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/8v88l7x1z3w9394fw5z84s12ai7va7q4-pkg-config-0.29.2/bin:/gnu/store/15j6iqyq3xlgr16x607i6cw6d42p0jpx-htslib-1.12/bin:/gnu/store/42s919l9a2zmiih1fnq7za8f51h7zjm8-ncurses-6.2.20210619/bin:/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin:/gnu/store/fmvmsjllz18d2hppxj723qjj788l1his-python-3.9.6/bin:/gnu/store/d8kx7i62bzcd8ladkzwrchcrd60f7bfj-tar-1.34/bin:/gnu/store/6ascvgl36zxymlpldh8x8igv7pkizi5s-gzip-1.10/bin:/gnu/store/dmca74p8b9ik05mrsnvbviflbxrz9qaw-bzip2-1.0.8/bin:/gnu/store/s3577mn5iz2gjgkrava2sm914bgbnkd8-xz-5.2.5/bin:/gnu/store/61b8q6rgdfgd2ffdnyqk6gq2ckrnm007-file-5.39/bin:/gnu/store/2mvffg3isy144py579g5ajwyjh04xbmp-diffutils-3.8/bin:/gnu/store/b34jl32gsdw4rvm78a82m4q50i6p1d7l-patch-2.7.6/bin:/gnu/store/zxaz9cg2b7x6c1z545x861zqllj8vz6h-findutils-4.8.0/bin:/gnu/store/sb75h0di8w5mhpn4wfhk7za6c7x3c97c-gawk-5.1.0/bin:/gnu/store/skrsx5h5h011al604grc3rqa2dhqp2wc-sed-4.8/bin:/gnu/store/vl9pxlycbk5ff0i7jbgyrh0rb2dl07lx-grep-3.6/bin:/gnu/store/firkqph0zalxwjv5g4cdjm4zh3kl3fax-coreutils-8.32/bin:/gnu/store/zjhq95bn5kmlhiqdsvcyy1nhyphxi8yb-make-4.3/bin:/gnu/store/7npwsymmqsb6qcn268cbdnd5558byfy2-bash-minimal-5.1.8/bin:/gnu/store/zhpqig154gpqkgc964wmdnf6b889jfsq-ld-wrapper-0/bin:/gnu/store/h8052068pq3a6rc903982ad2dd5ssxgk-binutils-2.37/bin:/gnu/store/ky9xbrj6slwvgwa4536xbs5lradbqfk5-gcc-10.3.0/bin:/gnu/store/skfhr2f8b7jnnpiarrrcjn6qx0xzfw00-glibc-2.33/bin:/gnu/store/skfhr2f8b7jnnpiarrrcjn6qx0xzfw00-glibc-2.33/sbin' environment variable `PKG_CONFIG_PATH' set to `/gnu/store/15j6iqyq3xlgr16x607i6cw6d42p0jpx-htslib-1.12/lib/pkgconfig:/gnu/store/42s919l9a2zmiih1fnq7za8f51h7zjm8-ncurses-6.2.20210619/lib/pkgconfig:/gnu/store/fmvmsjllz18d2hppxj723qjj788l1his-python-3.9.6/lib/pkgconfig:/gnu/store/rhrxyws0zzq02zpk6y9hhcbiibwag5ls-zlib-1.2.11/lib/pkgconfig:/gnu/store/s3577mn5iz2gjgkrava2sm914bgbnkd8-xz-5.2.5/lib/pkgconfig:/gnu/store/61b8q6rgdfgd2ffdnyqk6gq2ckrnm007-file-5.39/lib/pkgconfig' environment variable `TERMINFO_DIRS' set to `/gnu/store/42s919l9a2zmiih1fnq7za8f51h7zjm8-ncurses-6.2.20210619/share/terminfo' environment variable `PERL5LIB' set to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/lib/perl5/site_perl' environment variable `GUIX_PYTHONPATH' set to `/gnu/store/fmvmsjllz18d2hppxj723qjj788l1his-python-3.9.6/lib/python3.9/site-packages' environment variable `PYTHONTZPATH' unset environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/15j6iqyq3xlgr16x607i6cw6d42p0jpx-htslib-1.12/include:/gnu/store/42s919l9a2zmiih1fnq7za8f51h7zjm8-ncurses-6.2.20210619/include:/gnu/store/fmvmsjllz18d2hppxj723qjj788l1his-python-3.9.6/include:/gnu/store/rhrxyws0zzq02zpk6y9hhcbiibwag5ls-zlib-1.2.11/include:/gnu/store/dmca74p8b9ik05mrsnvbviflbxrz9qaw-bzip2-1.0.8/include:/gnu/store/s3577mn5iz2gjgkrava2sm914bgbnkd8-xz-5.2.5/include:/gnu/store/61b8q6rgdfgd2ffdnyqk6gq2ckrnm007-file-5.39/include:/gnu/store/sb75h0di8w5mhpn4wfhk7za6c7x3c97c-gawk-5.1.0/include:/gnu/store/zjhq95bn5kmlhiqdsvcyy1nhyphxi8yb-make-4.3/include:/gnu/store/h8052068pq3a6rc903982ad2dd5ssxgk-binutils-2.37/include:/gnu/store/ky9xbrj6slwvgwa4536xbs5lradbqfk5-gcc-10.3.0/include:/gnu/store/skfhr2f8b7jnnpiarrrcjn6qx0xzfw00-glibc-2.33/include:/gnu/store/swpaxgk7xzgs4lkmw450wiak8iy8snsm-linux-libre-headers-5.10.35/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/15j6iqyq3xlgr16x607i6cw6d42p0jpx-htslib-1.12/include:/gnu/store/42s919l9a2zmiih1fnq7za8f51h7zjm8-ncurses-6.2.20210619/include:/gnu/store/fmvmsjllz18d2hppxj723qjj788l1his-python-3.9.6/include:/gnu/store/rhrxyws0zzq02zpk6y9hhcbiibwag5ls-zlib-1.2.11/include:/gnu/store/dmca74p8b9ik05mrsnvbviflbxrz9qaw-bzip2-1.0.8/include:/gnu/store/s3577mn5iz2gjgkrava2sm914bgbnkd8-xz-5.2.5/include:/gnu/store/61b8q6rgdfgd2ffdnyqk6gq2ckrnm007-file-5.39/include:/gnu/store/sb75h0di8w5mhpn4wfhk7za6c7x3c97c-gawk-5.1.0/include:/gnu/store/zjhq95bn5kmlhiqdsvcyy1nhyphxi8yb-make-4.3/include:/gnu/store/h8052068pq3a6rc903982ad2dd5ssxgk-binutils-2.37/include:/gnu/store/ky9xbrj6slwvgwa4536xbs5lradbqfk5-gcc-10.3.0/include/c++:/gnu/store/ky9xbrj6slwvgwa4536xbs5lradbqfk5-gcc-10.3.0/include:/gnu/store/skfhr2f8b7jnnpiarrrcjn6qx0xzfw00-glibc-2.33/include:/gnu/store/swpaxgk7xzgs4lkmw450wiak8iy8snsm-linux-libre-headers-5.10.35/include' environment variable `LIBRARY_PATH' set to `/gnu/store/15j6iqyq3xlgr16x607i6cw6d42p0jpx-htslib-1.12/lib:/gnu/store/42s919l9a2zmiih1fnq7za8f51h7zjm8-ncurses-6.2.20210619/lib:/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/lib:/gnu/store/fmvmsjllz18d2hppxj723qjj788l1his-python-3.9.6/lib:/gnu/store/rhrxyws0zzq02zpk6y9hhcbiibwag5ls-zlib-1.2.11/lib:/gnu/store/dmca74p8b9ik05mrsnvbviflbxrz9qaw-bzip2-1.0.8/lib:/gnu/store/s3577mn5iz2gjgkrava2sm914bgbnkd8-xz-5.2.5/lib:/gnu/store/61b8q6rgdfgd2ffdnyqk6gq2ckrnm007-file-5.39/lib:/gnu/store/sb75h0di8w5mhpn4wfhk7za6c7x3c97c-gawk-5.1.0/lib:/gnu/store/h8052068pq3a6rc903982ad2dd5ssxgk-binutils-2.37/lib:/gnu/store/skfhr2f8b7jnnpiarrrcjn6qx0xzfw00-glibc-2.33/lib:/gnu/store/66nrq0ra6d3jnsc24cms9lgzbyb9spr8-glibc-2.33-static/lib:/gnu/store/mnxbr2w45qrfi4bi7khl2yj56rjz9vbi-glibc-utf8-locales-2.33/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/mnxbr2w45qrfi4bi7khl2yj56rjz9vbi-glibc-utf8-locales-2.33/lib/locale' phase `set-paths' succeeded after 0.1 seconds starting phase `install-locale' using 'en_US.utf8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' samtools-1.12/ samtools-1.12/AUTHORS samtools-1.12/ChangeLog.old samtools-1.12/INSTALL samtools-1.12/LICENSE samtools-1.12/Makefile samtools-1.12/NEWS samtools-1.12/README samtools-1.12/amplicon_stats.c samtools-1.12/bam.c samtools-1.12/bam.h samtools-1.12/bam2bcf.c samtools-1.12/bam2bcf.h samtools-1.12/bam2bcf_indel.c samtools-1.12/bam2depth.c samtools-1.12/bam_addrprg.c samtools-1.12/bam_ampliconclip.c samtools-1.12/bam_ampliconclip.h samtools-1.12/bam_aux.c samtools-1.12/bam_cat.c samtools-1.12/bam_color.c samtools-1.12/bam_endian.h samtools-1.12/bam_fastq.c samtools-1.12/bam_flags.c samtools-1.12/bam_index.c samtools-1.12/bam_lpileup.c samtools-1.12/bam_lpileup.h samtools-1.12/bam_markdup.c samtools-1.12/bam_mate.c samtools-1.12/bam_md.c samtools-1.12/bam_plbuf.c samtools-1.12/bam_plbuf.h samtools-1.12/bam_plcmd.c samtools-1.12/bam_quickcheck.c samtools-1.12/bam_reheader.c samtools-1.12/bam_rmdup.c samtools-1.12/bam_rmdupse.c samtools-1.12/bam_sort.c samtools-1.12/bam_split.c samtools-1.12/bam_stat.c samtools-1.12/bam_tview.c samtools-1.12/bam_tview.h samtools-1.12/bam_tview_curses.c samtools-1.12/bam_tview_html.c samtools-1.12/bamshuf.c samtools-1.12/bamtk.c samtools-1.12/bedcov.c samtools-1.12/bedidx.c samtools-1.12/bedidx.h samtools-1.12/config.h.in samtools-1.12/config.mk.in samtools-1.12/configure samtools-1.12/configure.ac samtools-1.12/coverage.c samtools-1.12/cut_target.c samtools-1.12/dict.c samtools-1.12/doc/ samtools-1.12/doc/samtools-addreplacerg.1 samtools-1.12/doc/samtools-ampliconclip.1 samtools-1.12/doc/samtools-ampliconstats.1 samtools-1.12/doc/samtools-bedcov.1 samtools-1.12/doc/samtools-calmd.1 samtools-1.12/doc/samtools-cat.1 samtools-1.12/doc/samtools-collate.1 samtools-1.12/doc/samtools-coverage.1 samtools-1.12/doc/samtools-depad.1 samtools-1.12/doc/samtools-depth.1 samtools-1.12/doc/samtools-dict.1 samtools-1.12/doc/samtools-faidx.1 samtools-1.12/doc/samtools-fasta.1 samtools-1.12/doc/samtools-fastq.1 samtools-1.12/doc/samtools-fixmate.1 samtools-1.12/doc/samtools-flags.1 samtools-1.12/doc/samtools-flagstat.1 samtools-1.12/doc/samtools-fqidx.1 samtools-1.12/doc/samtools-idxstats.1 samtools-1.12/doc/samtools-index.1 samtools-1.12/doc/samtools-markdup.1 samtools-1.12/doc/samtools-merge.1 samtools-1.12/doc/samtools-mpileup.1 samtools-1.12/doc/samtools-phase.1 samtools-1.12/doc/samtools-quickcheck.1 samtools-1.12/doc/samtools-reheader.1 samtools-1.12/doc/samtools-rmdup.1 samtools-1.12/doc/samtools-sort.1 samtools-1.12/doc/samtools-split.1 samtools-1.12/doc/samtools-stats.1 samtools-1.12/doc/samtools-targetcut.1 samtools-1.12/doc/samtools-tview.1 samtools-1.12/doc/samtools-view.1 samtools-1.12/doc/samtools.1 samtools-1.12/examples/ samtools-1.12/examples/00README.txt samtools-1.12/examples/ex1.fa samtools-1.12/examples/ex1.sam.gz samtools-1.12/examples/toy.fa samtools-1.12/examples/toy.sam samtools-1.12/faidx.c samtools-1.12/install-sh samtools-1.12/lz4/ samtools-1.12/lz4/LICENSE samtools-1.12/lz4/lz4.c samtools-1.12/lz4/lz4.h samtools-1.12/m4/ samtools-1.12/m4/ax_with_htslib.m4 samtools-1.12/m4/hts_prog_cc_warnings.m4 samtools-1.12/m4/hts_with_curses.m4 samtools-1.12/misc/ samtools-1.12/misc/HmmGlocal.java samtools-1.12/misc/ace2sam.c samtools-1.12/misc/blast2sam.pl samtools-1.12/misc/bowtie2sam.pl samtools-1.12/misc/export2sam.pl samtools-1.12/misc/fasta-sanitize.pl samtools-1.12/misc/interpolate_sam.pl samtools-1.12/misc/maq2sam.c samtools-1.12/misc/md5fa.c samtools-1.12/misc/md5sum-lite.c samtools-1.12/misc/novo2sam.pl samtools-1.12/misc/plot-ampliconstats samtools-1.12/misc/plot-bamstats samtools-1.12/misc/psl2sam.pl samtools-1.12/misc/r2plot.lua samtools-1.12/misc/sam2vcf.pl samtools-1.12/misc/samtools.pl samtools-1.12/misc/samtools_tab_completion samtools-1.12/misc/seq_cache_populate.pl samtools-1.12/misc/soap2sam.pl samtools-1.12/misc/vcfutils.lua samtools-1.12/misc/wgsim.1 samtools-1.12/misc/wgsim.c samtools-1.12/misc/wgsim_eval.pl samtools-1.12/misc/zoom2sam.pl samtools-1.12/padding.c samtools-1.12/phase.c samtools-1.12/sam.c samtools-1.12/sam.h samtools-1.12/sam_opts.c samtools-1.12/sam_opts.h samtools-1.12/sam_utils.c samtools-1.12/sam_view.c