starting phase `separate-from-pid1'
build process now running as PID 18
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/wp5sxc04bns6chy3ziykpr84ddp4rhbi-autoconf-2.69/bin:/gnu/store/pib9pv9587yn46pl31f0jwx06j9gjaql-automake-1.16.5/bin:/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/bin:/gnu/store/6a8nzjdrzqhi6ai3mz34fx4p938rihsy-tar-1.34/bin:/gnu/store/nz34ydn14l1r1mwqr0nwv207qn179db7-gzip-1.13/bin:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/bin:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/bin:/gnu/store/f8i87amlqmpxvca9damyf3925l7k67rb-diffutils-3.10/bin:/gnu/store/1wda77kxj74bz7icwj7zaiwamnlf8qdh-patch-2.7.6/bin:/gnu/store/kkr4i9hx0fibrdp4haqxli3qwd0wqsxp-findutils-4.9.0/bin:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/bin:/gnu/store/k1zvdjzr4zg47mh5rm41d7lpkg5ydy5y-zstd-1.5.2/bin:/gnu/store/wx7cvwj9vi4wsc1a06vq1pkgy3k1flpw-sed-4.8/bin:/gnu/store/bhz72a51ixagcjbmmswb98bnkbb6l327-grep-3.11/bin:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/bin:/gnu/store/y6w4s09jcvcc0as357d2vcm60c68agph-coreutils-9.1/bin:/gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/bin:/gnu/store/h1ap2ldl46a57fa3978w6pdbrq3zhzks-bash-minimal-5.1.16/bin:/gnu/store/fy0b225yfj0935gklyavxw81aak0zzc4-ld-wrapper-0/bin:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/bin:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/bin:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/bin:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/sbin'
environment variable `ACLOCAL_PATH' set to `/gnu/store/pib9pv9587yn46pl31f0jwx06j9gjaql-automake-1.16.5/share/aclocal'
environment variable `BASH_LOADABLES_PATH' unset
environment variable `C_INCLUDE_PATH' set to `/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include:/gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include:/gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include'
environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include:/gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include:/gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include'
environment variable `OBJC_INCLUDE_PATH' set to `/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include:/gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include:/gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include'
environment variable `OBJCPLUS_INCLUDE_PATH' set to `/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include:/gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include:/gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include'
environment variable `LIBRARY_PATH' set to `/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib'
environment variable `GUIX_LOCPATH' set to `/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-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/Doxyfile' -> `./Doxyfile'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/LICENSE' -> `./LICENSE'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/config.h.in' -> `./config.h.in'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/ChangeLog' -> `./ChangeLog'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/autogen.sh' -> `./autogen.sh'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/Makefile.am' -> `./Makefile.am'
`/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/README' -> `./README'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/AUTHORS' -> `./AUTHORS'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/NEWS' -> `./NEWS'
`/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/call_variants.sh' -> `./call_variants.sh'
`/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/workflows/clang-format-check.yml' -> `./.github/workflows/clang-format-check.yml'
`/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/.github/ISSUE_TEMPLATE/feature_request.md' -> `./.github/ISSUE_TEMPLATE/feature_request.md'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/pipeline/pipeline.png' -> `./pipeline/pipeline.png'
`/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/Snakefile' -> `./pipeline/Snakefile'
`/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/vcf_writer.cpp' -> `./src/vcf_writer.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/trim_primer_quality.cpp' -> `./src/trim_primer_quality.cpp'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/src/Makefile.am' -> `./src/Makefile.am'
`/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/parse_gff.h' -> `./src/parse_gff.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/get_common_variants.cpp' -> `./src/get_common_variants.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/primer_bed.h' -> `./src/primer_bed.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/alignment.h' -> `./src/alignment.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/call_variants.cpp' -> `./src/call_variants.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/ref_seq.cpp' -> `./src/ref_seq.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/suffix_tree.h' -> `./src/suffix_tree.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/get_common_variants.h' -> `./src/get_common_variants.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/bam_to_bed.cpp' -> `./src/bam_to_bed.cpp'
`/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/alignment.cpp' -> `./src/alignment.cpp'
`/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/ref_seq.h' -> `./src/ref_seq.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/parse_gff.cpp' -> `./src/parse_gff.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/pipeline_field/dag.svg' -> `./pipeline_field/dag.svg'
`/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/pipeline_field.png' -> `./pipeline_field/pipeline_field.png'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/INSTALLATION.md' -> `./docs/INSTALLATION.md'
`/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/footer.html' -> `./docs/footer.html'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/README.md' -> `./docs/README.md'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/docs/header.html' -> `./docs/header.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/manualpage.3' -> `./docs/man/man3/manualpage.3'
`/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/primer.3' -> `./docs/man/man3/primer.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/allele.3' -> `./docs/man/man3/allele.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/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/maj.3' -> `./docs/man/man3/maj.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/suffix_node.3' -> `./docs/man/man3/suffix_node.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/html/tab_ad.png' -> `./docs/html/tab_ad.png'
`/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/dir_68267d1309a1af8e8297ef4c3efbcdba.html' -> `./docs/html/dir_68267d1309a1af8e8297ef4c3efbcdba.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/classsuffix__node__coll__graph.dot' -> `./docs/html/classsuffix__node__coll__graph.dot'
`/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/_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/get__masked__amplicons_8cpp_source.html' -> `./docs/html/get__masked__amplicons_8cpp_source.html'
`/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/splitbar.png' -> `./docs/html/splitbar.png'
`/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/tabs.css' -> `./docs/html/tabs.css'
`/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/trim__primer__quality_8cpp_source.html' -> `./docs/html/trim__primer__quality_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/alignment_8cpp_source.html' -> `./docs/html/alignment_8cpp_source.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/tab_h.png' -> `./docs/html/tab_h.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/tab_b.png' -> `./docs/html/tab_b.png'
`/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/test_8cpp_source.html' -> `./docs/html/test_8cpp_source.html'
`/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/index.html' -> `./docs/html/index.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/classsuffix__node__coll__graph.md5' -> `./docs/html/classsuffix__node__coll__graph.md5'
`/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/tab_s.png' -> `./docs/html/tab_s.png'
