>]’ at ../source/contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../source/src/Utility.cpp:58:44: ../source/contrib/ttmath/ttmathint.h:652:61: warning: ‘result.ttmath::Big<4, 1>::exponent.ttmath::Int<4>::.ttmath::UInt<4>::table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ In file included from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: ../source/contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../source/contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In file included from ../source/contrib/ttmath/ttmathint.h:48, from ../source/contrib/ttmath/ttmathbig.h:46, from ../source/contrib/ttmath/ttmath.h:58, from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with long unsigned int value_size = 1]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<4, 1>]’ at ../source/contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../source/src/Utility.cpp:58:44: ../source/contrib/ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<4, 1>::mantissa.ttmath::UInt<1>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ In file included from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: ../source/contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../source/contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In file included from ../source/contrib/ttmath/ttmathbig.h:46, from ../source/contrib/ttmath/ttmath.h:58, from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: In member function ‘ttmath::uint ttmath::Int::FromUIntOrInt(const ttmath::UInt&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’, inlined from ‘ttmath::uint ttmath::Int::FromInt(const ttmath::Int&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:698:23, inlined from ‘ttmath::Int& ttmath::Int::operator=(const ttmath::Int&) [with long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:772:10, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3647:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<4, 1>]’ at ../source/contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../source/src/Utility.cpp:58:44: ../source/contrib/ttmath/ttmathint.h:652:61: warning: ‘result.ttmath::Big<4, 1>::exponent.ttmath::Int<4>::.ttmath::UInt<4>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ In file included from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: ../source/contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../source/contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In file included from ../source/contrib/ttmath/ttmathbig.h:46, from ../source/contrib/ttmath/ttmath.h:58, from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: In member function ‘ttmath::uint ttmath::Int::FromUIntOrInt(const ttmath::UInt&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’, inlined from ‘ttmath::uint ttmath::Int::FromInt(const ttmath::Int&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:698:23, inlined from ‘ttmath::Int& ttmath::Int::operator=(const ttmath::Int&) [with long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:772:10, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3647:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<4, 1>]’ at ../source/contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../source/src/Utility.cpp:58:44: ../source/contrib/ttmath/ttmathint.h:652:61: warning: ‘result.ttmath::Big<4, 1>::exponent.ttmath::Int<4>::.ttmath::UInt<4>::table[3]’ may be used uninitialized [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ In file included from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: ../source/contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../source/contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In file included from ../source/contrib/ttmath/ttmathbig.h:46, from ../source/contrib/ttmath/ttmath.h:58, from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: In member function ‘ttmath::uint ttmath::Int::FromUIntOrInt(const ttmath::UInt&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’, inlined from ‘ttmath::uint ttmath::Int::FromInt(const ttmath::Int&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:698:23, inlined from ‘ttmath::Int& ttmath::Int::operator=(const ttmath::Int&) [with long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:772:10, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3647:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<4, 1>]’ at ../source/contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../source/src/Utility.cpp:58:44: ../source/contrib/ttmath/ttmathint.h:652:61: warning: ‘result.ttmath::Big<4, 1>::exponent.ttmath::Int<4>::.ttmath::UInt<4>::table[2]’ may be used uninitialized [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ In file included from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: ../source/contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../source/contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In file included from ../source/contrib/ttmath/ttmathbig.h:46, from ../source/contrib/ttmath/ttmath.h:58, from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: In member function ‘ttmath::uint ttmath::Int::FromUIntOrInt(const ttmath::UInt&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’, inlined from ‘ttmath::uint ttmath::Int::FromInt(const