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/fwwa3gpk42r773gd492wfaz3smp3048m-autoconf-2.69/bin:/gnu/store/6fpkzhw6q09hqaiagnjg63fda2pn7sgq-automake-1.16.5/bin:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/bin:/gnu/store/crpic36n5wpk7vxyxw1idm99af9f20g7-binutils-cross-arm-linux-gnueabihf-2.41/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 `CROSS_LIBRARY_PATH' set to `/gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/lib:/gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/lib:/gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/lib:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib:/gnu/store/a6blq1zlgipcbangszn7p7s3nbhph5c8-glibc-cross-arm-linux-gnueabihf-2.39-static/lib'
environment variable `CROSS_C_INCLUDE_PATH' set to `/gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/include:/gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/include:/gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/include:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include:/gnu/store/q97gxljfvsmmd29w6i2caw8033hi42li-linux-libre-headers-cross-arm-linux-gnueabihf-5.15.49/include'
environment variable `CROSS_CPLUS_INCLUDE_PATH' set to `/gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/include:/gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/include:/gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/include:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include:/gnu/store/q97gxljfvsmmd29w6i2caw8033hi42li-linux-libre-headers-cross-arm-linux-gnueabihf-5.15.49/include'
environment variable `CROSS_OBJC_INCLUDE_PATH' set to `/gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/include:/gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/include:/gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/include:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include:/gnu/store/q97gxljfvsmmd29w6i2caw8033hi42li-linux-libre-headers-cross-arm-linux-gnueabihf-5.15.49/include'
environment variable `CROSS_OBJCPLUS_INCLUDE_PATH' set to `/gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/include:/gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/include:/gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/include:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include:/gnu/store/q97gxljfvsmmd29w6i2caw8033hi42li-linux-libre-headers-cross-arm-linux-gnueabihf-5.15.49/include'
environment variable `AWKPATH' unset
environment variable `AWKLIBPATH' unset
environment variable `ACLOCAL_PATH' set to `/gnu/store/6fpkzhw6q09hqaiagnjg63fda2pn7sgq-automake-1.16.5/share/aclocal'
environment variable `BASH_LOADABLES_PATH' unset
environment variable `C_INCLUDE_PATH' set to `/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include:/gnu/store/crpic36n5wpk7vxyxw1idm99af9f20g7-binutils-cross-arm-linux-gnueabihf-2.41/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/svghsdn1x3fyili8ij791nn25zba9bpf-linux-libre-headers-5.15.49/include'
environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include:/gnu/store/crpic36n5wpk7vxyxw1idm99af9f20g7-binutils-cross-arm-linux-gnueabihf-2.41/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/svghsdn1x3fyili8ij791nn25zba9bpf-linux-libre-headers-5.15.49/include'
environment variable `OBJC_INCLUDE_PATH' set to `/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include:/gnu/store/crpic36n5wpk7vxyxw1idm99af9f20g7-binutils-cross-arm-linux-gnueabihf-2.41/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/svghsdn1x3fyili8ij791nn25zba9bpf-linux-libre-headers-5.15.49/include'
environment variable `OBJCPLUS_INCLUDE_PATH' set to `/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include:/gnu/store/crpic36n5wpk7vxyxw1idm99af9f20g7-binutils-cross-arm-linux-gnueabihf-2.41/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/svghsdn1x3fyili8ij791nn25zba9bpf-linux-libre-headers-5.15.49/include'
environment variable `LIBRARY_PATH' set to `/gnu/store/crpic36n5wpk7vxyxw1idm99af9f20g7-binutils-cross-arm-linux-gnueabihf-2.41/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'
environment variable `GUIX_LOCPATH' set to `/gnu/store/zvlp3n8iwa1svxmwv4q22pv1pb1c9pjq-glibc-2.39/lib/locale'
environment variable `TZDIR' unset
phase `set-paths' succeeded after 0.0 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/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/.gitignore' -> `./.gitignore'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/.clang-format' -> `./.clang-format'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/call_variants.sh' -> `./call_variants.sh'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/LICENSE' -> `./LICENSE'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/README' -> `./README'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/ChangeLog' -> `./ChangeLog'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/AUTHORS' -> `./AUTHORS'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/README.md' -> `./README.md'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/Dockerfile' -> `./Dockerfile'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/configure.ac' -> `./configure.ac'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/Makefile.am' -> `./Makefile.am'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/NEWS' -> `./NEWS'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/Doxyfile' -> `./Doxyfile'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/autogen.sh' -> `./autogen.sh'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/config.h.in' -> `./config.h.in'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/pipeline_consensus/example_samples.tsv' -> `./pipeline_consensus/example_samples.tsv'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/pipeline_consensus/Snakefile' -> `./pipeline_consensus/Snakefile'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/pipeline_consensus/config.json' -> `./pipeline_consensus/config.json'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/MANUAL.md' -> `./docs/MANUAL.md'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/COOKBOOK.md' -> `./docs/COOKBOOK.md'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/README.md' -> `./docs/README.md'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/INSTALLATION.md' -> `./docs/INSTALLATION.md'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/header.html' -> `./docs/header.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/footer.html' -> `./docs/footer.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/customdoxygen.css' -> `./docs/customdoxygen.css'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/man/man3/md__r_e_a_d_m_e.3' -> `./docs/man/man3/md__r_e_a_d_m_e.3'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/man/man3/cookbookpage.3' -> `./docs/man/man3/cookbookpage.3'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/man/man3/md_docs__r_e_a_d_m_e.3' -> `./docs/man/man3/md_docs__r_e_a_d_m_e.3'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/man/man3/cigar_.3' -> `./docs/man/man3/cigar_.3'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/man/man3/args_t.3' -> `./docs/man/man3/args_t.3'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/man/man3/ret_t.3' -> `./docs/man/man3/ret_t.3'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/man/man3/installpage.3' -> `./docs/man/man3/installpage.3'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/man/man3/allele.3' -> `./docs/man/man3/allele.3'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/man/man3/ivar.cpp.3' -> `./docs/man/man3/ivar.cpp.3'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/man/man3/maj.3' -> `./docs/man/man3/maj.3'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/man/man3/primer.3' -> `./docs/man/man3/primer.3'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/man/man3/manualpage.3' -> `./docs/man/man3/manualpage.3'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/man/man3/suffix_node.3' -> `./docs/man/man3/suffix_node.3'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/ivar_8cpp.html' -> `./docs/html/ivar_8cpp.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/suffix__tree_8cpp_source.html' -> `./docs/html/suffix__tree_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/graph_legend.dot' -> `./docs/html/graph_legend.dot'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/ivar_8cpp__incl.dot' -> `./docs/html/ivar_8cpp__incl.dot'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/globals_func.html' -> `./docs/html/globals_func.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/structcigar__-members.html' -> `./docs/html/structcigar__-members.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/dir_49e56c817e5e54854c35e136979f97ca.html' -> `./docs/html/dir_49e56c817e5e54854c35e136979f97ca.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/index.html' -> `./docs/html/index.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/jquery.js' -> `./docs/html/jquery.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/_i_n_s_t_a_l_l_a_t_i_o_n_8md_source.html' -> `./docs/html/_i_n_s_t_a_l_l_a_t_i_o_n_8md_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/get__masked__amplicons_8h_source.html' -> `./docs/html/get__masked__amplicons_8h_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/remove__reads__from__amplicon_8h_source.html' -> `./docs/html/remove__reads__from__amplicon_8h_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/_readme_8md_source.html' -> `./docs/html/_readme_8md_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/doxygen.png' -> `./docs/html/doxygen.