`/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/structmaj-members.html' -> `./docs/html/structmaj-members.html'
`/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/nav_h.png' -> `./docs/html/nav_h.png'
`/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/trim__primer__quality_8h_source.html' -> `./docs/html/trim__primer__quality_8h_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/tab_bd.png' -> `./docs/html/tab_bd.png'
`/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/alignment_8h_source.html' -> `./docs/html/alignment_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/bc_s.png' -> `./docs/html/bc_s.png'
`/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/structmaj.html' -> `./docs/html/structmaj.html'
`/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/classes.html' -> `./docs/html/classes.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/folderclosed.png' -> `./docs/html/folderclosed.png'
`/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/suffix__tree_8h_source.html' -> `./docs/html/suffix__tree_8h_source.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/get__masked__amplicons_8h_source.html' -> `./docs/html/get__masked__amplicons_8h_source.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/call__variants_8h_source.html' -> `./docs/html/call__variants_8h_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/doxygen.png' -> `./docs/html/doxygen.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/graph_legend.md5' -> `./docs/html/graph_legend.md5'
`/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/call__consensus__pileup_8cpp_source.html' -> `./docs/html/call__consensus__pileup_8cpp_source.html'
`/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/installpage.html' -> `./docs/html/installpage.html'
`/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/files.html' -> `./docs/html/files.html'
`/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/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/bc_sd.png' -> `./docs/html/bc_sd.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/ivar_8cpp__incl.dot' -> `./docs/html/ivar_8cpp__incl.dot'
`/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/allele__functions_8cpp_source.html' -> `./docs/html/allele__functions_8cpp_source.html'
`/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/cookbookpage.html' -> `./docs/html/cookbookpage.html'
`/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/menu.js' -> `./docs/html/menu.js'
`/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/customdoxygen.css' -> `./docs/html/customdoxygen.css'
`/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/nav_f.png' -> `./docs/html/nav_f.png'
`/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/call__consensus__pileup_8h_source.html' -> `./docs/html/call__consensus__pileup_8h_source.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/closed.png' -> `./docs/html/closed.png'
`/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/annotated.html' -> `./docs/html/annotated.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/dir_49e56c817e5e54854c35e136979f97ca.html' -> `./docs/html/dir_49e56c817e5e54854c35e136979f97ca.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/menudata.js' -> `./docs/html/menudata.js'
`/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/primer__bed_8h_source.html' -> `./docs/html/primer__bed_8h_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/globals_func.html' -> `./docs/html/globals_func.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/call__variants_8cpp_source.html' -> `./docs/html/call__variants_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/get__common__consensus_8cpp_source.html' -> `./docs/html/get__common__consensus_8cpp_source.html'
`/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/ivar_8cpp__incl.md5' -> `./docs/html/ivar_8cpp__incl.md5'
`/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/search/all_1.js' -> `./docs/html/search/all_1.js'
`/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/classes_5.html' -> `./docs/html/search/classes_5.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_3.js' -> `./docs/html/search/all_3.js'
`/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/nomatches.html' -> `./docs/html/search/nomatches.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/mag_sel.svg' -> `./docs/html/search/mag_sel.svg'
`/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/mag.svg' -> `./docs/html/search/mag.svg'
`/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/pages_2.js' -> `./docs/html/search/pages_2.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/pages_1.html' -> `./docs/html/search/pages_1.html'
`/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/html/search/search_r.png' -> `./docs/html/search/search_r.png'
`/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_4.js' -> `./docs/html/search/classes_4.js'
`/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/functions_0.js' -> `./docs/html/search/functions_0.js'
`/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/classes_1.html' -> `./docs/html/search/classes_1.html'
`/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/close.svg' -> `./docs/html/search/close.svg'
`/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_4.html' -> `./docs/html/search/all_4.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/classes_5.js' -> `./docs/html/search/classes_5.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/all_6.js' -> `./docs/html/search/all_6.js'
`/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/all_2.html' -> `./docs/html/search/all_2.html'
`/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/classes_2.js' -> `./docs/html/search/classes_2.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/pages_0.js' -> `./docs/html/search/pages_0.js'
`/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/all_7.html' -> `./docs/html/search/all_7.html'
`/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/classes_0.html' -> `./docs/html/search/classes_0.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/all_0.html' -> `./docs/html/search/all_0.html'
`/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/pages_3.html' -> `./docs/html/search/pages_3.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_3.js' -> `./docs/html/search/pages_3.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/all_5.html' -> `./docs/html/search/all_5.html'
`/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/all_0.js' -> `./docs/html/search/all_0.js'
`/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_7.js' -> `./docs/html/search/all_7.js'
`/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/latex/structargs__t.tex' -> `./docs/latex/structargs__t.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/cookbookpage.tex' -> `./docs/latex/cookbookpage.tex'
`/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/structallele.tex' -> `./docs/latex/structallele.tex'
`/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/tabu_doxygen.sty' -> `./docs/latex/tabu_doxygen.sty'
`/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__coll__graph.md5' -> `./docs/latex/classsuffix__node__coll__graph.md5'
`/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/classprimer.tex' -> `./docs/latex/classprimer.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/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/longtable_doxygen.sty' -> `./docs/latex/longtable_doxygen.sty'
`/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/structmaj.tex' -> `./docs/latex/structmaj.tex'
`/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/ivar_8cpp.tex' -> `./docs/latex/ivar_8cpp.tex'
`/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/classsuffix__node.tex.tmp' -> `./docs/latex/classsuffix__node.tex.tmp'
`/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/index.tex' -> `./docs/latex/index.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/files.tex' -> `./docs/latex/files.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/tests/test_primer_trim.cpp' -> `./tests/test_primer_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/test_trim.cpp' -> `./tests/test_trim.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_consensus_seq_id.cpp' -> `./tests/test_consensus_seq_id.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_common_variants.cpp' -> `./tests/test_common_variants.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_unpaired_trim.cpp' -> `./tests/test_unpaired_trim.cpp'