samtools-1.12/sample.c samtools-1.12/sample.h samtools-1.12/samtools.h samtools-1.12/stats.c samtools-1.12/stats_isize.c samtools-1.12/stats_isize.h samtools-1.12/test/ samtools-1.12/test/addrprg/ samtools-1.12/test/addrprg/1_fixup.sam samtools-1.12/test/addrprg/1_fixup.sam.expected samtools-1.12/test/addrprg/1_fixup.sam.expected.err samtools-1.12/test/addrprg/2_fixup_orphan.sam samtools-1.12/test/addrprg/2_fixup_orphan.sam.expected samtools-1.12/test/addrprg/2_fixup_orphan.sam.expected.err samtools-1.12/test/addrprg/3_fixup.sam.expected samtools-1.12/test/addrprg/3_fixup.sam.expected.err samtools-1.12/test/addrprg/4_fixup_norg.sam samtools-1.12/test/addrprg/4_fixup_norg.sam.expected samtools-1.12/test/addrprg/4_fixup_norg.sam.expected.err samtools-1.12/test/ampliconclip/ samtools-1.12/test/ampliconclip/1_delete_tag.expected.sam samtools-1.12/test/ampliconclip/1_fail.expected.sam samtools-1.12/test/ampliconclip/1_filter.expected.sam samtools-1.12/test/ampliconclip/1_hard_clipped.expected.sam samtools-1.12/test/ampliconclip/1_original_tag.expected.sam samtools-1.12/test/ampliconclip/1_soft_clipped.expected.sam samtools-1.12/test/ampliconclip/1_soft_clipped_strand.expected.sam samtools-1.12/test/ampliconclip/1_test_data.sam samtools-1.12/test/ampliconclip/2_both_clipped.expected.sam samtools-1.12/test/ampliconclip/2_both_test_data.sam samtools-1.12/test/ampliconclip/ac_test.bed samtools-1.12/test/ampliconstats/ samtools-1.12/test/ampliconstats/stats.expected.txt samtools-1.12/test/bam2fq/ samtools-1.12/test/bam2fq/1.1.fq.expected samtools-1.12/test/bam2fq/1.2.fq.expected samtools-1.12/test/bam2fq/1.stdout.expected samtools-1.12/test/bam2fq/10.1.fq.expected samtools-1.12/test/bam2fq/10.2.fq.expected samtools-1.12/test/bam2fq/10.s.fq.expected samtools-1.12/test/bam2fq/11.fq.expected samtools-1.12/test/bam2fq/12.1.fq.expected samtools-1.12/test/bam2fq/12.2.fq.expected samtools-1.12/test/bam2fq/12.i.fq.expected samtools-1.12/test/bam2fq/12.s.fq.expected samtools-1.12/test/bam2fq/13.fq.expected samtools-1.12/test/bam2fq/2.1.fq.expected samtools-1.12/test/bam2fq/2.2.fq.expected samtools-1.12/test/bam2fq/2.s.fq.expected samtools-1.12/test/bam2fq/2.stdout.expected samtools-1.12/test/bam2fq/3.1.fq.expected samtools-1.12/test/bam2fq/3.2.fq.expected samtools-1.12/test/bam2fq/3.s.fq.expected samtools-1.12/test/bam2fq/3.stdout.expected samtools-1.12/test/bam2fq/4.1.fq.expected samtools-1.12/test/bam2fq/4.2.fq.expected samtools-1.12/test/bam2fq/4.s.fq.expected samtools-1.12/test/bam2fq/4.stdout.expected samtools-1.12/test/bam2fq/5.1.fq.expected samtools-1.12/test/bam2fq/5.2.fq.expected samtools-1.12/test/bam2fq/5.s.fq.expected samtools-1.12/test/bam2fq/6.1.fq.expected samtools-1.12/test/bam2fq/6.2.fq.expected samtools-1.12/test/bam2fq/6.s.fq.expected samtools-1.12/test/bam2fq/7.1.fq.expected samtools-1.12/test/bam2fq/7.2.fq.expected samtools-1.12/test/bam2fq/7.s.fq.expected samtools-1.12/test/bam2fq/8.1.fq.expected samtools-1.12/test/bam2fq/8.2.fq.expected samtools-1.12/test/bam2fq/8.i.fq.expected samtools-1.12/test/bam2fq/8.s.fq.expected samtools-1.12/test/bam2fq/9.1.fq.expected samtools-1.12/test/bam2fq/9.2.fq.expected samtools-1.12/test/bam2fq/bc.fq.expected samtools-1.12/test/bam2fq/bc10.fq.expected samtools-1.12/test/bam2fq/bc_split.fq.expected samtools-1.12/test/bedcov/ samtools-1.12/test/bedcov/bedcov.bam samtools-1.12/test/bedcov/bedcov.bam.bai samtools-1.12/test/bedcov/bedcov.bed samtools-1.12/test/bedcov/bedcov.expected samtools-1.12/test/bedcov/bedcov_gG.bed samtools-1.12/test/bedcov/bedcov_gG.expected samtools-1.12/test/bedcov/bedcov_j.expected samtools-1.12/test/collate/ samtools-1.12/test/collate/1_fast_collate.sam.expected samtools-1.12/test/collate/2_fast_collate_with_tmp_used.sam.expected samtools-1.12/test/collate/collate.expected.sam samtools-1.12/test/collate/fast_collate.sam samtools-1.12/test/dat/ samtools-1.12/test/dat/bam2fq.001.sam samtools-1.12/test/dat/bam2fq.002.sam samtools-1.12/test/dat/bam2fq.003.sam samtools-1.12/test/dat/bam2fq.004.sam samtools-1.12/test/dat/bam2fq.005.sam samtools-1.12/test/dat/bam2fq.010.sam samtools-1.12/test/dat/bam2fq.013.sam samtools-1.12/test/dat/bam2fq.703.sam samtools-1.12/test/dat/cat.hdr samtools-1.12/test/dat/cram_md5/ samtools-1.12/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468 samtools-1.12/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437 samtools-1.12/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4 samtools-1.12/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b samtools-1.12/test/dat/depad.001.fa samtools-1.12/test/dat/depad.001.fa.fai samtools-1.12/test/dat/depad.001p.sam samtools-1.12/test/dat/depad.001u.sam samtools-1.12/test/dat/dict.alias.fa samtools-1.12/test/dat/dict.alias.out samtools-1.12/test/dat/dict.fa samtools-1.12/test/dat/dict.out samtools-1.12/test/dat/empty.expected samtools-1.12/test/dat/large_chrom.out samtools-1.12/test/dat/large_chrom.sam samtools-1.12/test/dat/large_chrom_bai_index.err samtools-1.12/test/dat/mpileup.1.sam samtools-1.12/test/dat/mpileup.2.sam samtools-1.12/test/dat/mpileup.3.sam samtools-1.12/test/dat/mpileup.err.1 samtools-1.12/test/dat/mpileup.out.1 samtools-1.12/test/dat/mpileup.out.2 samtools-1.12/test/dat/mpileup.out.3 samtools-1.12/test/dat/mpileup.out.4 samtools-1.12/test/dat/mpileup.out.5 samtools-1.12/test/dat/mpileup.ref.fa samtools-1.12/test/dat/mpileup.ref.fa.fai samtools-1.12/test/dat/test_input_1_a.bam samtools-1.12/test/dat/test_input_1_a.bam.bai.expected samtools-1.12/test/dat/test_input_1_a.cram samtools-1.12/test/dat/test_input_1_a.sam samtools-1.12/test/dat/test_input_1_a_regex.sam samtools-1.12/test/dat/test_input_1_ab.X.expected samtools-1.12/test/dat/test_input_1_b.X.expected samtools-1.12/test/dat/test_input_1_b.bam samtools-1.12/test/dat/test_input_1_b.sam samtools-1.12/test/dat/test_input_1_b_regex.sam samtools-1.12/test/dat/test_input_1_c.bam samtools-1.12/test/dat/test_input_1_c.sam samtools-1.12/test/dat/test_input_1_d.sam samtools-1.12/test/dat/view.001.01.bed samtools-1.12/test/dat/view.001.02.bed samtools-1.12/test/dat/view.001.fa samtools-1.12/test/dat/view.001.fa.fai samtools-1.12/test/dat/view.001.sam samtools-1.12/test/dat/view.002.01.bed samtools-1.12/test/dat/view.002.02.bed samtools-1.12/test/dat/view.002.fa samtools-1.12/test/dat/view.002.fa.fai samtools-1.12/test/dat/view.002.sam samtools-1.12/test/dat/view.003.expected.sam samtools-1.12/test/dat/view.003.sam samtools-1.12/test/dat/view.004.expected.sam samtools-1.12/test/fixmate/ samtools-1.12/test/fixmate/1_coord_sort.sam samtools-1.12/test/fixmate/1_coord_sort.sam.expected samtools-1.12/test/fixmate/1_coord_sort.sam.expected.err samtools-1.12/test/fixmate/2_isize_overflow.sam samtools-1.12/test/fixmate/2_isize_overflow.sam.expected samtools-1.12/test/fixmate/3_reverse_read_pp_lt.sam samtools-1.12/test/fixmate/3_reverse_read_pp_lt.sam.expected samtools-1.12/test/fixmate/4_reverse_read_pp_equal.sam samtools-1.12/test/fixmate/4_reverse_read_pp_equal.sam.expected samtools-1.12/test/fixmate/5_ct.sam samtools-1.12/test/fixmate/5_ct.sam.expected samtools-1.12/test/fixmate/6_ct_replace.sam samtools-1.12/test/fixmate/6_ct_replace.sam.expected samtools-1.12/test/fixmate/7_two_read_mapped.sam samtools-1.12/test/fixmate/7_two_read_mapped.sam.expected samtools-1.12/test/fixmate/8_isize_overflow_64bit.sam samtools-1.12/test/fixmate/8_isize_overflow_64bit.sam.expected samtools-1.12/test/idxstats/ samtools-1.12/test/idxstats/test_input_1_a.bam.expected samtools-1.12/test/idxstats/test_input_1_a.bam.expected.err samtools-1.12/test/large_pos/ samtools-1.12/test/large_pos/depth.expected.out samtools-1.12/test/large_pos/depth_bed.expected.out samtools-1.12/test/large_pos/longref.sam samtools-1.12/test/large_pos/longref2.sam samtools-1.12/test/large_pos/longref3.expected.sam samtools-1.12/test/large_pos/longref3.sam samtools-1.12/test/large_pos/longref_idx.expected.sam samtools-1.12/test/large_pos/longref_name.sam samtools-1.12/test/large_pos/merge.expected.sam samtools-1.12/test/large_pos/test.bed samtools-1.12/test/large_pos/tview.expected.out samtools-1.12/test/maintainer/ samtools-1.12/test/maintainer/check_copyright.pl samtools-1.12/test/maintainer/check_spaces.pl samtools-1.12/test/markdup/ samtools-1.12/test/markdup/1_name_sort.expected.sam samtools-1.12/test/markdup/1_name_sort.expected.sam.err samtools-1.12/test/markdup/1_name_sort.sam samtools-1.12/test/markdup/2_bad_order.expected.sam samtools-1.12/test/markdup/2_bad_order.expected.sam.err samtools-1.12/test/markdup/2_bad_order.sam samtools-1.12/test/markdup/3_missing_mc.expected.sam samtools-1.12/test/markdup/3_missing_mc.expected.sam.err samtools-1.12/test/markdup/3_missing_mc.sam samtools-1.12/test/markdup/4_missing_ms.expected.sam samtools-1.12/test/markdup/4_missing_ms.expected.sam.err samtools-1.12/test/markdup/4_missing_ms.sam samtools-1.12/test/markdup/5_markdup.expected.sam samtools-1.12/test/markdup/5_markdup.sam samtools-1.12/test/markdup/6_remove_dups.expected.sam samtools-1.12/test/markdup/6_remove_dups.sam samtools-1.12/test/markdup/7_mark_supp_dup.expected.sam samtools-1.12/test/markdup/7_mark_supp_dup.sam samtools-1.12/test/markdup/8_optical_dup.expected.sam samtools-1.12/test/markdup/8_optical_dup.sam samtools-1.12/test/markdup/9_optical_dup_qcfail.expected.sam samtools-1.12/test/markdup/9_optical_dup_qcfail.sam samtools-1.12/test/merge/ samtools-1.12/test/merge/2.merge.expected.sam samtools-1.12/test/merge/3.merge.expected.err