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/remove__reads__from__amplicon_8cpp_source.html' -> `./docs/html/remove__reads__from__amplicon_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/test_8cpp_source.html' -> `./docs/html/test_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/tab_b.png' -> `./docs/html/tab_b.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/tab_hd.png' -> `./docs/html/tab_hd.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/classes.html' -> `./docs/html/classes.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/ivar_8cpp__incl.md5' -> `./docs/html/ivar_8cpp__incl.md5'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/primer__bed_8h_source.html' -> `./docs/html/primer__bed_8h_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/globals.html' -> `./docs/html/globals.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/nav_h.png' -> `./docs/html/nav_h.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/graph_legend.html' -> `./docs/html/graph_legend.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/menudata.js' -> `./docs/html/menudata.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/call__variants_8cpp_source.html' -> `./docs/html/call__variants_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/bdwn.png' -> `./docs/html/bdwn.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/nav_fd.png' -> `./docs/html/nav_fd.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/structret__t.html' -> `./docs/html/structret__t.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/graph_legend.md5' -> `./docs/html/graph_legend.md5'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/bc_sd.png' -> `./docs/html/bc_sd.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/structallele-members.html' -> `./docs/html/structallele-members.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/nav_g.png' -> `./docs/html/nav_g.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/tab_h.png' -> `./docs/html/tab_h.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/bam__to__bed_8cpp_source.html' -> `./docs/html/bam__to__bed_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/docd.png' -> `./docs/html/docd.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/sync_on.png' -> `./docs/html/sync_on.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/closed.png' -> `./docs/html/closed.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/get__masked__amplicons_8cpp_source.html' -> `./docs/html/get__masked__amplicons_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/dynsections.js' -> `./docs/html/dynsections.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/doxygen.svg' -> `./docs/html/doxygen.svg'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/manualpage.html' -> `./docs/html/manualpage.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/nav_hd.png' -> `./docs/html/nav_hd.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/structallele.html' -> `./docs/html/structallele.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/_m_a_n_u_a_l_8md_source.html' -> `./docs/html/_m_a_n_u_a_l_8md_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/trim__primer__quality_8h_source.html' -> `./docs/html/trim__primer__quality_8h_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/annotated.html' -> `./docs/html/annotated.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/files.html' -> `./docs/html/files.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/installpage.html' -> `./docs/html/installpage.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/call__variants_8h_source.html' -> `./docs/html/call__variants_8h_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/tab_a.png' -> `./docs/html/tab_a.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/call__consensus__pileup_8h_source.html' -> `./docs/html/call__consensus__pileup_8h_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/folderopen.png' -> `./docs/html/folderopen.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/ivar_8cpp_source.html' -> `./docs/html/ivar_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/nav_f.png' -> `./docs/html/nav_f.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/allele__functions_8h_source.html' -> `./docs/html/allele__functions_8h_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/alignment_8h_source.html' -> `./docs/html/alignment_8h_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/structargs__t.html' -> `./docs/html/structargs__t.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/open.png' -> `./docs/html/open.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/menu.js' -> `./docs/html/menu.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/bc_s.png' -> `./docs/html/bc_s.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/pages.html' -> `./docs/html/pages.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/classsuffix__node__coll__graph.dot' -> `./docs/html/classsuffix__node__coll__graph.dot'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/folderclosed.png' -> `./docs/html/folderclosed.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/splitbar.png' -> `./docs/html/splitbar.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/tabs.css' -> `./docs/html/tabs.css'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/allele__functions_8cpp_source.html' -> `./docs/html/allele__functions_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/get__common__consensus_8cpp_source.html' -> `./docs/html/get__common__consensus_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/_c_o_o_k_b_o_o_k_8md_source.html' -> `./docs/html/_c_o_o_k_b_o_o_k_8md_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/classprimer.html' -> `./docs/html/classprimer.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/structcigar__.html' -> `./docs/html/structcigar__.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/tab_s.png' -> `./docs/html/tab_s.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/suffix__tree_8h_source.html' -> `./docs/html/suffix__tree_8h_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/structargs__t-members.html' -> `./docs/html/structargs__t-members.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/md__r_e_a_d_m_e.html' -> `./docs/html/md__r_e_a_d_m_e.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/call__consensus_8cpp_source.html' -> `./docs/html/call__consensus_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/doc.png' -> `./docs/html/doc.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/cookbookpage.html' -> `./docs/html/cookbookpage.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/alignment_8cpp_source.html' -> `./docs/html/alignment_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/_r_e_a_d_m_e_8md_source.html' -> `./docs/html/_r_e_a_d_m_e_8md_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/tab_bd.png' -> `./docs/html/tab_bd.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/structmaj-members.html' -> `./docs/html/structmaj-members.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/tab_ad.png' -> `./docs/html/tab_ad.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/structmaj.html' -> `./docs/html/structmaj.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/doxygen.css' -> `./docs/html/doxygen.css'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/sync_off.png' -> `./docs/html/sync_off.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/customdoxygen.css' -> `./docs/html/customdoxygen.css'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/dir_68267d1309a1af8e8297ef4c3efbcdba.html' -> `./docs/html/dir_68267d1309a1af8e8297ef4c3efbcdba.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/tab_sd.png' -> `./docs/html/tab_sd.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/classprimer-members.html' -> `./docs/html/classprimer-members.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/call__consensus__pileup_8cpp_source.html' -> `./docs/html/call__consensus__pileup_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/md_docs__r_e_a_d_m_e.html' -> `./docs/html/md_docs__r_e_a_d_m_e.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/classsuffix__node-members.html' -> `./docs/html/classsuffix__node-members.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/classsuffix__node__coll__graph.md5' -> `./docs/html/classsuffix__node__coll__graph.md5'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/primer__bed_8cpp_source.html' -> `./docs/html/primer__bed_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/splitbard.png' -> `./docs/html/splitbard.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/structret__t-members.html' -> `./docs/html/structret__t-members.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/classsuffix__node.html' -> `./docs/html/classsuffix__node.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/trim__primer__quality_8cpp_source.html' -> `./docs/html/trim__primer__quality_8cpp_source.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/classes_0.html' -> `./docs/html/search/classes_0.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/classes_2.html' -> `./docs/html/search/classes_2.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_2.js' -> `./docs/html/search/all_2.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_7.js' -> `./docs/html/search/all_7.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_7.html' -> `./docs/html/search/all_7.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_4.html' -> `./docs/html/search/all_4.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/search.js' -> `./docs/html/search/search.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_0.html' -> `./docs/html/search/all_0.