`/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_interval_tree.cpp' -> `./tests/test_interval_tree.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/check_quality_trim.cpp' -> `./tests/check_quality_trim.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_allele_depth.cpp' -> `./tests/test_allele_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_call_consensus_from_plup.cpp' -> `./tests/test_call_consensus_from_plup.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_removereads.cpp' -> `./tests/test_removereads.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_primer_trim_pairs.cpp' -> `./tests/test_primer_trim_pairs.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/pipeline_consensus/config.json' -> `./pipeline_consensus/config.json'
`/gnu/store/8c9bxlsg6kcawvf7v0bghv14aw1j0n7b-ivar-1.4.2-checkout/pipeline_consensus/Snakefile' -> `./pipeline_consensus/Snakefile'
`/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/data/test.sorted.bam.bai' -> `./data/test.sorted.bam.bai'
`/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.indel.mpileup' -> `./data/test.indel.mpileup'
`/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.filtered.tsv' -> `./data/test.filtered.tsv'
`/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.bai' -> `./data/test.sim.merged.sorted.bam.bai'
`/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.gap.sorted.bam.bai' -> `./data/test.gap.sorted.bam.bai'
`/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.trimmed.sorted.bam' -> `./data/test.trimmed.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/pair_information.tsv' -> `./data/pair_information.tsv'
`/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/test.gap.sorted.bam' -> `./data/test.gap.sorted.bam'
`/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.gff' -> `./data/test.gff'
`/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.bed' -> `./data/test.bed'
`/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_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/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/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/scripts/Makefile.am' -> `./scripts/Makefile.am'
`/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'
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/h1ap2ldl46a57fa3978w6pdbrq3zhzks-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 4.9 seconds
starting phase `patch-usr-bin-file'
phase `patch-usr-bin-file' succeeded after 0.1 seconds
starting phase `patch-source-shebangs'
patch-shebang: ./call_variants.sh: changing `/bin/bash' to `/gnu/store/h1ap2ldl46a57fa3978w6pdbrq3zhzks-bash-minimal-5.1.16/bin/bash'
patch-shebang: ./compile: changing `/bin/sh' to `/gnu/store/h1ap2ldl46a57fa3978w6pdbrq3zhzks-bash-minimal-5.1.16/bin/sh'
patch-shebang: ./configure: changing `/bin/sh' to `/gnu/store/h1ap2ldl46a57fa3978w6pdbrq3zhzks-bash-minimal-5.1.16/bin/sh'
patch-shebang: ./depcomp: changing `/bin/sh' to `/gnu/store/h1ap2ldl46a57fa3978w6pdbrq3zhzks-bash-minimal-5.1.16/bin/sh'
patch-shebang: ./install-sh: changing `/bin/sh' to `/gnu/store/h1ap2ldl46a57fa3978w6pdbrq3zhzks-bash-minimal-5.1.16/bin/sh'
patch-shebang: ./missing: changing `/bin/sh' to `/gnu/store/h1ap2ldl46a57fa3978w6pdbrq3zhzks-bash-minimal-5.1.16/bin/sh'
patch-shebang: ./scripts/get_common_variants.sh: changing `/bin/bash' to `/gnu/store/h1ap2ldl46a57fa3978w6pdbrq3zhzks-bash-minimal-5.1.16/bin/bash'
patch-shebang: ./scripts/primer_bam_to_bed.sh: changing `/bin/bash' to `/gnu/store/h1ap2ldl46a57fa3978w6pdbrq3zhzks-bash-minimal-5.1.16/bin/bash'
patch-shebang: ./test-driver: changing `/bin/sh' to `/gnu/store/h1ap2ldl46a57fa3978w6pdbrq3zhzks-bash-minimal-5.1.16/bin/sh'
phase `patch-source-shebangs' succeeded after 0.1 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: ("CONFIG_SHELL=/gnu/store/h1ap2ldl46a57fa3978w6pdbrq3zhzks-bash-minimal-5.1.16/bin/bash" "SHELL=/gnu/store/h1ap2ldl46a57fa3978w6pdbrq3zhzks-bash-minimal-5.1.16/bin/bash" "--prefix=/gnu/store/b74vdvgy5wb4jpzryv67nm7a9gfdi9fz-ivar-1.4.2" "--enable-fast-install" "--build=arm-unknown-linux-gnueabihf")
configure: WARNING: unrecognized options: --enable-fast-install
checking for a BSD-compatible install... /gnu/store/y6w4s09jcvcc0as357d2vcm60c68agph-coreutils-9.1/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /gnu/store/y6w4s09jcvcc0as357d2vcm60c68agph-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 g++... 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... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... 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/bhz72a51ixagcjbmmswb98bnkbb6l327-grep-3.11/bin/grep
checking for egrep... /gnu/store/bhz72a51ixagcjbmmswb98bnkbb6l327-grep-3.11/bin/grep -E
checking for ANSI C header files... no
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 5.7 seconds
starting phase `patch-generated-file-shebangs'
phase `patch-generated-file-shebangs' succeeded after 0.1 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$||'`;\
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$||'`;\
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$||'`;\
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$||'`;\
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$||'`;\
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$||'`;\
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$||'`;\
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 $depbase.Po
Using built-in specs.
COLLECT_GCC=g++
Target: arm-unknown-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.4.0 (GCC) 
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'ivar.o' '-MD' '-MP' '-MF' '.deps/ivar.Tpo' '-c' '-o' 'ivar.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/cc1plus -quiet -v -I . -I .. -MD ivar.d -MF .deps/ivar.Tpo -MP -MT ivar.o -D_GNU_SOURCE -D HAVE_CONFIG_H ivar.cpp -quiet -dumpbase ivar.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mfpu=neon -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+simd -march=armv7-a+simd -g -Wall -Wextra -std=c++11 -version -o /tmp/guix-build-ivar-1.4.2.drv-0/ccIi0OiA.s
depbase=`echo primer_bed.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
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 $depbase.Po
Using built-in specs.
COLLECT_GCC=g++
Target: arm-unknown-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.4.0 (GCC) 
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'call_consensus_pileup.o' '-MD' '-MP' '-MF' '.deps/call_consensus_pileup.Tpo' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/cc1plus -quiet -v -I . -I .. -MD call_consensus_pileup.d -MF .deps/call_consensus_pileup.Tpo -MP -MT call_consensus_pileup.o -D_GNU_SOURCE -D HAVE_CONFIG_H call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mfpu=neon -mtls-dialect=gnu -mthumb -mlibarch=armv7-a+simd -march=armv7-a+simd -g -Wall -Wextra -std=c++11 -version -o /tmp/guix-build-ivar-1.4.2.drv-0/ccHEVfMX.s
depbase=`echo allele_functions.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT allele_functions.o -MD -MP -MF $depbase.Tpo -c -o allele_functions.o allele_functions.cpp &&\
mv -f $depbase.Tpo $depbase.Po
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
depbase=`echo get_masked_amplicons.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT get_masked_amplicons.o -MD -MP -MF $depbase.Tpo -c -o get_masked_amplicons.o get_masked_amplicons.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo get_common_variants.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT get_common_variants.o -MD -MP -MF $depbase.Tpo -c -o get_common_variants.o get_common_variants.cpp &&\
mv -f $depbase.Tpo $depbase.Po
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Using built-in specs.
Using built-in specs.
COLLECT_GCC=g++
COLLECT_GCC=g++
Target: arm-unknown-linux-gnueabihf
Target: arm-unknown-linux-gnueabihf
Configured with: 
Configured with: 
Thread model: posix
Thread model: posix
Supported LTO compression algorithms: zlibSupported LTO compression algorithms: zlib