samtools-1.12/test/merge/3.merge.expected.sam samtools-1.12/test/merge/4.merge.expected.sam samtools-1.12/test/merge/5.merge.expected.sam samtools-1.12/test/merge/6.merge.expected.sam samtools-1.12/test/merge/7.merge.expected.sam samtools-1.12/test/merge/merge.bed samtools-1.12/test/merge/merge.bed.1.sam samtools-1.12/test/merge/merge.bed.2.sam samtools-1.12/test/merge/merge.bed.expected.sam samtools-1.12/test/merge/tag.pg.merge.expected.sam samtools-1.12/test/merge/tag.pg.n.merge.expected.sam samtools-1.12/test/merge/test_3.fofn samtools-1.12/test/merge/test_bam_translate.c samtools-1.12/test/merge/test_header.sam samtools-1.12/test/merge/test_no_pg_rg_co.sam samtools-1.12/test/merge/test_rtrans_build.c samtools-1.12/test/merge/test_trans_tbl_init.c samtools-1.12/test/mpileup/ samtools-1.12/test/mpileup/1read.bam samtools-1.12/test/mpileup/1read.sam samtools-1.12/test/mpileup/anomalous.sam samtools-1.12/test/mpileup/c1#clip.bam samtools-1.12/test/mpileup/c1#pad1.bam samtools-1.12/test/mpileup/c1#pad2.bam samtools-1.12/test/mpileup/c1#pad3.bam samtools-1.12/test/mpileup/c1.fa samtools-1.12/test/mpileup/c1.fa.fai samtools-1.12/test/mpileup/ce#5b.bam samtools-1.12/test/mpileup/ce#5b.bam.bai samtools-1.12/test/mpileup/ce#5b.cram samtools-1.12/test/mpileup/ce#5b.cram.crai samtools-1.12/test/mpileup/ce#5b.sam samtools-1.12/test/mpileup/ce#large_seq.bam samtools-1.12/test/mpileup/ce#unmap.bam samtools-1.12/test/mpileup/ce#unmap1.bam samtools-1.12/test/mpileup/ce#unmap2.bam samtools-1.12/test/mpileup/ce.fa samtools-1.12/test/mpileup/ce.fa.fai samtools-1.12/test/mpileup/deep.sam samtools-1.12/test/mpileup/depth.reg samtools-1.12/test/mpileup/depth_del.sam samtools-1.12/test/mpileup/expected/ samtools-1.12/test/mpileup/expected/1.out.f3-6.gz samtools-1.12/test/mpileup/expected/10.out samtools-1.12/test/mpileup/expected/11.out samtools-1.12/test/mpileup/expected/12.out samtools-1.12/test/mpileup/expected/13.out samtools-1.12/test/mpileup/expected/14.out samtools-1.12/test/mpileup/expected/15.out samtools-1.12/test/mpileup/expected/16.out samtools-1.12/test/mpileup/expected/17.out samtools-1.12/test/mpileup/expected/18.out samtools-1.12/test/mpileup/expected/19.out samtools-1.12/test/mpileup/expected/2.out samtools-1.12/test/mpileup/expected/20.out samtools-1.12/test/mpileup/expected/21.out samtools-1.12/test/mpileup/expected/22.out samtools-1.12/test/mpileup/expected/23.out samtools-1.12/test/mpileup/expected/24.out samtools-1.12/test/mpileup/expected/25.out samtools-1.12/test/mpileup/expected/26.out samtools-1.12/test/mpileup/expected/27.out samtools-1.12/test/mpileup/expected/28.out samtools-1.12/test/mpileup/expected/29.out samtools-1.12/test/mpileup/expected/3.out samtools-1.12/test/mpileup/expected/30.out samtools-1.12/test/mpileup/expected/31.out samtools-1.12/test/mpileup/expected/32.out samtools-1.12/test/mpileup/expected/33.out samtools-1.12/test/mpileup/expected/34.out samtools-1.12/test/mpileup/expected/35.out samtools-1.12/test/mpileup/expected/37.out samtools-1.12/test/mpileup/expected/38.out samtools-1.12/test/mpileup/expected/39.out samtools-1.12/test/mpileup/expected/4.out samtools-1.12/test/mpileup/expected/40.out samtools-1.12/test/mpileup/expected/41.out samtools-1.12/test/mpileup/expected/42.out samtools-1.12/test/mpileup/expected/43.out samtools-1.12/test/mpileup/expected/44.out samtools-1.12/test/mpileup/expected/45.out samtools-1.12/test/mpileup/expected/46.out samtools-1.12/test/mpileup/expected/47.out samtools-1.12/test/mpileup/expected/48.out samtools-1.12/test/mpileup/expected/49.out samtools-1.12/test/mpileup/expected/5.out samtools-1.12/test/mpileup/expected/50.out samtools-1.12/test/mpileup/expected/51.out samtools-1.12/test/mpileup/expected/52.out samtools-1.12/test/mpileup/expected/53.out samtools-1.12/test/mpileup/expected/54.out samtools-1.12/test/mpileup/expected/55.out samtools-1.12/test/mpileup/expected/56.out samtools-1.12/test/mpileup/expected/57.out samtools-1.12/test/mpileup/expected/58.out samtools-1.12/test/mpileup/expected/59.out samtools-1.12/test/mpileup/expected/6.out samtools-1.12/test/mpileup/expected/60.out samtools-1.12/test/mpileup/expected/61.out samtools-1.12/test/mpileup/expected/62.out samtools-1.12/test/mpileup/expected/63.out samtools-1.12/test/mpileup/expected/64.out samtools-1.12/test/mpileup/expected/65.out samtools-1.12/test/mpileup/expected/66.out samtools-1.12/test/mpileup/expected/67.out samtools-1.12/test/mpileup/expected/68.out samtools-1.12/test/mpileup/expected/69.out samtools-1.12/test/mpileup/expected/7.out samtools-1.12/test/mpileup/expected/70.out samtools-1.12/test/mpileup/expected/71.out samtools-1.12/test/mpileup/expected/72.out samtools-1.12/test/mpileup/expected/73.out samtools-1.12/test/mpileup/expected/74.out samtools-1.12/test/mpileup/expected/75.out samtools-1.12/test/mpileup/expected/76.out samtools-1.12/test/mpileup/expected/77.out samtools-1.12/test/mpileup/expected/78.out samtools-1.12/test/mpileup/expected/79.out samtools-1.12/test/mpileup/expected/8.out samtools-1.12/test/mpileup/expected/9.out samtools-1.12/test/mpileup/expected/a0.out samtools-1.12/test/mpileup/expected/a1.out samtools-1.12/test/mpileup/expected/a10.out samtools-1.12/test/mpileup/expected/a11.out samtools-1.12/test/mpileup/expected/a13.out samtools-1.12/test/mpileup/expected/a14.out samtools-1.12/test/mpileup/expected/a15.out samtools-1.12/test/mpileup/expected/a16.out samtools-1.12/test/mpileup/expected/a17.out samtools-1.12/test/mpileup/expected/a2.out samtools-1.12/test/mpileup/expected/a3.out samtools-1.12/test/mpileup/expected/a4.out samtools-1.12/test/mpileup/expected/a5.out samtools-1.12/test/mpileup/expected/a6.out samtools-1.12/test/mpileup/expected/a8.out samtools-1.12/test/mpileup/expected/a9.out samtools-1.12/test/mpileup/expected/d1_1.out samtools-1.12/test/mpileup/expected/d1_12.out samtools-1.12/test/mpileup/expected/d1_2.out samtools-1.12/test/mpileup/expected/d2_12r.out samtools-1.12/test/mpileup/expected/d3_12.out samtools-1.12/test/mpileup/expected/d3_12r1a.out samtools-1.12/test/mpileup/expected/d3_12r2a.out samtools-1.12/test/mpileup/expected/d3_3.out samtools-1.12/test/mpileup/expected/d4_12.out samtools-1.12/test/mpileup/expected/d4_12b.out samtools-1.12/test/mpileup/expected/d4_12r.out samtools-1.12/test/mpileup/expected/d5_all1.out samtools-1.12/test/mpileup/expected/d5_all2.out samtools-1.12/test/mpileup/expected/d5_all3.out samtools-1.12/test/mpileup/expected/d5_all4.out samtools-1.12/test/mpileup/expected/d5_b3.out samtools-1.12/test/mpileup/expected/d5_b3a.out samtools-1.12/test/mpileup/expected/d5_b3aa.out samtools-1.12/test/mpileup/expected/d5_blank.out samtools-1.12/test/mpileup/expected/d5_xx1.out samtools-1.12/test/mpileup/expected/d5_xx2.out samtools-1.12/test/mpileup/expected/d5_xx3.out samtools-1.12/test/mpileup/expected/d5_xy1.out samtools-1.12/test/mpileup/expected/d6_nodel.out samtools-1.12/test/mpileup/expected/d6_wdel.out samtools-1.12/test/mpileup/expected/d7_nodup.out samtools-1.12/test/mpileup/expected/m5_all1.out samtools-1.12/test/mpileup/expected/m5_all2.out samtools-1.12/test/mpileup/expected/m5_all3.out samtools-1.12/test/mpileup/expected/m5_b3.out samtools-1.12/test/mpileup/expected/m5_b3a.out samtools-1.12/test/mpileup/expected/m5_b3aa.out samtools-1.12/test/mpileup/expected/m5_blank.out samtools-1.12/test/mpileup/expected/m5_xx1.out samtools-1.12/test/mpileup/expected/m5_xx2.out samtools-1.12/test/mpileup/expected/m5_xx3.out samtools-1.12/test/mpileup/expected/m5_xy1.out samtools-1.12/test/mpileup/expected/mp_D.out samtools-1.12/test/mpileup/expected/mp_DI.out samtools-1.12/test/mpileup/expected/mp_I.out samtools-1.12/test/mpileup/expected/mp_ID.out samtools-1.12/test/mpileup/expected/mp_ID_rev.out samtools-1.12/test/mpileup/expected/mp_N.out samtools-1.12/test/mpileup/expected/mp_N2.out samtools-1.12/test/mpileup/expected/mp_P.out samtools-1.12/test/mpileup/indels.sam samtools-1.12/test/mpileup/md5/ samtools-1.12/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae samtools-1.12/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d samtools-1.12/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de samtools-1.12/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc samtools-1.12/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1 samtools-1.12/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e samtools-1.12/test/mpileup/mp.fa samtools-1.12/test/mpileup/mp.fa.fai samtools-1.12/test/mpileup/mp_D.sam samtools-1.12/test/mpileup/mp_DI.sam samtools-1.12/test/mpileup/mp_I.sam samtools-1.12/test/mpileup/mp_ID.sam samtools-1.12/test/mpileup/mp_ID_rev.sam samtools-1.12/test/mpileup/mp_N.sam samtools-1.12/test/mpileup/mp_N2.sam samtools-1.12/test/mpileup/mp_P.sam samtools-1.12/test/mpileup/mpileup-E.bam samtools-1.12/test/mpileup/mpileup.1.bam samtools-1.12/test/mpileup/mpileup.1.bam.bai samtools-1.12/test/mpileup/mpileup.2.bam samtools-1.12/test/mpileup/mpileup.3.bam samtools-1.12/test/mpileup/mpileup.ref.fa samtools-1.12/test/mpileup/mpileup.ref.fa.fai samtools-1.12/test/mpileup/mpileup.reg samtools-1.12/test/mpileup/overlap.bam samtools-1.12/test/mpileup/overlap50.sam samtools-1.12/test/mpileup/overlapIllumina.bam samtools-1.12/test/mpileup/regions samtools-1.12/test/mpileup/regression.sh samtools-1.12/test/mpileup/xx#depth1.sam samtools-1.12/test/mpileup/xx#depth2.sam samtools-1.12/test/mpileup/xx#depth3.sam samtools-1.12/test/mpileup/xx#depth4.sam samtools-1.12/test/mpileup/xx#minimal.bam samtools-1.12/test/mpileup/xx#triplet.bam