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/mag_d.svg' -> `./docs/html/search/mag_d.svg'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/search.css' -> `./docs/html/search/search.css'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/pages_0.js' -> `./docs/html/search/pages_0.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/mag.svg' -> `./docs/html/search/mag.svg'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/pages_1.js' -> `./docs/html/search/pages_1.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/classes_0.js' -> `./docs/html/search/classes_0.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/classes_3.html' -> `./docs/html/search/classes_3.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_3.js' -> `./docs/html/search/all_3.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/pages_3.html' -> `./docs/html/search/pages_3.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/search_m.png' -> `./docs/html/search/search_m.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/files_0.html' -> `./docs/html/search/files_0.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/pages_2.html' -> `./docs/html/search/pages_2.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_2.html' -> `./docs/html/search/all_2.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_5.js' -> `./docs/html/search/all_5.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_6.js' -> `./docs/html/search/all_6.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_1.html' -> `./docs/html/search/all_1.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/classes_1.js' -> `./docs/html/search/classes_1.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/search_r.png' -> `./docs/html/search/search_r.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/mag_sel.png' -> `./docs/html/search/mag_sel.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/pages_1.html' -> `./docs/html/search/pages_1.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/functions_0.js' -> `./docs/html/search/functions_0.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/close.svg' -> `./docs/html/search/close.svg'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/mag_sel.svg' -> `./docs/html/search/mag_sel.svg'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_6.html' -> `./docs/html/search/all_6.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/close.png' -> `./docs/html/search/close.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/classes_4.html' -> `./docs/html/search/classes_4.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/classes_3.js' -> `./docs/html/search/classes_3.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/classes_1.html' -> `./docs/html/search/classes_1.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/classes_4.js' -> `./docs/html/search/classes_4.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_1.js' -> `./docs/html/search/all_1.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/search_l.png' -> `./docs/html/search/search_l.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_4.js' -> `./docs/html/search/all_4.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_3.html' -> `./docs/html/search/all_3.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/pages_3.js' -> `./docs/html/search/pages_3.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/nomatches.html' -> `./docs/html/search/nomatches.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_0.js' -> `./docs/html/search/all_0.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/classes_5.js' -> `./docs/html/search/classes_5.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/classes_2.js' -> `./docs/html/search/classes_2.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/files_0.js' -> `./docs/html/search/files_0.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/pages_2.js' -> `./docs/html/search/pages_2.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/all_5.html' -> `./docs/html/search/all_5.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/mag_seld.svg' -> `./docs/html/search/mag_seld.svg'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/functions_0.html' -> `./docs/html/search/functions_0.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/classes_5.html' -> `./docs/html/search/classes_5.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/searchdata.js' -> `./docs/html/search/searchdata.js'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/html/search/pages_0.html' -> `./docs/html/search/pages_0.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/ivar_8cpp__incl.dot' -> `./docs/latex/ivar_8cpp__incl.dot'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/md_docs__r_e_a_d_m_e.tex' -> `./docs/latex/md_docs__r_e_a_d_m_e.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/classsuffix__node.tex' -> `./docs/latex/classsuffix__node.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/structallele.tex' -> `./docs/latex/structallele.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/files.tex' -> `./docs/latex/files.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/manualpage.tex' -> `./docs/latex/manualpage.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/ivar_8cpp__incl.md5' -> `./docs/latex/ivar_8cpp__incl.md5'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/annotated.tex' -> `./docs/latex/annotated.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/classsuffix__node.tex.tmp' -> `./docs/latex/classsuffix__node.tex.tmp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/structcigar__.tex' -> `./docs/latex/structcigar__.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/ivar_8cpp.tex.tmp' -> `./docs/latex/ivar_8cpp.tex.tmp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/installpage.tex' -> `./docs/latex/installpage.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/tabu_doxygen.sty' -> `./docs/latex/tabu_doxygen.sty'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/md__r_e_a_d_m_e.tex' -> `./docs/latex/md__r_e_a_d_m_e.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/refman.tex' -> `./docs/latex/refman.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/classsuffix__node__coll__graph.dot' -> `./docs/latex/classsuffix__node__coll__graph.dot'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/index.tex' -> `./docs/latex/index.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/cookbookpage.tex' -> `./docs/latex/cookbookpage.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/classprimer.tex' -> `./docs/latex/classprimer.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/structret__t.tex' -> `./docs/latex/structret__t.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/structargs__t.tex' -> `./docs/latex/structargs__t.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/structmaj.tex' -> `./docs/latex/structmaj.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/doxygen.sty' -> `./docs/latex/doxygen.sty'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/classsuffix__node__coll__graph.md5' -> `./docs/latex/classsuffix__node__coll__graph.md5'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/longtable_doxygen.sty' -> `./docs/latex/longtable_doxygen.sty'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/latex/ivar_8cpp.tex' -> `./docs/latex/ivar_8cpp.tex'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_isize_trim.cpp' -> `./tests/test_isize_trim.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_consensus_seq_id.cpp' -> `./tests/test_consensus_seq_id.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/check_quality_trim.cpp' -> `./tests/check_quality_trim.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_consensus_threshold.cpp' -> `./tests/test_consensus_threshold.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_primer_trim_edge_cases.cpp' -> `./tests/test_primer_trim_edge_cases.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_consensus_min_depth.cpp' -> `./tests/test_consensus_min_depth.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_ref_seq.cpp' -> `./tests/test_ref_seq.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_removereads.cpp' -> `./tests/test_removereads.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_unpaired_trim.cpp' -> `./tests/test_unpaired_trim.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_primer_bed.cpp' -> `./tests/test_primer_bed.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/Makefile.am' -> `./tests/Makefile.am'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_primer_trim.cpp' -> `./tests/test_primer_trim.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_call_consensus_from_plup.cpp' -> `./tests/test_call_consensus_from_plup.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_variants.cpp' -> `./tests/test_variants.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_allele_depth.cpp' -> `./tests/test_allele_depth.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_consensus_min_insert_threshold.cpp' -> `./tests/test_consensus_min_insert_threshold.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_trim.cpp' -> `./tests/test_trim.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_interval_tree.cpp' -> `./tests/test_interval_tree.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_primer_trim_pairs.cpp' -> `./tests/test_primer_trim_pairs.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_getmasked.cpp' -> `./tests/test_getmasked.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_common_variants.cpp' -> `./tests/test_common_variants.