ttmath::Int&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:698:23, inlined from ‘ttmath::Int& ttmath::Int::operator=(const ttmath::Int&) [with long unsigned int value_size = 4]’ at ../source/contrib/ttmath/ttmathint.h:772:10, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3647:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../source/contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ttmath::ErrorCode*) [with ValueType = ttmath::Big<4, 1>]’ at ../source/contrib/ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../source/src/Utility.cpp:58:44: ../source/contrib/ttmath/ttmathint.h:652:61: warning: ‘result.ttmath::Big<4, 1>::exponent.ttmath::Int<4>::.ttmath::UInt<4>::table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ In file included from ../source/src/Utility.h:18, from ../source/src/Utility.cpp:3: ../source/contrib/ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../source/contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ [28/35] Compiling C++ object bamleftalign.p/src_bamleftalign.cpp.o [29/35] Compiling C++ object libfreebayes_common.a.p/src_Genotype.cpp.o [30/35] Compiling C++ object libfreebayes_common.a.p/src_AlleleParser.cpp.o [31/35] Compiling C++ object freebayes.p/src_freebayes.cpp.o [32/35] Compiling C++ object libfreebayes_common.a.p/src_ResultData.cpp.o [33/35] Linking static target libfreebayes_common.a [34/35] Linking target bamleftalign [35/35] Linking target freebayes phase `build' succeeded after 96.3 seconds starting phase `check' ninja: Entering directory `/tmp/guix-build-freebayes-1.3.7.drv-0/build' ninja: no work to do. 1/5 T03 FAIL 0.53s exit status 1 >>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=242 MESON_TEST_ITERATION=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /gnu/store/v6bivyjbg6bj07s8iqfzdm6hpvypc0p1-perl-5.36.0/bin/prove -e bash -v t/03_reference_bases.t ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/03_reference_bases.t .. 1..3 ok 1 - freebayes rejects invalid reference not ok 2 - freebayes does not put uppercase IUPAC bases in VCFs # got: '' # expected: 'ref 14 . A G # ref 16 . CNNNNNNNNNNN TAAAAAAAAAAA # ref 29 . C G # ref 31 . A T' not ok 3 - freebayes does not put lowercase IUPAC bases in VCFs # got: '' # expected: 'ref 14 . A G # ref 16 . CNNNNNNNNNNN TAAAAAAAAAAA # ref 29 . C G # ref 31 . A T' Failed 2/3 subtests Test Summary Report ------------------- t/03_reference_bases.t (Wstat: 0 Tests: 3 Failed: 2) Failed tests: 2-3 Files=1, Tests=3, 0 wallclock secs ( 0.03 usr 0.00 sys + 0.07 cusr 0.04 csys = 0.14 CPU) Result: FAIL ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 2/5 T00 FAIL 0.95s exit status 1 >>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=151 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MESON_TEST_ITERATION=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /gnu/store/v6bivyjbg6bj07s8iqfzdm6hpvypc0p1-perl-5.36.0/bin/prove -e bash -v t/00_region_and_target_handling.t ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― stdout: t/00_region_and_target_handling.t .. 1..12 ok 1 - ref:4-5 ref:6-7 are empty ok 2 - ref:4 ref:6 are empty not ok 3 - ref:5-6 ref:7-8 not ok 4 - ref:5 ref:7 not ok 5 - ref:5- not ok 6 - full output not ok 7 - --targets t/../00_region_and_target_handling.t.bed not ok 8 - --region ref not ok 9 - ref:1,0- not ok 10 - ref:1,0-1,1 not ok 11 - ref:0-1 ok 12 - region outside of bounds error Failed 9/12 subtests Test Summary Report ------------------- t/00_region_and_target_handling.t (Wstat: 0 Tests: 12 Failed: 9) Failed tests: 3-11 Files=1, Tests=12, 0 wallclock secs ( 0.02 usr 0.01 sys + 0.18 cusr 0.14 csys = 0.35 CPU) Result: FAIL stderr: # Failed test 'ref:5-6 ref:7-8' # at t/00_region_and_target_handling.t line 101. # Failed test 'ref:5 ref:7' # at t/00_region_and_target_handling.t line 104. # Failed test 'ref:5-' # at t/00_region_and_target_handling.t line 113. # Failed test 'full output' # at t/00_region_and_target_handling.t line 124. # Failed test '--targets t/../00_region_and_target_handling.t.bed' # at t/00_region_and_target_handling.t line 127. # Failed test '--region ref' # at t/00_region_and_target_handling.t line 130. # Failed test 'ref:1,0-' # at t/00_region_and_target_handling.t line 138. # Failed test 'ref:1,0-1,1' # at t/00_region_and_target_handling.t line 141. # Failed test 'ref:0-1' # at t/00_region_and_target_handling.t line 145. Output: ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 3/5 T02 FAIL 1.00s exit status 1 >>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=243 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MESON_TEST_ITERATION=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /gnu/store/v6bivyjbg6bj07s8iqfzdm6hpvypc0p1-perl-5.36.0/bin/prove -e bash -v t/02_multi_bam.t ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/02_multi_bam.t .. 