gcc version 11.4.0 (GCC) 
gcc version 11.4.0 (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/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/cc1plus -quiet -v -I . -I .. -MD trim_primer_quality.d -MF .deps/trim_primer_quality.Tpo -MP -MT trim_primer_quality.o -D_GNU_SOURCE -D HAVE_CONFIG_H trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.cppCOLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'alignment.o' '-MD' ' -dumpbase-ext-MP' '-MF' '.deps/alignment.Tpo' '-c' '-o' 'alignment.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' ' .cpp-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 -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/cctXpTXC.s
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/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 -g -Wall -Wextra -std=c++11 -version -o /tmp/guix-build-ivar-1.4.2.drv-0/cczoVt5Z.s
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
depbase=`echo parse_gff.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT parse_gff.o -MD -MP -MF $depbase.Tpo -c -o parse_gff.o parse_gff.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ref_seq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT ref_seq.o -MD -MP -MF $depbase.Tpo -c -o ref_seq.o ref_seq.cpp &&\
mv -f $depbase.Tpo $depbase.Po
Using built-in specs.
COLLECT_GCC=g++
Target: arm-unknown-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.4.0 (GCC) 
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/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/cc1plus -quiet -v -I . -I .. -MD suffix_tree.d -MF .deps/suffix_tree.Tpo -MP -MT suffix_tree.o -D_GNU_SOURCE -D HAVE_CONFIG_H suffix_tree.cpp -quiet -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/ccPLIEkh.s
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
Using built-in specs.
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
COLLECT_GCC=g++
Target: arm-unknown-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.4.0 (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/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/cc1plus -quiet -v -I . -I .. -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/cczT8pml.s
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
depbase=`echo interval_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -v -g -std=c++11 -Wall -Wextra  -MT interval_tree.o -MD -MP -MF $depbase.Tpo -c -o interval_tree.o interval_tree.cpp &&\
mv -f $depbase.Tpo $depbase.Po
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Using built-in specs.
ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
COLLECT_GCC=g++
Target: arm-unknown-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.4.0 (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/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/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/ccmqk26t.s
Compiler executable checksum: 45679312f4708c35e2Using built-in specs.
75Using built-in specs.
74f7COLLECT_GCC=g++
Target: arm-unknown-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.4.0 (GCC) 
COLLECT_GCC=g++
Target: arm-unknown-linux-gnueabihf
Configured with: 
Thread model: posix
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'primer_bed.o' '-MD' Supported LTO compression algorithms: zlib'-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'
gcc version 11.4.0 (GCC) 
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/cc1plus -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/ccWRdNge.s
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'allele_functions.o' '-MD' '-MP' '-MF' '.deps/allele_functions.Tpo' '-c' '-o' 'allele_functions.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/cc1plus -quiet -v -I . -I .. -MD allele_functions.d -MF .deps/allele_functions.Tpo -MP -MT allele_functions.o -D_GNU_SOURCE -D HAVE_CONFIG_H allele_functions.cpp -quiet -dumpbase allele_functions.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/cc0rGGSm.s
a34cGNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 45679312f4708c35e27574f7a34c99a8
Compiler executable checksum: 45679312f4708c35e27574f7a34c99a8
99a8
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
Using built-in specs.
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, Compiler executable checksum: GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
45679312f4708c35e27574f7a34c99a8GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072

ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
COLLECT_GCC=g++
Target: arm-unknown-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.4.0 (GCC) 
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'get_masked_amplicons.o' '-MD' '-MP' '-MF' '.deps/get_masked_amplicons.Tpo' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/cc1plus -quiet -v -I . -I .. -MD get_masked_amplicons.d -MF .deps/get_masked_amplicons.Tpo -MP -MT get_masked_amplicons.o -D_GNU_SOURCE -D HAVE_CONFIG_H get_masked_amplicons.cpp -quiet -dumpbase get_masked_amplicons.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/ccEx4JZf.s
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 45679312f4708c35e27574f7a34c99a8
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Using built-in specs.
COLLECT_GCC=g++
Target: arm-unknown-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.4.0 (GCC) 
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'get_common_variants.o' '-MD' '-MP' '-MF' '.deps/get_common_variants.Tpo' '-c' '-o' 'get_common_variants.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/cc1plus -quiet -v -I . -I .. -MD get_common_variants.d -MF .deps/get_common_variants.Tpo -MP -MT get_common_variants.o -D_GNU_SOURCE -D HAVE_CONFIG_H get_common_variants.cpp -quiet -dumpbase get_common_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/cc7PpQAs.s
Compiler executable checksum: 45679312f4708c35e27574f7a34c99a8
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 45679312f4708c35e27574f7a34c99a8
Using built-in specs.
COLLECT_GCC=g++
Target: arm-unknown-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.4.0 (GCC) 
Using built-in specs.
COLLECT_GCC=g++
Target: arm-unknown-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.4.0 (GCC) 
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'interval_tree.o' '-MD' '-MP' '-MF' '.deps/interval_tree.Tpo' '-c' '-o' 'interval_tree.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/cc1plus -quiet -v -I . -I .. -MD interval_tree.d -MF .deps/interval_tree.Tpo -MP -MT interval_tree.o -D_GNU_SOURCE -D HAVE_CONFIG_H interval_tree.cpp -quiet -dumpbase interval_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/ccHysUc6.s
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'parse_gff.o' '-MD' '-MP' '-MF' '.deps/parse_gff.Tpo' '-c' '-o' 'parse_gff.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/cc1plus -quiet -v -I . -I .. -MD parse_gff.d -MF .deps/parse_gff.Tpo -MP -MT parse_gff.o -D_GNU_SOURCE -D HAVE_CONFIG_H parse_gff.cpp -quiet -dumpbase parse_gff.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/cc1FgeZY.s
Using built-in specs.
COLLECT_GCC=g++
Target: arm-unknown-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.4.0 (GCC) 
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'ref_seq.o' '-MD' '-MP' '-MF' '.deps/ref_seq.Tpo' '-c' '-o' 'ref_seq.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/cc1plus -quiet -v -I . -I .. -MD ref_seq.d -MF .deps/ref_seq.Tpo -MP -MT ref_seq.o -D_GNU_SOURCE -D HAVE_CONFIG_H ref_seq.cpp -quiet -dumpbase ref_seq.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/ccG57RBm.s
Compiler executable checksum: 45679312f4708c35e27574f7a34c99a8
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 45679312f4708c35e27574f7a34c99a8
Compiler executable checksum: 45679312f4708c35e27574f7a34c99a8
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++"
ignoring nonexistent directory "/no-gcc-local-prefix/include"
ignoring nonexistent directory "/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../../../../../arm-unknown-linux-gnueabihf/include"
ignoring duplicate directory "/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/include
 /gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/include
 /gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/include
 /gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/include
 /gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/include
 /gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/include
 /gnu/store/5i82l9hfcz3iqshsb7ys14088lj5n39q-make-4.4.1/include
 /gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include
 /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/include
 /gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/include
 /gnu/store/hs72i1aq263cgprjdindfqsi12ivz49d-linux-libre-headers-5.15.49/include
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/arm-unknown-linux-gnueabihf
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/backward
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include
 /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/include-fixed
End of search list.
GNU C++11 (GCC) version 11.4.0 (arm-unknown-linux-gnueabihf)
	compiled by GNU C version 11.4.0, GMP version 6.0.0, MPFR version 4.2.1, MPC version 1.3.1, isl version none
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 45679312f4708c35e27574f7a34c99a8
Compiler executable checksum: 45679312f4708c35e27574f7a34c99a8
Compiler executable checksum: 45679312f4708c35e27574f7a34c99a8
Compiler executable checksum: 45679312f4708c35e27574f7a34c99a8
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'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o remove_reads_from_amplicon.o /tmp/guix-build-ivar-1.4.2.drv-0/cczT8pml.s
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-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' 'get_masked_amplicons.o' '-MD' '-MP' '-MF' '.deps/get_masked_amplicons.Tpo' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o get_masked_amplicons.o /tmp/guix-build-ivar-1.4.2.drv-0/ccEx4JZf.s
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'get_masked_amplicons.o' '-MD' '-MP' '-MF' '.deps/get_masked_amplicons.Tpo' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'get_masked_amplicons.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'interval_tree.o' '-MD' '-MP' '-MF' '.deps/interval_tree.Tpo' '-c' '-o' 'interval_tree.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o interval_tree.o /tmp/guix-build-ivar-1.4.2.drv-0/ccHysUc6.s
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
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'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o alignment.o /tmp/guix-build-ivar-1.4.2.drv-0/cczoVt5Z.s
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-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.'
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'interval_tree.o' '-MD' '-MP' '-MF' '.deps/interval_tree.Tpo' '-c' '-o' 'interval_tree.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'interval_tree.'
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'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o suffix_tree.o /tmp/guix-build-ivar-1.4.2.drv-0/ccPLIEkh.s
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
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'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o trim_primer_quality.o /tmp/guix-build-ivar-1.4.2.drv-0/cctXpTXC.s
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-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.'
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-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' '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'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o primer_bed.o /tmp/guix-build-ivar-1.4.2.drv-0/ccWRdNge.s
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'allele_functions.o' '-MD' '-MP' '-MF' '.deps/allele_functions.Tpo' '-c' '-o' 'allele_functions.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o allele_functions.o /tmp/guix-build-ivar-1.4.2.drv-0/cc0rGGSm.s
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib
COLLECT_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' '-dumpdir' 'primer_bed.'
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'allele_functions.o' '-MD' '-MP' '-MF' '.deps/allele_functions.Tpo' '-c' '-o' 'allele_functions.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'allele_functions.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'get_common_variants.o' '-MD' '-MP' '-MF' '.deps/get_common_variants.Tpo' '-c' '-o' 'get_common_variants.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o get_common_variants.o /tmp/guix-build-ivar-1.4.2.drv-0/cc7PpQAs.s
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'get_common_variants.o' '-MD' '-MP' '-MF' '.deps/get_common_variants.Tpo' '-c' '-o' 'get_common_variants.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'get_common_variants.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'ref_seq.o' '-MD' '-MP' '-MF' '.deps/ref_seq.Tpo' '-c' '-o' 'ref_seq.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o ref_seq.o /tmp/guix-build-ivar-1.4.2.drv-0/ccG57RBm.s
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'ref_seq.o' '-MD' '-MP' '-MF' '.deps/ref_seq.Tpo' '-c' '-o' 'ref_seq.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'ref_seq.'
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'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o call_consensus_pileup.o /tmp/guix-build-ivar-1.4.2.drv-0/ccHEVfMX.s
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-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'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o call_variants.o /tmp/guix-build-ivar-1.4.2.drv-0/ccmqk26t.s
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-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'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o ivar.o /tmp/guix-build-ivar-1.4.2.drv-0/ccIi0OiA.s
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-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.'
In file included from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/vector:67,
                 from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/regex:51,
                 from parse_gff.h:5,
                 from parse_gff.cpp:1:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_vector.h: In copy constructor ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_vector.h:558:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  558 |           std::__uninitialized_copy_a(__x.begin(), __x.end(),
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
  559 |                                       this->_M_impl._M_start,
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~
  560 |                                       _M_get_Tp_allocator());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
 1198 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/memory:66,
                 from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/regex:45,
                 from parse_gff.h:5,
                 from parse_gff.cpp:1:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  331 |     __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:333:37: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  333 |     { return std::uninitialized_copy(__first, __last, __result); }
      |              ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/vector:72,
                 from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/regex:51,
                 from parse_gff.h:5,
                 from parse_gff.cpp:1:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  121 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/memory:66,
                 from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/regex:45,
                 from parse_gff.h:5,
                 from parse_gff.cpp:1:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  126 |     uninitialized_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:151:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  148 |       return std::__uninitialized_copy<__is_trivial(_ValueType1)