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/tests/test_amplicon_search.cpp' -> `./tests/test_amplicon_search.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/.github/workflows/clang-format-check.yml' -> `./.github/workflows/clang-format-check.yml'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/.github/workflows/ccpp.yml' -> `./.github/workflows/ccpp.yml'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/.github/ISSUE_TEMPLATE/feature_request.md' -> `./.github/ISSUE_TEMPLATE/feature_request.md'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/.github/ISSUE_TEMPLATE/bug_report.md' -> `./.github/ISSUE_TEMPLATE/bug_report.md'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/bam_to_bed.cpp' -> `./src/bam_to_bed.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/call_variants.h' -> `./src/call_variants.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/allele_functions.cpp' -> `./src/allele_functions.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/get_masked_amplicons.h' -> `./src/get_masked_amplicons.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/trim_primer_quality.h' -> `./src/trim_primer_quality.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/suffix_tree.h' -> `./src/suffix_tree.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/primer_bed.h' -> `./src/primer_bed.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/get_common_variants.cpp' -> `./src/get_common_variants.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/trim_primer_quality.cpp' -> `./src/trim_primer_quality.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/vcf_writer.h' -> `./src/vcf_writer.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/interval_tree.cpp' -> `./src/interval_tree.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/call_consensus.cpp' -> `./src/call_consensus.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/parse_gff.cpp' -> `./src/parse_gff.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/alignment.h' -> `./src/alignment.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/alignment.cpp' -> `./src/alignment.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/call_consensus_pileup.h' -> `./src/call_consensus_pileup.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/ref_seq.h' -> `./src/ref_seq.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/call_consensus_pileup.cpp' -> `./src/call_consensus_pileup.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/allele_functions.h' -> `./src/allele_functions.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/ivar.cpp' -> `./src/ivar.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/primer_bed.cpp' -> `./src/primer_bed.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/Makefile.am' -> `./src/Makefile.am'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/vcf_writer.cpp' -> `./src/vcf_writer.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/interval_tree.h' -> `./src/interval_tree.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/ref_seq.cpp' -> `./src/ref_seq.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/get_masked_amplicons.cpp' -> `./src/get_masked_amplicons.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/parse_gff.h' -> `./src/parse_gff.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/remove_reads_from_amplicon.h' -> `./src/remove_reads_from_amplicon.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/remove_reads_from_amplicon.cpp' -> `./src/remove_reads_from_amplicon.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/get_common_variants.h' -> `./src/get_common_variants.h'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/suffix_tree.cpp' -> `./src/suffix_tree.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/call_variants.cpp' -> `./src/call_variants.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/pipeline_field/Snakefile' -> `./pipeline_field/Snakefile'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/pipeline_field/pipeline_field.dot' -> `./pipeline_field/pipeline_field.dot'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/pipeline_field/dag.svg' -> `./pipeline_field/dag.svg'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/pipeline_field/pipeline_field.png' -> `./pipeline_field/pipeline_field.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test.gff' -> `./data/test.gff'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test.sorted.bam' -> `./data/test.sorted.bam'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test.unmapped.sorted.bam' -> `./data/test.unmapped.sorted.bam'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test.gap.sorted.bam.bai' -> `./data/test.gap.sorted.bam.bai'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test.gap.sorted.bam' -> `./data/test.gap.sorted.bam'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/pair_info_2.tsv' -> `./data/pair_info_2.tsv'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test.gap.sorted.mpileup' -> `./data/test.gap.sorted.mpileup'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test.sorted.bam.bai' -> `./data/test.sorted.bam.bai'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test.indel.mpileup' -> `./data/test.indel.mpileup'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test.filtered.tsv' -> `./data/test.filtered.tsv'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test_isize.bed' -> `./data/test_isize.bed'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test.sim.merged.sorted.bam.bai' -> `./data/test.sim.merged.sorted.bam.bai'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test_isize.sorted.bam' -> `./data/test_isize.sorted.bam'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/pair_information.tsv' -> `./data/pair_information.tsv'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test_merged.bed' -> `./data/test_merged.bed'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test.bed' -> `./data/test.bed'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test_amplicon.sorted.bam' -> `./data/test_amplicon.sorted.bam'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test.sim.merged.sorted.bam' -> `./data/test.sim.merged.sorted.bam'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/test.trimmed.sorted.bam' -> `./data/test.trimmed.sorted.bam'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/primer_only/primer_edge_cases.bam.bai' -> `./data/primer_only/primer_edge_cases.bam.bai'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/primer_only/primer_edge_cases.bam' -> `./data/primer_only/primer_edge_cases.bam'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/db/test_ref.fa' -> `./data/db/test_ref.fa'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/primer_pair_test/test_primer_pair.bed' -> `./data/primer_pair_test/test_primer_pair.bed'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/primer_pair_test/test_primer_pair_trim.tsv' -> `./data/primer_pair_test/test_primer_pair_trim.tsv'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/data/primer_pair_test/test_primer_pair_trim.untrimmed.bam' -> `./data/primer_pair_test/test_primer_pair_trim.untrimmed.bam'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/pipeline/Snakefile' -> `./pipeline/Snakefile'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/pipeline/pipeline.dot' -> `./pipeline/pipeline.dot'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/pipeline/dag.svg' -> `./pipeline/dag.svg'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/pipeline/pipeline.png' -> `./pipeline/pipeline.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/scripts/get_common_variants.sh' -> `./scripts/get_common_variants.sh'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/scripts/primer_bam_to_bed.sh' -> `./scripts/primer_bam_to_bed.sh'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/scripts/Makefile.am' -> `./scripts/Makefile.am'
phase `unpack' succeeded after 0.1 seconds
starting phase `patch-CXXFLAGS'
phase `patch-CXXFLAGS' succeeded after 0.0 seconds
starting phase `bootstrap'
running './autogen.sh'
patch-shebang: ./autogen.sh: changing `/bin/bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash'
configure.ac:12: installing './compile'
configure.ac:6: installing './install-sh'
configure.ac:6: installing './missing'
src/Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
phase `bootstrap' succeeded after 14.9 seconds
starting phase `patch-usr-bin-file'
phase `patch-usr-bin-file' succeeded after 1.3 seconds
starting phase `patch-source-shebangs'
patch-shebang: ./call_variants.sh: changing `/bin/bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash'
patch-shebang: ./compile: changing `/bin/sh' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/sh'
patch-shebang: ./configure: changing `/bin/sh' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/sh'
patch-shebang: ./depcomp: changing `/bin/sh' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/sh'
patch-shebang: ./install-sh: changing `/bin/sh' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/sh'
patch-shebang: ./missing: changing `/bin/sh' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/sh'
patch-shebang: ./scripts/get_common_variants.sh: changing `/bin/bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash'
patch-shebang: ./scripts/primer_bam_to_bed.sh: changing `/bin/bash' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash'
patch-shebang: ./test-driver: changing `/bin/sh' to `/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/sh'
phase `patch-source-shebangs' succeeded after 1.3 seconds
starting phase `configure'
source directory: "/tmp/guix-build-ivar-1.4.2.drv-0/source" (relative from build: ".")