samtools-1.12/test/mpileup/xx.bed samtools-1.12/test/mpileup/xx.bed2 samtools-1.12/test/mpileup/xx.bed3 samtools-1.12/test/mpileup/xx.fa samtools-1.12/test/mpileup/xx.fa.fai samtools-1.12/test/quickcheck/ samtools-1.12/test/quickcheck/1.quickcheck.badeof.bam samtools-1.12/test/quickcheck/10.quickcheck.notargets.bam samtools-1.12/test/quickcheck/2.quickcheck.badheader.bam samtools-1.12/test/quickcheck/3.quickcheck.ok.bam samtools-1.12/test/quickcheck/4.quickcheck.ok.bam samtools-1.12/test/quickcheck/5.quickcheck.scramble30.truncated.cram samtools-1.12/test/quickcheck/6.quickcheck.cram21.ok.cram samtools-1.12/test/quickcheck/7.quickcheck.cram30.ok.cram samtools-1.12/test/quickcheck/8.quickcheck.cram21.truncated.cram samtools-1.12/test/quickcheck/9.quickcheck.cram30.truncated.cram samtools-1.12/test/quickcheck/all.expected samtools-1.12/test/reheader/ samtools-1.12/test/reheader/1_view1.sam.expected samtools-1.12/test/reheader/1_view1.sam.expected.err samtools-1.12/test/reheader/2_view1.sam.expected samtools-1.12/test/reheader/2_view1.sam.expected.err samtools-1.12/test/reheader/3_view1.sam.expected samtools-1.12/test/reheader/3_view1.sam.expected.err samtools-1.12/test/reheader/4_view1.sam.expected samtools-1.12/test/reheader/5_view1.sam.expected samtools-1.12/test/reheader/hdr.sam samtools-1.12/test/sort/ samtools-1.12/test/sort/name.sort.expected.sam samtools-1.12/test/sort/pos.sort.expected.sam samtools-1.12/test/sort/tag.as.sort.expected.sam samtools-1.12/test/sort/tag.fi.sort.expected.sam samtools-1.12/test/sort/tag.rg.n.sort.expected.sam samtools-1.12/test/sort/tag.rg.sort.expected.sam samtools-1.12/test/split/ samtools-1.12/test/split/split.expected.grp1.sam samtools-1.12/test/split/split.expected.grp2.sam samtools-1.12/test/split/split.expected.unk.sam samtools-1.12/test/split/split.sam samtools-1.12/test/split/test_count_rg.c samtools-1.12/test/split/test_expand_format_string.c samtools-1.12/test/split/test_filter_header_rg.c samtools-1.12/test/split/test_parse_args.c samtools-1.12/test/stat/ samtools-1.12/test/stat/1.stats.expected samtools-1.12/test/stat/1.stats.large.expected samtools-1.12/test/stat/10.stats.expected samtools-1.12/test/stat/10_map_cigar.sam samtools-1.12/test/stat/10_map_cigar.sam_s1_a_1.expected.bamstat samtools-1.12/test/stat/10_map_cigar.sam_s1_b_1.expected.bamstat samtools-1.12/test/stat/11.stats.expected samtools-1.12/test/stat/11.stats.g4.expected samtools-1.12/test/stat/11.stats.targets samtools-1.12/test/stat/11_target.bam samtools-1.12/test/stat/11_target.bam.bai samtools-1.12/test/stat/11_target.sam samtools-1.12/test/stat/12.2reads.nooverlap.expected samtools-1.12/test/stat/12.2reads.overlap.expected samtools-1.12/test/stat/12.3reads.nooverlap.expected samtools-1.12/test/stat/12.3reads.overlap.expected samtools-1.12/test/stat/12_2reads.bed samtools-1.12/test/stat/12_3reads.bed samtools-1.12/test/stat/12_overlaps.bam samtools-1.12/test/stat/13.barcodes.bc.ok.expected samtools-1.12/test/stat/13.barcodes.ox.ok.expected samtools-1.12/test/stat/13_barcodes_fail_bc_length.sam samtools-1.12/test/stat/13_barcodes_fail_hyphen.sam samtools-1.12/test/stat/13_barcodes_fail_qt_length.sam samtools-1.12/test/stat/13_barcodes_ok.sam samtools-1.12/test/stat/13_barcodes_ok_ox_bz.sam samtools-1.12/test/stat/1_map_cigar.sam samtools-1.12/test/stat/1_map_cigar.sam_s1_a_1.expected.bamstat samtools-1.12/test/stat/1_map_cigar_large.sam samtools-1.12/test/stat/2.stats.expected samtools-1.12/test/stat/2.stats.large.expected samtools-1.12/test/stat/2_equal_cigar_full_seq.sam samtools-1.12/test/stat/2_equal_cigar_full_seq_large.sam samtools-1.12/test/stat/3.stats.expected samtools-1.12/test/stat/3.stats.large.expected samtools-1.12/test/stat/3_map_cigar_equal_seq.sam samtools-1.12/test/stat/3_map_cigar_equal_seq_large.sam samtools-1.12/test/stat/4.stats.expected samtools-1.12/test/stat/4.stats.large.expected samtools-1.12/test/stat/4_X_cigar_full_seq.sam samtools-1.12/test/stat/4_X_cigar_full_seq_large.sam samtools-1.12/test/stat/5.stats.expected samtools-1.12/test/stat/5.stats.large.expected samtools-1.12/test/stat/5_insert_cigar.sam samtools-1.12/test/stat/5_insert_cigar_large.sam samtools-1.12/test/stat/6.stats.expected samtools-1.12/test/stat/7.stats.expected samtools-1.12/test/stat/7.stats.large.expected samtools-1.12/test/stat/7_supp.sam samtools-1.12/test/stat/7_supp_large.sam samtools-1.12/test/stat/8.stats.expected samtools-1.12/test/stat/8.stats.large.expected samtools-1.12/test/stat/8_secondary.sam samtools-1.12/test/stat/8_secondary_large.sam samtools-1.12/test/stat/9.stats.expected samtools-1.12/test/stat/test.fa samtools-1.12/test/stat/test.fa.fai samtools-1.12/test/test.c samtools-1.12/test/test.h samtools-1.12/test/test.pl samtools-1.12/test/tview/ samtools-1.12/test/tview/test_get_rg_sample.c samtools-1.12/test/vcf-miniview.c samtools-1.12/tmp_file.c samtools-1.12/tmp_file.h samtools-1.12/version.sh phase `unpack' succeeded after 0.5 seconds starting phase `patch-tests' phase `patch-tests' succeeded after 0.0 seconds starting phase `bootstrap' GNU build system bootstrapping not needed phase `bootstrap' succeeded after 0.0 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.1 seconds starting phase `patch-source-shebangs' patch-shebang: ./configure: changing `/bin/sh' to `/gnu/store/7npwsymmqsb6qcn268cbdnd5558byfy2-bash-minimal-5.1.8/bin/sh' patch-shebang: ./install-sh: changing `/bin/sh' to `/gnu/store/7npwsymmqsb6qcn268cbdnd5558byfy2-bash-minimal-5.1.8/bin/sh' patch-shebang: ./misc/blast2sam.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/bowtie2sam.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/export2sam.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/fasta-sanitize.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/interpolate_sam.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/novo2sam.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/plot-ampliconstats: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/plot-bamstats: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/psl2sam.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/r2plot.lua: warning: no binary for interpreter `luajit' found in $PATH patch-shebang: ./misc/sam2vcf.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/samtools.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/seq_cache_populate.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/soap2sam.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/vcfutils.lua: warning: no binary for interpreter `luajit' found in $PATH patch-shebang: ./misc/wgsim_eval.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./misc/zoom2sam.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./test/maintainer/check_copyright.pl: changing `/usr/bin/perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./test/maintainer/check_spaces.pl: changing `/usr/bin/perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./test/mpileup/regression.sh: changing `/bin/sh' to `/gnu/store/7npwsymmqsb6qcn268cbdnd5558byfy2-bash-minimal-5.1.8/bin/sh' patch-shebang: ./test/test.pl: changing `/usr/bin/env perl' to `/gnu/store/v26gmmw0xakfw4g46bc437srbj70hl0b-perl-5.34.0/bin/perl' patch-shebang: ./version.sh: changing `/bin/sh' to `/gnu/store/7npwsymmqsb6qcn268cbdnd5558byfy2-bash-minimal-5.1.8/bin/sh' phase `patch-source-shebangs' succeeded after 0.1 seconds starting phase `configure' source directory: "/tmp/guix-build-samtools-1.12.drv-0/samtools-1.12" (relative from build: ".") build directory: "/tmp/guix-build-samtools-1.12.drv-0/samtools-1.12" configure flags: ("CONFIG_SHELL=/gnu/store/7npwsymmqsb6qcn268cbdnd5558byfy2-bash-minimal-5.1.8/bin/bash" "SHELL=/gnu/store/7npwsymmqsb6qcn268cbdnd5558byfy2-bash-minimal-5.1.8/bin/bash" "--prefix=/gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12" "--enable-fast-install" "--build=aarch64-unknown-linux-gnu" "--with-ncurses") checking for gawk... gawk checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /gnu/store/vl9pxlycbk5ff0i7jbgyrh0rb2dl07lx-grep-3.6/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking location of HTSlib source tree... none found checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for NcursesW wide-character library... yes checking for working ncursesw/curses.h... no checking for working ncursesw.h... no checking for working ncurses.h... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h phase `configure' succeeded after 3.9 seconds starting phase `patch-generated-file-shebangs' patch-shebang: ./misc/r2plot.lua: warning: no binary for interpreter `luajit' found in $PATH patch-shebang: ./misc/vcfutils.lua: warning: no binary for interpreter `luajit' found in $PATH phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `build' gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_index.o bam_index.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_plcmd.o bam_plcmd.c gcc -Wall -g -O2 -I. -I./lz4 -c -o sam_view.o sam_view.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_fastq.o bam_fastq.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_cat.o bam_cat.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_md.o bam_md.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_reheader.o bam_reheader.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_sort.o bam_sort.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_rmdup.o bam_rmdup.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_rmdupse.o bam_rmdupse.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_mate.o bam_mate.