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  149 |                                        && __is_trivial(_ValueType2)
      |                                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  150 |                                        && __assignable>::
      |                                        ~~~~~~~~~~~~~~~~~~
  151 |         __uninit_copy(__first, __last, __result);
      |         ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/vector:72,
                 from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/regex:51,
                 from parse_gff.h:5,
                 from parse_gff.cpp:1:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/memory:66,
                 from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/regex:45,
                 from parse_gff.h:5,
                 from parse_gff.cpp:1:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gff3_feature*; _ForwardIterator = gff3_feature*; _Allocator = std::allocator<gff3_feature>]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:355:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  354 |       return std::__uninitialized_copy_a
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~
  355 |         (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  356 |          _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
   85 |         __uninit_copy(_InputIterator __first, _InputIterator __last,
      |         ^~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  331 |     __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:333:37: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  333 |     { return std::uninitialized_copy(__first, __last, __result); }
      |              ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  126 |     uninitialized_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:151:22: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  148 |       return std::__uninitialized_copy<__is_trivial(_ValueType1)
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  149 |                                        && __is_trivial(_ValueType2)
      |                                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  150 |                                        && __assignable>::
      |                                        ~~~~~~~~~~~~~~~~~~
  151 |         __uninit_copy(__first, __last, __result);
      |         ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
   85 |         __uninit_copy(_InputIterator __first, _InputIterator __last,
      |         ^~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'parse_gff.o' '-MD' '-MP' '-MF' '.deps/parse_gff.Tpo' '-c' '-o' 'parse_gff.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd'
 as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=neon -meabi=5 -o parse_gff.o /tmp/guix-build-ivar-1.4.2.drv-0/cc1FgeZY.s
GNU assembler version 2.41 (arm-unknown-linux-gnueabihf) using BFD version (GNU Binutils) 2.41
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-MT' 'parse_gff.o' '-MD' '-MP' '-MF' '.deps/parse_gff.Tpo' '-c' '-o' 'parse_gff.o' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'parse_gff.'
g++  -v -g -std=c++11 -Wall -Wextra    -o ivar ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/lto-wrapper
Target: arm-unknown-linux-gnueabihf
Configured with: 
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.4.0 (GCC) 
COMPILER_PATH=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/
LIBRARY_PATH=/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib/:/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib/:/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib/:/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib/:/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib/:/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib/:/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib/:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/:/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib/:/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/:/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../../:/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib
COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-o' 'ivar' '-shared-libgcc'  '-mfloat-abi=hard' '-mfpu=neon' '-mtls-dialect=gnu' '-mthumb' '-mlibarch=armv7-a+simd' '-march=armv7-a+simd' '-dumpdir' 'ivar.'
 /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/collect2 -plugin /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/liblto_plugin.so -plugin-opt=/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/libexec/gcc/arm-unknown-linux-gnueabihf/11.4.0/lto-wrapper -plugin-opt=-fresolution=/tmp/guix-build-ivar-1.4.2.drv-0/cctQZzOh.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --eh-frame-hdr -dynamic-linker /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/ld-linux-armhf.so.3 -X -m armelf_linux_eabi -o ivar /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/crt1.o /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/crti.o /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/crtbegin.o -L/gnu/store/b5v4zb7m95f5p9l41dwkf2158mi83c2n-htslib-1.19/lib -L/gnu/store/6hmdzziaq3nvqkc6l71s5pwk6r6qq13x-zlib-1.3/lib -L/gnu/store/hfcal1gx8g4cyvrgfz9pik2y8y5mkvx1-bzip2-1.0.8/lib -L/gnu/store/amzrvv5bgxpzknl3gg4k7dfvcln76q4b-file-5.45/lib -L/gnu/store/alksjnrf32dx2p6w25ifk6pir4rj4hxl-gawk-5.3.0/lib -L/gnu/store/0jhdrfxfsqvss9273d2pvgqxyrmsdf66-xz-5.4.5/lib -L/gnu/store/03i3civrmcfpc0212jdir7hvgz776iv1-binutils-2.41/lib -L/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib -L/gnu/store/diy4fnn93542sdrcgnfqkkwxp50bbmi7-glibc-2.39-static/lib -L/gnu/store/n1x9x5mvf1vhhpgxb0pghhga9rs8j928-htscodecs-1.6.0/lib -L/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0 -L/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/../../.. -L/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -L/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib -rpath=/gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib -rpath=/gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib -lgcc_s -lc -lgcc_s -lgcc /gnu/store/zc0labqnpq44i3ysrknr8rhz8kqs6nrk-gcc-11.4.0-lib/lib/gcc/arm-unknown-linux-gnueabihf/11.4.0/crtend.o /gnu/store/hqpnggqlr3r9l6v2wpc9s98cfpxqksql-glibc-2.39/lib/crtn.o
COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-o' 'ivar' '-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'
Making all in tests
make[2]: Entering directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/tests'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/tests'
make[2]: Entering directory '/tmp/guix-build-ivar-1.4.2.drv-0/source'
make[2]: Leaving directory '/tmp/guix-build-ivar-1.4.2.drv-0/source'
make[1]: Leaving directory '/tmp/guix-build-ivar-1.4.2.drv-0/source'
phase `build' succeeded after 11.3 seconds
starting phase `check'
Making check in src
make[1]: Entering directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/src'
make[1]: Nothing to be done for 'check'.
make[1]: Leaving directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/src'
Making check in tests
make[1]: Entering directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/tests'
make  check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search check_consensus_min_insert_threshold
make[2]: Entering directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/tests'
depbase=`echo test_primer_trim.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_primer_trim.o -MD -MP -MF $depbase.Tpo -c -o test_primer_trim.o test_primer_trim.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ../src/trim_primer_quality.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT ../src/trim_primer_quality.o -MD -MP -MF $depbase.Tpo -c -o ../src/trim_primer_quality.o ../src/trim_primer_quality.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ../src/primer_bed.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT ../src/primer_bed.o -MD -MP -MF $depbase.Tpo -c -o ../src/primer_bed.o ../src/primer_bed.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ../src/interval_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT ../src/interval_tree.o -MD -MP -MF $depbase.Tpo -c -o ../src/interval_tree.o ../src/interval_tree.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_primer_trim test_primer_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o  -lhts -lz -lpthread
depbase=`echo test_trim.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_trim.o -MD -MP -MF $depbase.Tpo -c -o test_trim.o test_trim.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_trim test_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o  -lhts -lz -lpthread
depbase=`echo check_quality_trim.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT check_quality_trim.o -MD -MP -MF $depbase.Tpo -c -o check_quality_trim.o check_quality_trim.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_quality_trim check_quality_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o  -lhts -lz -lpthread
depbase=`echo test_call_consensus_from_plup.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_call_consensus_from_plup.o -MD -MP -MF $depbase.Tpo -c -o test_call_consensus_from_plup.o test_call_consensus_from_plup.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ../src/call_consensus_pileup.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT ../src/call_consensus_pileup.o -MD -MP -MF $depbase.Tpo -c -o ../src/call_consensus_pileup.o ../src/call_consensus_pileup.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ../src/allele_functions.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT ../src/allele_functions.o -MD -MP -MF $depbase.Tpo -c -o ../src/allele_functions.o ../src/allele_functions.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_consensus test_call_consensus_from_plup.o ../src/call_consensus_pileup.o ../src/allele_functions.o  -lhts -lz -lpthread
depbase=`echo test_allele_depth.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_allele_depth.o -MD -MP -MF $depbase.Tpo -c -o test_allele_depth.o test_allele_depth.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_allele_depth test_allele_depth.o ../src/allele_functions.o  -lhts -lz -lpthread
depbase=`echo test_consensus_threshold.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_consensus_threshold.o -MD -MP -MF $depbase.Tpo -c -o test_consensus_threshold.o test_consensus_threshold.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_consensus_threshold test_consensus_threshold.o ../src/call_consensus_pileup.o ../src/allele_functions.o  -lhts -lz -lpthread
depbase=`echo test_consensus_min_depth.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_consensus_min_depth.o -MD -MP -MF $depbase.Tpo -c -o test_consensus_min_depth.o test_consensus_min_depth.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_consensus_min_depth test_consensus_min_depth.o ../src/call_consensus_pileup.o ../src/allele_functions.o  -lhts -lz -lpthread
depbase=`echo test_consensus_seq_id.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_consensus_seq_id.o -MD -MP -MF $depbase.Tpo -c -o test_consensus_seq_id.o test_consensus_seq_id.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_consensus_seq_id test_consensus_seq_id.o ../src/call_consensus_pileup.o ../src/allele_functions.o  -lhts -lz -lpthread
depbase=`echo test_primer_bed.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_primer_bed.o -MD -MP -MF $depbase.Tpo -c -o test_primer_bed.o test_primer_bed.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_primer_bed test_primer_bed.o ../src/primer_bed.o  -lhts -lz -lpthread