build directory: "/tmp/guix-build-ivar-1.4.2.drv-0/source"
configure flags: ("CC_FOR_BUILD=gcc" "CONFIG_SHELL=/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash" "SHELL=/gnu/store/3jhfhxdf6v5ms10x5zmnl166dh3yhbr1-bash-minimal-5.1.16/bin/bash" "--prefix=/gnu/store/4j3w55czkj8p7id21yvlfadbf6qyfxv4-ivar-1.4.2" "--enable-fast-install" "--build=x86_64-unknown-linux-gnu" "--host=arm-linux-gnueabihf")
configure: WARNING: unrecognized options: --enable-fast-install
checking for a BSD-compatible install... /gnu/store/7h0mnlwalw23j9jmvz5n1i5mqkgb4d06-coreutils-9.1/bin/install -c
checking whether build environment is sane... yes
checking for arm-linux-gnueabihf-strip... arm-linux-gnueabihf-strip
checking for a thread-safe mkdir -p... /gnu/store/7h0mnlwalw23j9jmvz5n1i5mqkgb4d06-coreutils-9.1/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... no
checking whether make supports nested variables... yes
checking for gawk... (cached) gawk
checking for arm-linux-gnueabihf-g++... arm-linux-gnueabihf-g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... yes
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether arm-linux-gnueabihf-g++ accepts -g... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of arm-linux-gnueabihf-g++... gcc3
checking for arm-linux-gnueabihf-gcc... arm-linux-gnueabihf-gcc
checking whether we are using the GNU C compiler... yes
checking whether arm-linux-gnueabihf-gcc accepts -g... yes
checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed
checking whether arm-linux-gnueabihf-gcc understands -c and -o together... yes
checking dependency style of arm-linux-gnueabihf-gcc... gcc3
checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E
checking for main in -lhts... no
checking for main in -lpthread... no
checking for main in -lz... no
checking for grep that handles long lines and -e... /gnu/store/7k8b93779dqpwcg2qjdvnf4nl43jv7hf-grep-3.11/bin/grep
checking for egrep... /gnu/store/7k8b93779dqpwcg2qjdvnf4nl43jv7hf-grep-3.11/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for int16_t... yes
checking for int32_t... yes
checking for int8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint8_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... no
checking for memmove... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --enable-fast-install
phase `configure' succeeded after 8.8 seconds
starting phase `patch-generated-file-shebangs'
phase `patch-generated-file-shebangs' succeeded after 0.0 seconds
starting phase `build'
make  all-recursive
make[1]: Entering directory '/tmp/guix-build-ivar-1.4.2.drv-0/source'
Making all in src
make[2]: Entering directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/src'
depbase=`echo ivar.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT ivar.o -MD -MP -MF $depbase.Tpo -c -o ivar.o ivar.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo call_consensus_pileup.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT call_consensus_pileup.o -MD -MP -MF $depbase.Tpo -c -o call_consensus_pileup.o call_consensus_pileup.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo alignment.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT alignment.o -MD -MP -MF $depbase.Tpo -c -o alignment.o alignment.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo suffix_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT suffix_tree.o -MD -MP -MF $depbase.Tpo -c -o suffix_tree.o suffix_tree.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo trim_primer_quality.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT trim_primer_quality.o -MD -MP -MF $depbase.Tpo -c -o trim_primer_quality.o trim_primer_quality.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo remove_reads_from_amplicon.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT remove_reads_from_amplicon.o -MD -MP -MF $depbase.Tpo -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo call_variants.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT call_variants.o -MD -MP -MF $depbase.Tpo -c -o call_variants.o call_variants.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo primer_bed.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
arm-linux-gnueabihf-g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT primer_bed.o -MD -MP -MF $depbase.Tpo -c -o primer_bed.o primer_bed.cpp &&\
mv -f $depbase.Tpo $depbase.Po
Using built-in specs.
Using built-in specs.
COLLECT_GCC=arm-linux-gnueabihf-g++
COLLECT_GCC=arm-linux-gnueabihf-g++
Target: arm-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
Target: arm-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 14.2.0 (GCC) 
gcc version 14.2.0 (GCC) 
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'alignment.o' '-MD' '-MP' '-MF' '.deps/alignment.Tpo' '-c' '-o' 'alignment.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/cc1plus -quiet -v -I . -I .. -MD alignment.d -MF .deps/alignment.Tpo -MP -MT alignment.o -D_GNU_SOURCE -D HAVE_CONFIG_H alignment.cpp -quiet -dumpbase alignment.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mfpu=neon -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+simd -march=armv7-a+simd -gUsing built-in specs.
 -Wall -Wextra -std=c++11 -version -o /tmp/guix-build-ivar-1.4.2.drv-0/ccqhEj1n.s
COLLECT_GCC=arm-linux-gnueabihf-g++
Target: arm-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 14.2.0 (GCC) 
Using built-in specs.
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'call_consensus_pileup.o' '-MD' '-MP' '-MF' '.deps/call_consensus_pileup.Tpo' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/cc1plus -quietUsing built-in specs.
 -v -I . -I .. -MD call_consensus_pileup.d -MF .deps/call_consensus_pileup.Tpo -MP -MT call_consensus_pileup.o -D_GNU_SOURCE -D HAVE_CONFIG_H call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mfpu=neon -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+simd -march=armv7-a+simd -g -Wall -Wextra -std=c++11 -version -o /tmp/guix-build-ivar-1.4.2.drv-0/ccocMFWj.s
COLLECT_GCC=arm-linux-gnueabihf-g++
Target: arm-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 14.2.0 (GCC) 
COLLECT_GCC=arm-linux-gnueabihf-g++
Target: arm-linux-gnueabihf
Configured with: 
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'ivar.o' '-MD' '-MP' Thread model: posix
'-MF' '.deps/ivar.Tpo' '-c' '-o' 'ivar.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/cc1plusSupported LTO compression algorithms: zlib -quiet -v -I . -I .. -MD ivar.d -MF .deps/ivar.Tpo -MP -MT ivar.o -D_GNU_SOURCE -D HAVE_CONFIG_H ivar.cpp -quiet -dumpbase ivar.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mfpu=neon -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+simd -march=armv7-a+simd -g -Wall -Wextra -std=c++11 -version -o /tmp/guix-build-ivar-1.4.2.drv-0/ccz40tnZ.s

gcc version 14.2.0 (GCC) 
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'trim_primer_quality.o' '-MD' '-MP' '-MF' '.deps/trim_primer_quality.Tpo' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/cc1plus -quiet -v -I .COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'suffix_tree.o' '-MD' -I '-MP' '-MF' '.deps/suffix_tree.Tpo' '-c' '-o' 'suffix_tree.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect= ..gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 -MD trim_primer_quality.d -MF .deps/trim_primer_quality.Tpo -MP -MT trim_primer_quality.o -D_GNU_SOURCE -D HAVE_CONFIG_H /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/cc1plus trim_primer_quality.cpp -quiet -quiet -v -dumpbase -I trim_primer_quality.cpp . -dumpbase-ext -I .cpp .. -mfloat-abi=hard -MD -mfpu=neon suffix_tree.d -mtls-dialect=gnu -MF -mthumb .deps/suffix_tree.Tpo -mlibarch=armv7-a+simd -MP -march=armv7-a+simd -MT -g suffix_tree.o -Wall -D_GNU_SOURCE -Wextra -D -std=c++11 HAVE_CONFIG_H -version suffix_tree.cpp -o -quiet /tmp/guix-build-ivar-1.4.2.drv-0/ccrT4Ifj.s -dumpbase
 suffix_tree.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mfpu=neon -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+simd -march=armv7-a+simd -g -Wall -Wextra -std=c++11 -version -o /tmp/guix-build-ivar-1.4.2.drv-0/ccvHToPI.s
Using built-in specs.
Using built-in specs.
COLLECT_GCC=arm-linux-gnueabihf-g++
Target: arm-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 14.2.0 (GCC) 
COLLECT_GCC=arm-linux-gnueabihf-g++
Target: arm-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 14.2.0 (GCC) 
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'remove_reads_from_amplicon.o' '-MD' '-MP' '-MF' '.deps/remove_reads_from_amplicon.Tpo' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/cc1plus -quiet -v -I . -ICOLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'primer_bed.o' '-MD' '-MP' '-MF' '.deps/primer_bed.Tpo' '-c' '-o' 'primer_bed.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/cc1plus .. -MD remove_reads_from_amplicon.d -MF .deps/remove_reads_from_amplicon.Tpo -MP -MT remove_reads_from_amplicon.o -D_GNU_SOURCE -D HAVE_CONFIG_H remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mfpu=neon -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+simd -march=armv7-a+simd -g -Wall -Wextra -std=c++11 -version -o /tmp/guix-build-ivar-1.4.2.drv-0/ccEh0Fyb.s
 -quiet -v -I . -I .. -MD primer_bed.d -MF .deps/primer_bed.Tpo -MP -MT primer_bed.o -D_GNU_SOURCE -D HAVE_CONFIG_H primer_bed.cpp -quiet -dumpbase primer_bed.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mfpu=neon -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+simd -march=armv7-a+simd -g -Wall -Wextra -std=c++11 -version -o /tmp/guix-build-ivar-1.4.2.drv-0/ccohe4Ln.s
Using built-in specs.