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_stat.o bam_stat.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.12"' > version.h gcc -Wall -g -O2 -I. -I./lz4 -c -o bam2bcf.o bam2bcf.c echo '#define SAMTOOLS_CC "gcc"' >> version.h gcc -Wall -g -O2 -I. -I./lz4 -c -o bam2bcf_indel.o bam2bcf_indel.c echo '#define SAMTOOLS_CPPFLAGS ""' >> version.h echo '#define SAMTOOLS_CFLAGS "-Wall -g -O2"' >> version.h echo '#define SAMTOOLS_LDFLAGS ""' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> version.h gcc -Wall -g -O2 -I. -I./lz4 -c -o sample.o sample.c gcc -Wall -g -O2 -I. -I./lz4 -c -o cut_target.o cut_target.c gcc -Wall -g -O2 -I. -I./lz4 -c -o phase.o phase.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam2depth.o bam2depth.c gcc -Wall -g -O2 -I. -I./lz4 -c -o coverage.o coverage.c gcc -Wall -g -O2 -I. -I./lz4 -c -o padding.o padding.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bedcov.o bedcov.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bamshuf.o bamshuf.c gcc -Wall -g -O2 -I. -I./lz4 -c -o faidx.o faidx.c gcc -Wall -g -O2 -I. -I./lz4 -c -o dict.o dict.c gcc -Wall -g -O2 -I. -I./lz4 -c -o stats.o stats.c gcc -Wall -g -O2 -I. -I./lz4 -c -o stats_isize.o stats_isize.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_flags.o bam_flags.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_split.o bam_split.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_tview.o bam_tview.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_tview_curses.o bam_tview_curses.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_tview_html.o bam_tview_html.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_lpileup.o bam_lpileup.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_quickcheck.o bam_quickcheck.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_addrprg.o bam_addrprg.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_markdup.o bam_markdup.c gcc -Wall -g -O2 -I. -I./lz4 -c -o tmp_file.o tmp_file.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_ampliconclip.o bam_ampliconclip.c gcc -Wall -g -O2 -I. -I./lz4 -c -o amplicon_stats.o amplicon_stats.c gcc -Wall -g -O2 -I. -I./lz4 -c -o lz4/lz4.o lz4/lz4.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_aux.o bam_aux.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam.o bam.c gcc -Wall -g -O2 -I. -I./lz4 -c -o sam.o sam.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bam_plbuf.o bam_plbuf.c gcc -Wall -g -O2 -I. -I./lz4 -c -o sam_opts.o sam_opts.c gcc -Wall -g -O2 -I. -I./lz4 -c -o sam_utils.o sam_utils.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bedidx.o bedidx.c gcc -Wall -g -O2 -I. -I./lz4 -c -o misc/ace2sam.o misc/ace2sam.c gcc -Wall -g -O2 -DMAQ_LONGREADS -I. -I./lz4 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -Wall -g -O2 -I. -I./lz4 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -Wall -g -O2 -I. -I./lz4 -c -o misc/md5fa.o misc/md5fa.c gcc -Wall -g -O2 -I. -I./lz4 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -Wall -g -O2 -I. -I./lz4 -c -o misc/wgsim.o misc/wgsim.c gcc -Wall -g -O2 -I. -I./lz4 -c -o test/test.o test/test.c gcc -Wall -g -O2 -I. -I./lz4 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -Wall -g -O2 -I. -I./lz4 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -Wall -g -O2 -I. -I./lz4 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -Wall -g -O2 -I. -I./lz4 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -Wall -g -O2 -I. -I./lz4 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -Wall -g -O2 -I. -I./lz4 -c -o bamtk.o bamtk.c ar -csru libbam.a bam_aux.o bam.o sam.o bam_plbuf.o ar: `u' modifier ignored since `D' is the default (see `U') gcc -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o gcc -L./lz4 -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -L./lz4 -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -o samtools bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o ./lz4/lz4.o libbam.a libst.a -lhts -lncursesw -lm -lz -lpthread gcc -Wall -g -O2 -I. -I./lz4 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -Wall -g -O2 -I. -I./lz4 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -Wall -g -O2 -I. -I./lz4 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -L./lz4 -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread phase `build' succeeded after 19.8 seconds starting phase `check' test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip= ${TEST_OPTS:-} bgzip -c -b 65272 -s 5 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/bgzip.dat.gz .. ok bgzip -c -b 979200 -s 6 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/bgzip.dat.gz .. ok bgzip -c -b 652804 -s 6 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/bgzip.dat.gz .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools faidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/faidx.fa 3:11-13 | grep -v '^>' .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools faidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools faidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/faidx.fa 2:998-1003 | grep -v '^>' .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools faidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools faidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/faidx.fa 1:100-104 | grep -v '^>' .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools faidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools faidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools faidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fqidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/fqidx.fq 3:11-13 .. ok .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fqidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/fqidx.fq.gz 3:11-13 .. ok .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fqidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/fqidx.fq 2:998-1003 .. ok .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fqidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/fqidx.fq.gz 2:998-1003 .. ok .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fqidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/fqidx.fq 1:100-104 .. ok .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fqidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/fqidx.fq.gz 1:100-104 .. ok .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fqidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/fqidx.fq 1:99998-100007 .. ok .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fqidx /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/dict.fa .. ok test_dict: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/dict.fa.gz .. ok test_dict: cat /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/dict.fa | /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools dict -AH < /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/dict.alias.fa .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/large_chrom.bam ref2 .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/large_chrom.bam ref2:1-541556283 .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools index /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam && cat /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam.bai .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -X /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/test_input_1_b.bam.bai ref2 .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -O sam - -X -cp -R ref2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.bam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam.bai /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/test_input_1_b.bam.bai .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools index -c /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/auto_indexed.tmp.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/auto_indexed.csi && cat /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/auto_indexed.csi .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools index /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/auto_indexed.tmp.cram /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/auto_indexed.crai && cat /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/auto_indexed.crai .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools index -c /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/auto_indexed.tmp.sam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/auto_indexed.csi && cat /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/auto_indexed.csi .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -@ 2 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/large_chrom.bam ref2 .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -@ 2 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/large_chrom.bam ref2:1-541556283 .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools index -@ 2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam && cat /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam.bai .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -@ 2 -X /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/test_input_1_b.bam.bai ref2 .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -@ 2 -O sam - -X -cp -R ref2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.bam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam.bai /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/test_input_1_b.bam.bai .