depbase=`echo test_getmasked.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_getmasked.o -MD -MP -MF $depbase.Tpo -c -o test_getmasked.o test_getmasked.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ../src/get_masked_amplicons.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT ../src/get_masked_amplicons.o -MD -MP -MF $depbase.Tpo -c -o ../src/get_masked_amplicons.o ../src/get_masked_amplicons.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_getmasked test_getmasked.o ../src/get_masked_amplicons.o ../src/primer_bed.o  -lhts -lz -lpthread
depbase=`echo test_removereads.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_removereads.o -MD -MP -MF $depbase.Tpo -c -o test_removereads.o test_removereads.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ../src/remove_reads_from_amplicon.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT ../src/remove_reads_from_amplicon.o -MD -MP -MF $depbase.Tpo -c -o ../src/remove_reads_from_amplicon.o ../src/remove_reads_from_amplicon.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_removereads test_removereads.o ../src/remove_reads_from_amplicon.o ../src/primer_bed.o ../src/trim_primer_quality.o ../src/interval_tree.o  -lhts -lz -lpthread
depbase=`echo test_variants.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_variants.o -MD -MP -MF $depbase.Tpo -c -o test_variants.o test_variants.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ../src/call_variants.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT ../src/call_variants.o -MD -MP -MF $depbase.Tpo -c -o ../src/call_variants.o ../src/call_variants.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ../src/parse_gff.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT ../src/parse_gff.o -MD -MP -MF $depbase.Tpo -c -o ../src/parse_gff.o ../src/parse_gff.cpp &&\
mv -f $depbase.Tpo $depbase.Po
In file included from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/vector:67,
                 from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/regex:51,
                 from ../src/parse_gff.h:5,
                 from ../src/parse_gff.cpp:1:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_vector.h: In copy constructor ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_vector.h:558:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  558 |           std::__uninitialized_copy_a(__x.begin(), __x.end(),
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
  559 |                                       this->_M_impl._M_start,
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~
  560 |                                       _M_get_Tp_allocator());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
 1198 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/memory:66,
                 from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/regex:45,
                 from ../src/parse_gff.h:5,
                 from ../src/parse_gff.cpp:1:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  331 |     __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:333:37: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  333 |     { return std::uninitialized_copy(__first, __last, __result); }
      |              ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/vector:72,
                 from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/regex:51,
                 from ../src/parse_gff.h:5,
                 from ../src/parse_gff.cpp:1:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  121 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/memory:66,
                 from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/regex:45,
                 from ../src/parse_gff.h:5,
                 from ../src/parse_gff.cpp:1:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  126 |     uninitialized_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:151:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  148 |       return std::__uninitialized_copy<__is_trivial(_ValueType1)
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  149 |                                        && __is_trivial(_ValueType2)
      |                                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  150 |                                        && __assignable>::
      |                                        ~~~~~~~~~~~~~~~~~~
  151 |         __uninit_copy(__first, __last, __result);
      |         ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/vector:72,
                 from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/regex:51,
                 from ../src/parse_gff.h:5,
                 from ../src/parse_gff.cpp:1:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/memory:66,
                 from /gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/regex:45,
                 from ../src/parse_gff.h:5,
                 from ../src/parse_gff.cpp:1:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gff3_feature*; _ForwardIterator = gff3_feature*; _Allocator = std::allocator<gff3_feature>]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:355:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  354 |       return std::__uninitialized_copy_a
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~
  355 |         (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  356 |          _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
   85 |         __uninit_copy(_InputIterator __first, _InputIterator __last,
      |         ^~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  331 |     __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:333:37: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  333 |     { return std::uninitialized_copy(__first, __last, __result); }
      |              ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  126 |     uninitialized_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:151:22: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  148 |       return std::__uninitialized_copy<__is_trivial(_ValueType1)
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  149 |                                        && __is_trivial(_ValueType2)
      |                                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  150 |                                        && __assignable>::
      |                                        ~~~~~~~~~~~~~~~~~~
  151 |         __uninit_copy(__first, __last, __result);
      |         ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’:
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
   85 |         __uninit_copy(_InputIterator __first, _InputIterator __last,
      |         ^~~~~~~~~~~~~
/gnu/store/r4bj333lsb6xan75wsy24y9r4fidb6x0-gcc-11.4.0/include/c++/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
depbase=`echo ../src/ref_seq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT ../src/ref_seq.o -MD -MP -MF $depbase.Tpo -c -o ../src/ref_seq.o ../src/ref_seq.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_variants test_variants.o ../src/call_variants.o ../src/allele_functions.o ../src/parse_gff.o ../src/ref_seq.o  -lhts -lz -lpthread
depbase=`echo test_common_variants.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_common_variants.o -MD -MP -MF $depbase.Tpo -c -o test_common_variants.o test_common_variants.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ../src/get_common_variants.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT ../src/get_common_variants.o -MD -MP -MF $depbase.Tpo -c -o ../src/get_common_variants.o ../src/get_common_variants.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_common_variants test_common_variants.o ../src/get_common_variants.o  -lhts -lz -lpthread
depbase=`echo test_unpaired_trim.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_unpaired_trim.o -MD -MP -MF $depbase.Tpo -c -o test_unpaired_trim.o test_unpaired_trim.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_unpaired_trim test_unpaired_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o  -lhts -lz -lpthread
depbase=`echo test_primer_trim_edge_cases.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_primer_trim_edge_cases.o -MD -MP -MF $depbase.Tpo -c -o test_primer_trim_edge_cases.o test_primer_trim_edge_cases.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_primer_trim_edge_cases test_primer_trim_edge_cases.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o  -lhts -lz -lpthread
depbase=`echo test_isize_trim.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_isize_trim.o -MD -MP -MF $depbase.Tpo -c -o test_isize_trim.o test_isize_trim.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_isize_trim test_isize_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o  -lhts -lz -lpthread
depbase=`echo test_interval_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_interval_tree.o -MD -MP -MF $depbase.Tpo -c -o test_interval_tree.o test_interval_tree.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_interval_tree test_interval_tree.o ../src/primer_bed.o ../src/interval_tree.o  -lhts -lz -lpthread
depbase=`echo test_amplicon_search.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_amplicon_search.o -MD -MP -MF $depbase.Tpo -c -o test_amplicon_search.o test_amplicon_search.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_amplicon_search test_amplicon_search.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o  -lhts -lz -lpthread
depbase=`echo test_consensus_min_insert_threshold.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..     -g -std=c++11 -Wall -Wextra  -MT test_consensus_min_insert_threshold.o -MD -MP -MF $depbase.Tpo -c -o test_consensus_min_insert_threshold.o test_consensus_min_insert_threshold.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -std=c++11 -Wall -Wextra    -o check_consensus_min_insert_threshold test_consensus_min_insert_threshold.o ../src/call_consensus_pileup.o ../src/allele_functions.o  -lhts -lz -lpthread
make[2]: Leaving directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/tests'
make  check-TESTS
make[2]: Entering directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/tests'
make[3]: Entering directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/tests'
PASS: check_primer_trim
PASS: check_trim
PASS: check_quality_trim
PASS: check_consensus
PASS: check_allele_depth
PASS: check_consensus_threshold
PASS: check_consensus_min_depth
PASS: check_consensus_seq_id
PASS: check_primer_bed
PASS: check_getmasked
PASS: check_removereads
PASS: check_variants
PASS: check_common_variants
FAIL: check_unpaired_trim
PASS: check_primer_trim_edge_cases
PASS: check_isize_trim
PASS: check_interval_tree
PASS: check_amplicon_search
PASS: check_consensus_min_insert_threshold
============================================================================
Testsuite summary for ivar 1.4.2
============================================================================
# TOTAL: 19
# PASS:  18
# SKIP:  0
# XFAIL: 0
# FAIL:  1
# XPASS: 0
# ERROR: 0
============================================================================
See tests/test-suite.log
Please report to gkarthik@scripps.edu
============================================================================
make[3]: *** [Makefile:922: test-suite.log] Error 1
make[3]: Leaving directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/tests'
make[2]: *** [Makefile:1030: check-TESTS] Error 2
make[2]: Leaving directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/tests'
make[1]: *** [Makefile:1229: check-am] Error 2
make[1]: Leaving directory '/tmp/guix-build-ivar-1.4.2.drv-0/source/tests'
make: *** [Makefile:361: check-recursive] Error 1