COLLECT_GCC=arm-linux-gnueabihf-g++
Target: arm-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 14.2.0 (GCC) 
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'call_variants.o' '-MD' '-MP' '-MF' '.deps/call_variants.Tpo' '-c' '-o' 'call_variants.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/cc1plus -quiet -v -I . -I .. -MD call_variants.d -MF .deps/call_variants.Tpo -MP -MT call_variants.o -D_GNU_SOURCE -D HAVE_CONFIG_H call_variants.cpp -quiet -dumpbase call_variants.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mfpu=neon -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+simd -march=armv7-a+simd -g -Wall -Wextra -std=c++11 -version -o /tmp/guix-build-ivar-1.4.2.drv-0/ccE3S6R0.s
GNU C++11 (GCC) version 14.2.0 (arm-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.24-GMP

GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
GNU C++11 (GCC) version 14.2.0 (arm-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GNU C++11 (GCC) version 14.2.0 (arm-linux-gnueabihf)
	compiled by GNU C version 11.4.0, ignoring nonexistent directory "/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../../../../arm-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include"
GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.24-GMP

#include "..." search starts here:
GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.24-GMP

#include <...> search starts here:
 .
 ..
 /gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/include
 /gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/include
 /gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include
 /gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include
 /gnu/store/q97gxljfvsmmd29w6i2caw8033hi42li-linux-libre-headers-cross-arm-linux-gnueabihf-5.15.49/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/arm-linux-gnueabihf
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/backward
 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include
 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/includeGGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
-fixed
End of search list.
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++"
ignoring duplicate directory "/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../../../../arm-linux-gnueabihf/include"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring duplicate directory "/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
ignoring nonexistent directory "/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm .
-linux-gnueabihf/14.2.0/../../../../../../../arm-linux-gnueabihf/include"
 ..
 /gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/include
 /gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/include
 /gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/include
ignoring duplicate directory "/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include"
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include
 /gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include
 /gnu/store/q97gxljfvsmmd29w6i2caw8033hi42li-linux-libre-headers-cross-arm-linux-gnueabihf-5.15.49/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/arm-linux-gnueabihf
#include "..." search starts here:
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/backward
#include <...> search starts here:
 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include .

 ..
 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include /gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/include
-fixed
 /gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/include
End of search list.
 /gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include
 /gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include
 /gnu/store/q97gxljfvsmmd29w6i2caw8033hi42li-linux-libre-headers-cross-arm-linux-gnueabihf-5.15.49/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/arm-linux-gnueabihf
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/backward
 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include
 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include-fixed
End of search list.
GNU C++11 (GCC) version 14.2.0 (arm-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.24-GMP

GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../../../../arm-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/include
 /gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/include
 /gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include
 /gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include
 /gnu/store/q97gxljfvsmmd29w6i2caw8033hi42li-linux-libre-headers-cross-arm-linux-gnueabihf-5.15.49/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/arm-linux-gnueabihf
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/backward
 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include
 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include-fixed
End of search list.
GNU C++11 (GCC) version 14.2.0 (arm-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GNU C++11 (GCC) version 14.2.0 (arm-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.24-GMP

GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.24-GMP

GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++"
ignoring duplicate directory "/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../../../../arm-linux-gnueabihf/include"
ignoring nonexistent directory "/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../../../../arm-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include"
ignoring duplicate directory "/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include"
#include "..." search starts here:
#include "..." search starts here:
#include <...> search starts here:
#include <...> search starts here:
 .
 .
 ..
 ..
 /gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/include
 /gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/include
 /gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/include
 /gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/include
 /gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/include
 /gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include
 /gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include
 /gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include
 /gnu/store/q97gxljfvsmmd29w6i2caw8033hi42li-linux-libre-headers-cross-arm-linux-gnueabihf-5.15.49/include
 /gnu/store/q97gxljfvsmmd29w6i2caw8033hi42li-linux-libre-headers-cross-arm-linux-gnueabihf-5.15.49/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/arm-linux-gnueabihf
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/arm-linux-gnueabihf
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/backward
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/backward
 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include

 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include-fixed
-fixed
End of search list.
End of search list.
GNU C++11 (GCC) version 14.2.0 (arm-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.24-GMP

GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../../../../arm-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/include
 /gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/include
 /gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include
 /gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include
 /gnu/store/q97gxljfvsmmd29w6i2caw8033hi42li-linux-libre-headers-cross-arm-linux-gnueabihf-5.15.49/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/arm-linux-gnueabihf
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/backward
 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include
 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include-fixed
End of search list.
Compiler executable checksum: 7288a54875b90d34207572fa1a57fbfc
Compiler executable checksum: 7288a54875b90d34207572fa1a57fbfc
Compiler executable checksum: 7288a54875b90d34207572fa1a57fbfc
Compiler executable checksum: 7288a548Compiler executable checksum: 75Compiler executable checksum: b9720d72883488a520a54875487572b975fab90d1a0d34573420fb2075fc757272
fafa1a1a5757fbfbfcfc

Compiler executable checksum: 7288a54875b90d34207572fa1a57fbfc
GNU C++11 (GCC) version 14.2.0 (arm-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.24-GMP

GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../../../../arm-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/include
 /gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/include
 /gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include
 /gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/include
 /gnu/store/q97gxljfvsmmd29w6i2caw8033hi42li-linux-libre-headers-cross-arm-linux-gnueabihf-5.15.49/include
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/arm-linux-gnueabihf
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/backward
 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include
 /gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/include-fixed
End of search list.