1..7 not ok 1 - freebayes calls from two identical BAMs # got: '' # expected: 'ref 2 . A G # ref 4 . CG TA # ref 7 . C G # ref 9 . A T' not ok 2 - freebayes calls from two BAMs with different samples for different read groups # got: '' # expected: 'ref 2 . A G # ref 4 . CG TA # ref 7 . C G # ref 9 . A T' not ok 3 - freebayes calls from two BAMs with different technologies for different read groups # got: '' # expected: 'ref 2 . A G # ref 4 . CG TA # ref 7 . C G # ref 9 . A T' ok 4 - freebayes rejects two BAMs with different samples for same read groups ok 5 - freebayes rejects two BAMs with different technologies for same read groups not ok 6 - freebayes calls multiple alts from two different BAMs # got: '' # expected: 'ref 2 . A C,G # ref 4 . CG TA # ref 7 . C G # ref 9 . A T' ok 7 - freebayes rejects two BAMs with the same name Failed 4/7 subtests Test Summary Report ------------------- t/02_multi_bam.t (Wstat: 0 Tests: 7 Failed: 4) Failed tests: 1-3, 6 Files=1, Tests=7, 1 wallclock secs ( 0.03 usr 0.01 sys + 0.20 cusr 0.18 csys = 0.42 CPU) Result: FAIL ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 4/5 T01 FAIL 1.86s exit status 1 >>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=76 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MESON_TEST_ITERATION=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /gnu/store/v6bivyjbg6bj07s8iqfzdm6hpvypc0p1-perl-5.36.0/bin/prove -e bash -v t/01_call_variants.t ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― stdout: t/01_call_variants.t .. 1..16 not ok 1 - variant calling recovers most of the GiAB variants in a test region # got: '0' # expected: '1' ok 2 - freebayes produces the same number of calls if targeted per site or called without targets ok 3 - a targets bed file can be used with the same effect as running by region ok 4 - reading from stdin or not makes no difference not ok 5 - freebayes processes all alignments in BAM input # got: '3333' # expected: '51' ok 6 - freebayes processes all alignments in CRAM input not ok 7 - freebayes correctly handles variant input # got: '0' # expected: '16' not ok 8 - freebayes puts required variants in output # got: '0' # expected: '3' not ok 9 - freebayes limits calls to input variants correctly # got: '0' # expected: '3' not ok 10 - freebayes reports all input variants even when there is no input data # got: '0' # expected: '16' not ok 11 - freebayes handles region and variant input # got: '0' # expected: '2' not ok 12 - freebayes limits to variant input correctly when region is given # got: '0' # expected: '2' not ok 13 - freebayes handles variant input and reading from stdin # got: '0' # expected: '3' not ok 14 - freebayes limits to variant input when reading from stdin # got: '0' # expected: '3' not ok 15 - freebayes handles region, stdin, and variant input # got: '0' # expected: '2' ok 16 - ! Failed 11/16 subtests Test Summary Report ------------------- t/01_call_variants.t (Wstat: 0 Tests: 16 Failed: 11) Failed tests: 1, 5, 7-15 Files=1, Tests=16, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.66 cusr 0.38 csys = 1.07 CPU) Result: FAIL stderr: egrep: warning: egrep is obsolescent; using grep -E [E::idx_find_and_load] Could not retrieve index file for '-' Random access with SetRegion not available for STDIN reading (no index file) ERROR(freebayes): Could not SetRegion to q:1..10000 t/01_call_variants.t: line 107: 856 Aborted freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 5/5 T01b FAIL 1.80s exit status 1 >>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=97 MESON_TEST_ITERATION=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /gnu/store/v6bivyjbg6bj07s8iqfzdm6hpvypc0p1-perl-5.36.0/bin/prove -e bash -v t/01b_call_variants.t ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/01b_call_variants.t .. 1..10 ok 1 - running in parallel makes no difference ok 2 - freebayes handles spaces in file names not ok 3 - freebayes handles region and variant input even with : in contig names # got: '0' # expected: '2' not ok 4 - freebayes can handle spliced reads # got: '0' # expected: '3' not ok 5 - freebayes produces the expected number of lines of gVCF output # got: '0' # expected: '20' not ok 6 - freebayes produces the expected number of lines of gVCF output # got: '3' # expected: '250' not ok 7 - freebayes produces the expected number of lines of gVCF output # got: '176' # expected: '12250' not ok 8 - the CNV map may be used to specify per-sample copy numbers # got: '0' # expected: '19' not ok 9 - freebayes makes the expected number of calls when capping coverage # got: '0' # expected: '22' not ok 10 - freebayes correctly uses CNV map with multiple entries # got: '0:0' # expected: '0:19' Failed 8/10 subtests Test Summary Report ------------------- t/01b_call_variants.t (Wstat: 0 Tests: 10 Failed: 8) Failed tests: 3-10 Files=1, Tests=10, 1 wallclock secs ( 0.02 usr 0.02 sys + 1.02 cusr 0.43 csys = 1.49 CPU) Result: FAIL ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― Summary of Failures: 1/5 T03 FAIL 0.53s exit status 1 2/5 T00 FAIL 0.95s exit status 1 3/5 T02 FAIL 1.00s exit status 1 4/5 T01 FAIL 1.86s exit status 1 5/5 T01b FAIL 1.80s exit status 1 Ok: 0 Expected Fail: 0 Fail: 5 Unexpected Pass: 0 Skipped: 0 Timeout: 0 Full log written to /tmp/guix-build-freebayes-1.3.7.drv-0/build/meson-logs/testlog.txt error: in phase 'check': uncaught exception: %exception #<&invoke-error program: "meson" arguments: ("test" "--print-errorlogs" "-t" "0") exit-status: 5 term-signal: #f stop-signal: #f> phase `check' failed after 2.5 seconds command "meson" "test" "--print-errorlogs" "-t" "0" failed with status 5 build process 10 exited with status 256