Test suite failed, dumping logs.

--- ./tests/test-suite.log --------------------------------------------------

======================================
   ivar 1.4.2: tests/test-suite.log
======================================

# TOTAL: 19
# PASS:  18
# SKIP:  0
# XFAIL: 0
# FAIL:  1
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

FAIL: check_unpaired_trim
=========================

Found 8 primers in BED file
test_72_280_12:1:0_11:0:0_2

Forward

Reverse

Condensing cigar ... 
test_92_337_8:0:0_10:0:0_21

Forward

Reverse
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 56
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 56 Got 1
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 6
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 3
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 3 Got 99
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 99 Got 2
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 2 Got 65

Condensing cigar ... 
Cigar length didn't match after condense! Expected 19 Got 75
Cigar length didn't match after condense! Expected 56 Got 6
Cigar length didn't match after condense! Expected 1 Got 3
Cigar length didn't match after condense! Expected 6 Got 99
Cigar length didn't match after condense! Expected 3 Got 2
Cigar length didn't match after condense! Expected 99 Got 65
test_147_337_11:1:0_11:1:0_11

Forward

Reverse

Condensing cigar ... 
test_149_298_7:0:0_11:0:0_d

Forward

Reverse

Condensing cigar ... 
test_184_379_11:1:0_8:1:0_26

Forward

Reverse
Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 6 Got 0
Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 2 Got 89
Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 0 Got 4
Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 89 Got 18

Condensing cigar ... 
Cigar length didn't match after condense! Expected 71 Got 160
Cigar flag didn't match! Expected  Got 4
Cigar length didn't match after condense! Expected 2 Got 18
FAIL check_unpaired_trim (exit status: 255)


error: in phase 'check': uncaught exception:
%exception #<&invoke-error program: "make" arguments: ("check") exit-status: 2 term-signal: #f stop-signal: #f> 
phase `check' failed after 56.3 seconds
command "make" "check" failed with status 2
build process 18 exited with status 256