Compiler executable checksum: 7288a54875b90d34207572fa1a57fbfc
In file included from primer_bed.cpp:1:
primer_bed.h:13:3: error: ‘uint32_t’ does not name a type
   13 |   uint32_t start;  // 0 based
      |   ^~~~~~~~
primer_bed.h:6:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
    5 | #include <vector>
  +++ |+#include <cstdint>
    6 | 
primer_bed.h:14:3: error: ‘uint32_t’ does not name a type
   14 |   uint32_t end;    // 0 based
      |   ^~~~~~~~
primer_bed.h:14:3: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
primer_bed.h:20:3: error: ‘uint32_t’ does not name a type
   20 |   uint32_t read_count = 0;
      |   ^~~~~~~~
primer_bed.h:20:3: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
primer_bed.h:26:3: error: ‘uint32_t’ does not name a type
   26 |   uint32_t get_start() const;
      |   ^~~~~~~~
primer_bed.h:26:3: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
primer_bed.h:27:3: error: ‘uint32_t’ does not name a type
   27 |   uint32_t get_end() const;
      |   ^~~~~~~~
primer_bed.h:27:3: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
primer_bed.h:32:3: error: ‘uint32_t’ does not name a type
   32 |   uint32_t get_read_count() const;
      |   ^~~~~~~~
primer_bed.h:32:3: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
primer_bed.h:33:18: error: ‘uint32_t’ has not been declared
   33 |   void set_start(uint32_t s);
      |                  ^~~~~~~~
primer_bed.h:34:16: error: ‘uint32_t’ has not been declared
   34 |   void set_end(uint32_t e);
      |                ^~~~~~~~
primer_bed.h:41:23: error: ‘uint32_t’ has not been declared
   41 |   void set_read_count(uint32_t rc);
      |                       ^~~~~~~~
primer_bed.h:42:23: error: ‘uint32_t’ has not been declared
   42 |   void add_read_count(uint32_t rc);
      |                       ^~~~~~~~
primer_bed.cpp:9:1: error: ‘uint32_t’ does not name a type
    9 | uint32_t primer::get_start() const { return start; }
      | ^~~~~~~~
primer_bed.cpp:2:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
    1 | #include "primer_bed.h"
  +++ |+#include <cstdint>
    2 | 
primer_bed.cpp:11:1: error: ‘uint32_t’ does not name a type
   11 | uint32_t primer::get_end() const { return end; }
      | ^~~~~~~~
primer_bed.cpp:11:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
primer_bed.cpp: In member function ‘int primer::get_length()’:
primer_bed.cpp:15:35: error: ‘end’ was not declared in this scope; did you mean ‘std::end’?
   15 | int primer::get_length() { return end - start + 1; }
      |                                   ^~~
      |                                   std::end
In file included from /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/string:53,
                 from /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/bits/locale_classes.h:40,
                 from /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/bits/ios_base.h:41,
                 from /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/ios:44,
                 from /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/istream:40,
                 from /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/fstream:40,
                 from primer_bed.h:2:
/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/include/c++/bits/range_access.h:106:5: note: ‘std::end’ declared here
  106 |     end(_Tp (&__arr)[_Nm]) noexcept
      |     ^~~
primer_bed.cpp:15:41: error: ‘start’ was not declared in this scope
   15 | int primer::get_length() { return end - start + 1; }
      |                                         ^~~~~
primer_bed.cpp: At global scope:
primer_bed.cpp:21:1: error: ‘uint32_t’ does not name a type
   21 | uint32_t primer::get_read_count() const { return read_count; }
      | ^~~~~~~~
primer_bed.cpp:21:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
primer_bed.cpp:23:6: error: variable or field ‘set_start’ declared void
   23 | void primer::set_start(uint32_t s) { start = s; }
      |      ^~~~~~
primer_bed.cpp:23:24: error: ‘uint32_t’ was not declared in this scope
   23 | void primer::set_start(uint32_t s) { start = s; }
      |                        ^~~~~~~~
primer_bed.cpp:23:24: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
primer_bed.cpp:25:6: error: variable or field ‘set_end’ declared void
   25 | void primer::set_end(uint32_t e) { end = e; }
      |      ^~~~~~
primer_bed.cpp:25:22: error: ‘uint32_t’ was not declared in this scope
   25 | void primer::set_end(uint32_t e) { end = e; }
      |                      ^~~~~~~~
primer_bed.cpp:25:22: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
primer_bed.cpp:39:6: error: variable or field ‘set_read_count’ declared void
   39 | void primer::set_read_count(uint32_t rc) { read_count = rc; }
      |      ^~~~~~
primer_bed.cpp:39:29: error: ‘uint32_t’ was not declared in this scope
   39 | void primer::set_read_count(uint32_t rc) { read_count = rc; }
      |                             ^~~~~~~~
primer_bed.cpp:39:29: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
primer_bed.cpp:41:6: error: variable or field ‘add_read_count’ declared void
   41 | void primer::add_read_count(uint32_t rc) { read_count += rc; }
      |      ^~~~~~
primer_bed.cpp:41:29: error: ‘uint32_t’ was not declared in this scope
   41 | void primer::add_read_count(uint32_t rc) { read_count += rc; }
      |                             ^~~~~~~~
primer_bed.cpp:41:29: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
primer_bed.cpp: In function ‘std::vector<primer> get_primers(std::vector<primer>, unsigned int)’:
primer_bed.cpp:208:13: error: ‘class primer’ has no member named ‘get_start’; did you mean ‘set_start’?
  208 |     if (it->get_start() <= pos && it->get_end() >= pos) {
      |             ^~~~~~~~~
      |             set_start
primer_bed.cpp:208:39: error: ‘class primer’ has no member named ‘get_end’; did you mean ‘set_end’?
  208 |     if (it->get_start() <= pos && it->get_end() >= pos) {
      |                                       ^~~~~~~
      |                                       set_end
primer_bed.cpp: In lambda function:
primer_bed.cpp:292:47: error: ‘class primer’ has no member named ‘get_start’; did you mean ‘set_start’?
  292 |       [](primer lhs, primer rhs) { return lhs.get_start() < rhs.get_start(); });
      |                                               ^~~~~~~~~
      |                                               set_start
primer_bed.cpp:292:65: error: ‘class primer’ has no member named ‘get_start’; did you mean ‘set_start’?
  292 |       [](primer lhs, primer rhs) { return lhs.get_start() < rhs.get_start(); });
      |                                                                 ^~~~~~~~~
      |                                                                 set_start
primer_bed.cpp: In lambda function:
primer_bed.cpp:299:47: error: ‘class primer’ has no member named ‘get_end’; did you mean ‘set_end’?
  299 |       [](primer lhs, primer rhs) { return lhs.get_end() < rhs.get_end(); });
      |                                               ^~~~~~~
      |                                               set_end
primer_bed.cpp:299:63: error: ‘class primer’ has no member named ‘get_end’; did you mean ‘set_end’?
  299 |       [](primer lhs, primer rhs) { return lhs.get_end() < rhs.get_end(); });
      |                                                               ^~~~~~~
      |                                                               set_end
primer_bed.cpp: In function ‘void print_all_primer_info(std::vector<primer>)’:
primer_bed.cpp:307:42: error: ‘class primer’ has no member named ‘get_start’; did you mean ‘set_start’?
  307 |     std::cerr << "Primer start: " << it->get_start() << std::endl;
      |                                          ^~~~~~~~~
      |                                          set_start
primer_bed.cpp:308:40: error: ‘class primer’ has no member named ‘get_end’; did you mean ‘set_end’?
  308 |     std::cerr << "Primer end: " << it->get_end() << std::endl;
      |                                        ^~~~~~~
      |                                        set_end
primer_bed.cpp: In function ‘void print_primer_info(primer)’:
primer_bed.cpp:316:43: error: ‘class primer’ has no member named ‘get_start’; did you mean ‘set_start’?
  316 |   std::cerr << "Primer start: " << primer.get_start() << std::endl;
      |                                           ^~~~~~~~~
      |                                           set_start
primer_bed.cpp:317:41: error: ‘class primer’ has no member named ‘get_end’; did you mean ‘set_end’?