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools index -@ 2 -c /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/auto_indexed.tmp.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/auto_indexed.csi && cat /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/auto_indexed.csi .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools index -@ 2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/auto_indexed.tmp.cram /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/auto_indexed.crai && cat /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/auto_indexed.crai .. ok test_index: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools index -@ 2 -c /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/auto_indexed.tmp.sam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/auto_indexed.csi && cat /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/auto_indexed.csi .. ok test_mpileup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools mpileup -b /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.bam.list -f /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools mpileup -b /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.cram.list -f /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools mpileup -b /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.bam.urllist -f /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools mpileup -b /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.cram.urllist -f /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools mpileup -uvDV -b /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.bam.list -f /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools mpileup -uvDV -b /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.cram.list -f /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.cram.list -f /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.cram.list -f /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools mpileup -B --ff 0x14 -f /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.ref.fa.gz -r17:1050-1060 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools mpileup -B --ff 0x14 -f /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.ref.fa.gz -r17:1050-1060 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools mpileup /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/mpileup/overlap.bam | grep 128814202 test/test.pl: no IO::Pty module or can't open pty; skipping usage tests .. ok test_usage: samtools test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (SAM input).. ok 50: Count -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (SAM input).. ok 51: Filter -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (BAM input).. ok 52: Count -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (BAM input).. ok 53: Filter -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (CRAM input).. ok 54: Count -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (CRAM input).. ok 55: Filter -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.forn (SAM input).. ok 68: Count -N /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.forn (SAM input).. ok 69: Filter -N /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.forn (BAM input).. ok 70: Count -N /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.forn (BAM input).. ok 71: Filter -N /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.forn (CRAM input).. ok 72: Count -N /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.forn (CRAM input).. ok 73: Filter -d BC (SAM input) .. ok 74: Count -d BC (SAM input) .. ok 75: Filter -d BC (BAM input) .. ok 76: Count -d BC (BAM input) .. ok 77: Filter -d BC (CRAM input) .. ok 78: Count -d BC (CRAM input) .. ok 79: Filter -d BC:TGCA (SAM input) .. ok 80: Count -d BC:TGCA (SAM input) .. ok 81: Filter -d BC:TGCA (BAM input) .. ok 82: Count -d BC:TGCA (BAM input) .. ok 83: Filter -d BC:TGCA (CRAM input) .. ok 84: Count -d BC:TGCA (CRAM input) .. ok 85: Filter -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (SAM input).. ok 86: Count -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (SAM input).. ok 87: Filter -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (BAM input).. ok 88: Count -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (BAM input).. ok 89: Filter -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (CRAM input).. ok 90: Count -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (CRAM input).. ok 91: Filter -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (SAM input).. ok 104: Count -D RG:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (SAM input).. ok 105: Filter -D RG:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (BAM input).. ok 106: Count -D RG:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (BAM input).. ok 107: Filter -D RG:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fogn (CRAM input).. ok 109: Filter -d NE:TGCA (SAM input) .. ok 110: Count -d NE:TGCA (SAM input) .. ok 111: Filter -d NE:TGCA (BAM input) .. ok 112: Count -d NE:TGCA (BAM input) .. ok 113: Filter -d NE:TGCA (CRAM input) .. ok 114: Count -d NE:TGCA (CRAM input) .. ok 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -o /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test115.sam -h -d TGCA /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -c -d TGCA /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -o /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test117.sam -h -d TGCA /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -c -d TGCA /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -o /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test119.sam -h -d TGCA /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -c -d TGCA /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc": No such file or directory Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -o /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test121.sam -h -D BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc": No such file or directory Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -c -D BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc": No such file or directory Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -o /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test123.sam -h -D BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc": No such file or directory Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -c -D BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc": No such file or directory Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -o /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test125.sam -h -D BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc": No such file or directory Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -c -D BClong:/tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.fobc /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test006.cram --no-PG .. expected failure 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -o /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.sam --no-PG .. expected failure 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.001.sam --no-PG .. expected failure 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -o /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test001.bam --no-PG .. expected failure 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test001.bam --no-PG .. expected failure 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -o /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test006.cram --no-PG .. expected failure 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/view.test006.cram --no-PG .. expected failure 133: Filter -d NM:13 (SAM input) .. ok 134: Count -d NM:13 (SAM input) .. ok 135: Filter -d NM:13 (BAM input) .. ok 136: Count -d NM:13 (BAM input) .. ok 137: Filter -d NM:13 (CRAM input) .. ok 138: Count -d NM:13 (CRAM input) .. ok 139: Filter -d ab:z (SAM input) .. ok 140: Count -d ab:z (SAM input) .. ok 141: Filter -d ab:z (BAM input) .. ok 142: Count -d ab:z (BAM input) .. ok 143: Filter -d ab:z (CRAM input) .. ok 144: Count -d ab:z (CRAM input) .. ok 145: Filter -l Library 2 (SAM input) .. ok 146: Count -l Library 2 (SAM input) .. ok 147: Filter -l Library 2 (BAM input) .. ok 148: Count -l Library 2 (BAM input) .. ok 149: Filter -l Library 2 (CRAM input) .. ok 150: Count -l Library 2 (CRAM input) .. ok 151: Filter -l Library 3 (SAM input) .. ok 152: Count -l Library 3 (SAM input) .. ok 153: Filter -l Library 3 (BAM input) .. ok 154: Count -l Library 3 (BAM input) .. ok 155: Filter -l Library 3 (CRAM input) .. ok 156: Count -l Library 3 (CRAM input) .. ok 157: Filter -q 50 (SAM input) .. ok 158: Count -q 50 (SAM input) .. ok 159: Filter -q 50 (BAM input) .. ok 160: Count -q 50 (BAM input) .. ok 161: Filter -q 50 (CRAM input) .. ok 162: Count -q 50 (CRAM input) .. ok 163: Filter -q 99 (SAM input) .. ok 164: Count -q 99 (SAM input) .. ok 165: Filter -q 99 (BAM input) .. ok 166: Count -q 99 (BAM input) .. ok 167: Filter -q 99 (CRAM input) .. ok 168: Count -q 99 (CRAM input) .. ok 169: Filter -q 100 (SAM input) .. ok 170: Count -q 100 (SAM input) .. ok 171: Filter -q 100 (BAM input) .. ok 172: Count -q 100 (BAM input) .. ok 173: Filter -q 100 (CRAM input) .. ok 174: Count -q 100 (CRAM input) .. ok 175: Filter -x fa (SAM input) .. ok 176: Count -x fa (SAM input) .. ok 177: Filter -x fa (BAM input) .. ok 178: Count -x fa (BAM input) .. ok 179: Filter -x fa (CRAM input) .. ok 180: Count -x fa (CRAM input) .. ok 181: Filter -x