  317 |   std::cerr << "Primer end: " << primer.get_end() << std::endl;
      |                                         ^~~~~~~
      |                                         set_end
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'alignment.o' '-MD' '-MP' '-MF' '.deps/alignment.Tpo' '-c' '-o' 'alignment.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/as -v -I . -I .. -march=armv7-a+simd -mfloat-abi=hard -mfpu=neon -meabi=5 -o alignment.o /tmp/guix-build-ivar-1.4.2.drv-0/ccqhEj1n.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
make[2]: *** [Makefile:384: primer_bed.o] Error 1
make[2]: *** Waiting for unfinished jobs....
COMPILER_PATH=/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/
CROSS_LIBRARY_PATH=/gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/lib/:/gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/lib/:/gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib/:/gnu/store/a6blq1zlgipcbangszn7p7s3nbhph5c8-glibc-cross-arm-linux-gnueabihf-2.39-static/lib/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../arm-linux-gnueabihf/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'alignment.o' '-MD' '-MP' '-MF' '.deps/alignment.Tpo' '-c' '-o' 'alignment.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'alignment.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'remove_reads_from_amplicon.o' '-MD' '-MP' '-MF' '.deps/remove_reads_from_amplicon.Tpo' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/as -v -I . -I .. -march=armv7-a+simd -mfloat-abi=hard -mfpu=neon -meabi=5 -o remove_reads_from_amplicon.o /tmp/guix-build-ivar-1.4.2.drv-0/ccEh0Fyb.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/
CROSS_LIBRARY_PATH=/gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/lib/:/gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/lib/:/gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib/:/gnu/store/a6blq1zlgipcbangszn7p7s3nbhph5c8-glibc-cross-arm-linux-gnueabihf-2.39-static/lib/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../arm-linux-gnueabihf/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'remove_reads_from_amplicon.o' '-MD' '-MP' '-MF' '.deps/remove_reads_from_amplicon.Tpo' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'remove_reads_from_amplicon.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'suffix_tree.o' '-MD' '-MP' '-MF' '.deps/suffix_tree.Tpo' '-c' '-o' 'suffix_tree.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/as -v -I . -I .. -march=armv7-a+simd -mfloat-abi=hard -mfpu=neon -meabi=5 -o suffix_tree.o /tmp/guix-build-ivar-1.4.2.drv-0/ccvHToPI.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/
CROSS_LIBRARY_PATH=/gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/lib/:/gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/lib/:/gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib/:/gnu/store/a6blq1zlgipcbangszn7p7s3nbhph5c8-glibc-cross-arm-linux-gnueabihf-2.39-static/lib/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../arm-linux-gnueabihf/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'suffix_tree.o' '-MD' '-MP' '-MF' '.deps/suffix_tree.Tpo' '-c' '-o' 'suffix_tree.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'suffix_tree.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'trim_primer_quality.o' '-MD' '-MP' '-MF' '.deps/trim_primer_quality.Tpo' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/as -v -I . -I .. -march=armv7-a+simd -mfloat-abi=hard -mfpu=neon -meabi=5 -o trim_primer_quality.o /tmp/guix-build-ivar-1.4.2.drv-0/ccrT4Ifj.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/
CROSS_LIBRARY_PATH=/gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/lib/:/gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/lib/:/gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib/:/gnu/store/a6blq1zlgipcbangszn7p7s3nbhph5c8-glibc-cross-arm-linux-gnueabihf-2.39-static/lib/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../arm-linux-gnueabihf/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'trim_primer_quality.o' '-MD' '-MP' '-MF' '.deps/trim_primer_quality.Tpo' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'trim_primer_quality.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'call_consensus_pileup.o' '-MD' '-MP' '-MF' '.deps/call_consensus_pileup.Tpo' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/as -v -I . -I .. -march=armv7-a+simd -mfloat-abi=hard -mfpu=neon -meabi=5 -o call_consensus_pileup.o /tmp/guix-build-ivar-1.4.2.drv-0/ccocMFWj.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/
CROSS_LIBRARY_PATH=/gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/lib/:/gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/lib/:/gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib/:/gnu/store/a6blq1zlgipcbangszn7p7s3nbhph5c8-glibc-cross-arm-linux-gnueabihf-2.39-static/lib/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../arm-linux-gnueabihf/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'call_consensus_pileup.o' '-MD' '-MP' '-MF' '.deps/call_consensus_pileup.Tpo' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'call_consensus_pileup.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'call_variants.o' '-MD' '-MP' '-MF' '.deps/call_variants.Tpo' '-c' '-o' 'call_variants.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/as -v -I . -I .. -march=armv7-a+simd -mfloat-abi=hard -mfpu=neon -meabi=5 -o call_variants.o /tmp/guix-build-ivar-1.4.2.drv-0/ccE3S6R0.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/
CROSS_LIBRARY_PATH=/gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/lib/:/gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/lib/:/gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib/:/gnu/store/a6blq1zlgipcbangszn7p7s3nbhph5c8-glibc-cross-arm-linux-gnueabihf-2.39-static/lib/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../arm-linux-gnueabihf/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'call_variants.o' '-MD' '-MP' '-MF' '.deps/call_variants.Tpo' '-c' '-o' 'call_variants.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'call_variants.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'ivar.o' '-MD' '-MP' '-MF' '.deps/ivar.Tpo' '-c' '-o' 'ivar.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/as -v -I . -I .. -march=armv7-a+simd -mfloat-abi=hard -mfpu=neon -meabi=5 -o ivar.o /tmp/guix-build-ivar-1.4.2.drv-0/ccz40tnZ.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/87q3p0k9kary1vzpci4pmg99scm6zvwk-gcc-cross-arm-linux-gnueabihf-14.2.0/libexec/gcc/arm-linux-gnueabihf/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/
CROSS_LIBRARY_PATH=/gnu/store/iqf68qlpsn4agrrx095fbn5mw6k8zhl4-htslib-1.19/lib/:/gnu/store/xcwqplswjbmvb113hbns7ysr4kp1jg87-zlib-1.3/lib/:/gnu/store/1qc1hd6afsqh05prnrx429cghafdjig8-htscodecs-1.6.0/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib/:/gnu/store/a6blq1zlgipcbangszn7p7s3nbhph5c8-glibc-cross-arm-linux-gnueabihf-2.39-static/lib/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/:/gnu/store/n352gyvqpjh84xwbbdyh98gh0lckj0la-gcc-cross-arm-linux-gnueabihf-14.2.0-lib/lib/gcc/arm-linux-gnueabihf/14.2.0/../../../../arm-linux-gnueabihf/lib/:/gnu/store/kdk5c2va0v32x9xbsziwpdlh29x63vb7-glibc-cross-arm-linux-gnueabihf-2.39/lib
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'ivar.o' '-MD' '-MP' '-MF' '.deps/ivar.Tpo' '-c' '-o' 'ivar.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'ivar.'
make[2]: Leaving directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/src'
make[1]: *** [Makefile:361: all-recursive] Error 1
make[1]: Leaving directory '/tmp/guix-build-ivar-1.4.2.drv-0/source'
make: *** [Makefile:302: all] Error 2
error: in phase 'build': uncaught exception:
%exception #<&invoke-error program: "make" arguments: ("-j" "8") exit-status: 2 term-signal: #f stop-signal: #f> 
phase `build' failed after 1.8 seconds
command "make" "-j" "8" failed with status 2
build process 10 exited with status 256