fa -x ha (SAM input) .. ok 182: Count -x fa -x ha (SAM input) .. ok 183: Filter -x fa -x ha (BAM input) .. ok 184: Count -x fa -x ha (BAM input) .. ok 185: Filter -x fa -x ha (CRAM input) .. ok 186: Count -x fa -x ha (CRAM input) .. ok 187: Filter -x fa -r grp2 (SAM input) .. ok 188: Count -x fa -r grp2 (SAM input) .. ok 189: Filter -x fa -r grp2 (BAM input) .. ok 190: Count -x fa -r grp2 (BAM input) .. ok 191: Filter -x fa -r grp2 (CRAM input) .. ok 192: Count -x fa -r grp2 (CRAM input) .. ok 193: Filter -x RG -r grp2 (SAM input) .. ok 194: Count -x RG -r grp2 (SAM input) .. ok 195: Filter -x RG -r grp2 (BAM input) .. ok 196: Count -x RG -r grp2 (BAM input) .. ok 197: Filter -x RG -r grp2 (CRAM input) .. ok 198: Count -x RG -r grp2 (CRAM input) .. ok 199: Filter -m 10 (SAM input) .. ok 200: Count -m 10 (SAM input) .. ok 201: Filter -m 10 (BAM input) .. ok 202: Count -m 10 (BAM input) .. ok 203: Filter -m 10 (CRAM input) .. ok 204: Count -m 10 (CRAM input) .. ok 205: Filter -m 11 (SAM input) .. ok 206: Count -m 11 (SAM input) .. ok 207: Filter -m 11 (BAM input) .. ok 208: Count -m 11 (BAM input) .. ok 209: Filter -m 11 (CRAM input) .. ok 210: Count -m 11 (CRAM input) .. ok 211: Filter -m 15 (SAM input) .. ok 212: Count -m 15 (SAM input) .. ok 213: Filter -m 15 (BAM input) .. ok 214: Count -m 15 (BAM input) .. ok 215: Filter -m 15 (CRAM input) .. ok 216: Count -m 15 (CRAM input) .. ok 217: Filter -m 16 (SAM input) .. ok 218: Count -m 16 (SAM input) .. ok 219: Filter -m 16 (BAM input) .. ok 220: Count -m 16 (BAM input) .. ok 221: Filter -m 16 (CRAM input) .. ok 222: Count -m 16 (CRAM input) .. ok 223: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 224: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 225: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 226: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 227: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 228: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 229: Filter -e [BC] (SAM input) .. ok 230: Count -e [BC] (SAM input) .. ok 231: Filter -e [BC] (BAM input) .. ok 232: Count -e [BC] (BAM input) .. ok 233: Filter -e [BC] (CRAM input) .. ok 234: Count -e [BC] (CRAM input) .. ok 235: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 236: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 237: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 238: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 239: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 240: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 241: Filter -e mapq >= 50 (SAM input) .. ok 242: Count -e mapq >= 50 (SAM input) .. ok 243: Filter -e mapq >= 50 (BAM input) .. ok 244: Count -e mapq >= 50 (BAM input) .. ok 245: Filter -e mapq >= 50 (CRAM input) .. ok 246: Count -e mapq >= 50 (CRAM input) .. ok 247: Filter -e mapq >= 99 (SAM input) .. ok 248: Count -e mapq >= 99 (SAM input) .. ok 249: Filter -e mapq >= 99 (BAM input) .. ok 250: Count -e mapq >= 99 (BAM input) .. ok 251: Filter -e mapq >= 99 (CRAM input) .. ok 252: Count -e mapq >= 99 (CRAM input) .. ok 253: Filter -e mapq >= 100 (SAM input) .. ok 254: Count -e mapq >= 100 (SAM input) .. ok 255: Filter -e mapq >= 100 (BAM input) .. ok 256: Count -e mapq >= 100 (BAM input) .. ok 257: Filter -e mapq >= 100 (CRAM input) .. ok 258: Count -e mapq >= 100 (CRAM input) .. ok 259: 1bp reads file SAM -> BAM -> SAM .. ok 260: 1bp reads file SAM -> CRAM -> SAM .. ok 260: Region Z (BAM input) .. ok 261: Count Z (BAM input) .. ok 262: Region Z (CRAM input) .. ok 263: Count Z (CRAM input) .. ok 264: Region Z:30 (BAM input) .. ok 265: Count Z:30 (BAM input) .. ok 266: Region Z:30 (CRAM input) .. ok 267: Count Z:30 (CRAM input) .. ok 268: Region Z:20-40 (BAM input) .. ok 269: Count Z:20-40 (BAM input) .. ok 270: Region Z:20-40 (CRAM input) .. ok 271: Count Z:20-40 (CRAM input) .. ok 272: Region ref1 (BAM input) .. ok 273: Count ref1 (BAM input) .. ok 274: Region ref1 (CRAM input) .. ok 275: Count ref1 (CRAM input) .. ok 276: Region ref1:15 (BAM input) .. ok 277: Count ref1:15 (BAM input) .. ok 278: Region ref1:15 (CRAM input) .. ok 279: Count ref1:15 (CRAM input) .. ok 280: Region ref1:15-45 (BAM input) .. ok 281: Count ref1:15-45 (BAM input) .. ok 282: Region ref1:15-45 (CRAM input) .. ok 283: Count ref1:15-45 (CRAM input) .. ok 284: Region ref1:15-45 ref2 (BAM input) .. ok 285: Count ref1:15-45 ref2 (BAM input) .. ok 286: Region ref1:15-45 ref2 (CRAM input) .. ok 287: Count ref1:15-45 ref2 (CRAM input) .. ok 288: Region ref1:15-45 ref2:16 (BAM input) .. ok 289: Count ref1:15-45 ref2:16 (BAM input) .. ok 290: Region ref1:15-45 ref2:16 (CRAM input) .. ok 291: Count ref1:15-45 ref2:16 (CRAM input) .. ok 292: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 293: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 294: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 295: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 296: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 297: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 298: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 299: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 300: Region -f 128 ref1 (BAM input) .. ok 301: Count -f 128 ref1 (BAM input) .. ok 302: Region -f 128 ref1 (CRAM input) .. ok 303: Count -f 128 ref1 (CRAM input) .. ok 304: Region -q 50 ref1:15-45 (BAM input) .. ok 305: Count -q 50 ref1:15-45 (BAM input) .. ok 306: Region -q 50 ref1:15-45 (CRAM input) .. ok 307: Count -q 50 ref1:15-45 (CRAM input) .. ok 308: Region -r grp2 ref1:15-45 (BAM input) .. ok 309: Count -r grp2 ref1:15-45 (BAM input) .. ok 310: Region -r grp2 ref1:15-45 (CRAM input) .. ok 311: Count -r grp2 ref1:15-45 (CRAM input) .. ok 312: Region * (BAM input) .. ok 313: Count * (BAM input) .. ok 314: Region * (CRAM input) .. ok 315: Count * (CRAM input) .. ok 316: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed (BAM input).. ok 317: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed (BAM input).. ok 318: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed (CRAM input).. ok 319: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed (CRAM input).. ok 320: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.02.bed (BAM input).. ok 321: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.02.bed (BAM input).. ok 322: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.02.bed (CRAM input).. ok 323: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.02.bed (CRAM input).. ok 324: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed (BAM input).. ok 325: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed (BAM input).. ok 326: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed (CRAM input).. ok 327: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed (CRAM input).. ok 328: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.02.bed (BAM input).. ok 329: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.02.bed (BAM input).. ok 330: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.02.bed (CRAM input).. ok 331: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.02.bed (CRAM input).. ok 332: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z (BAM input).. ok 333: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z (BAM input).. ok 334: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z (CRAM input).. ok 335: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z (CRAM input).. ok 336: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z:30 (BAM input).. ok 337: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z:30 (BAM input).. ok 338: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 339: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 340: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 341: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 342: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 343: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 344: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 345: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 346: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 347: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 348: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 349: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 350: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 351: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 352: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed ref2 (BAM input).. ok 353: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed ref2 (BAM input).. ok 354: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed ref2 (CRAM input).. ok 355: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed ref2 (CRAM input).. ok 356: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 357: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 358: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 359: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 360: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 361: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 362: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 363: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 364: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -f 128 (BAM input).. ok 365: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -f 128 (BAM input).. ok 366: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 367: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 368: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -q 5 (BAM input).. ok 369: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -q 5 (BAM input).. ok 370: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 371: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 372: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 373: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 374: Region -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 375: Count -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 376: Make BAM with no M5/UR tags .. ok 377: Add @SQ with -t (SAM -> SAM) .. ok 378: Add @SQ with -T (SAM -> SAM) .. ok 379: Add @SQ with -t (BAM -> SAM) .. ok 380: Add @SQ with -T (BAM -> SAM) .. ok 381: Add @SQ with -t (SAM -> BAM) .. ok 382: Add @SQ with -T (SAM -> BAM) .. ok 383: Add @SQ with -t (BAM -> BAM) .. ok 384: Add @SQ with -T (BAM -> BAM) .. ok 385: Add @SQ with -t (SAM -> CRAM) .. ok 386: Add @SQ with -T (SAM -> CRAM) .. ok 387: Add @SQ with -t (BAM -> CRAM) .. ok 388: Add @SQ with -T (BAM -> CRAM) .. ok 389: Make CRAM with no UR field .. ok 390: Decoding CRAM with no UR field via -T .. ok 391: CIGAR B-operator removal .. ok 392: Big SAM -> BAM .. ok 393: Big SAM -> BAM (2 threads) .. ok 394: Big SAM -> BAM (4 threads) .. ok 395: Big SAM -> CRAM .. ok 396: Big SAM -> CRAM (2 threads) .. ok 397: Big SAM -> CRAM (4 threads) .. ok 398: Subsample 0.2 (SAM input) ............ ok 399: Subsample 0.5 (SAM input) ............ ok 400: Subsample 0.8 (SAM input) ............ ok 401: Subsample 0.2 (BAM input) ............ ok 402: Subsample 0.5 (BAM input) ............ ok 403: Subsample 0.8 (BAM input) ............ ok 404: Subsample 0.2 (CRAM input) ............ ok 405: Subsample 0.5 (CRAM input) ............ ok 406: Subsample 0.8 (CRAM input) ............ ok 407: SAM add PG .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_bam2fq: Generate BAM file .. ok Generate CRAM file .. ok 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.001.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.001.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.002.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.003.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bc.fq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.004.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bc.fq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.004.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bc.fq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.010.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bc_split.fq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.005.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -N -t -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.005.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -N -t -T MD,ia -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.005.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/i.fq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.004.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/i.fq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.005.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -i --index-format 'i*i*' -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.005.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.703.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -N -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/o.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/o.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.001.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -N -o /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/o.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.001.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -N -s /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/bam2fq.discard.s.fq -0 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/bam2fq.discard.0.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.001.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -T ba,bb,bc,bd,be,bf,bg /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.013.sam .. ok test_bam2fq: Generate BAM file (2 threads) .. ok Generate CRAM file (2 threads) .. ok 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.001.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.001.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.002.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.003.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bc.fq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.004.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bc.fq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.004.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bc.fq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.010.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bc_split.fq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.005.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 -N -t -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.005.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 -N -t -T MD,ia -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.005.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/i.fq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.004.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/i.fq -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.005.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 -i --index-format 'i*i*' -s /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/s.fq -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.005.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/1.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/2.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.703.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 -N -1 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/o.fq -2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/o.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.001.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 -N -o /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/o.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.001.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 -N -s /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/bam2fq.discard.s.fq -0 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/bam2fq.discard.0.fq /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.001.sam .. ok test_bam2fq: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/bam2fq.013.sam .. ok test_depad: Generate BAM file .. ok depad (SAM input) .. ok depad -s (SAM input) .. ok depad -u (SAM input) .. ok depad -1 (SAM input) .. ok depad (BAM input) .. ok depad -s (BAM input) .. ok depad -u (BAM input) .. ok depad -1 (BAM input) .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats -r /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/test.fa /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats -r /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/test.fa /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats -r /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/test.fa /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats -r /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/test.fa /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats -r /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/test.fa /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats -r /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/test.fa -i 0 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats -r /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/test.fa /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats -r /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/test.fa /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats -S RG -r /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/test.fa /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats -S RG -r /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/test.fa /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats -t /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/11.stats.targets /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats -g 4 -t /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/11.stats.targets /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats -g 4 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/12_overlaps.bam -t /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/12_overlaps.bam -p -t /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/12_overlaps.bam -t /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/12_overlaps.bam -p -t /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools stats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -s 1 -O sam - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_c.sam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -s 1 -O sam - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.bam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_c.bam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -s 1 -O sam -b /tmp/guix-build-samtools-1.12.drv-0/6GiYzNaD7M - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -s 1 -O sam - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.bam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -r -s 1 -O sam - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_c.sam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -cp -s 1 -O sam - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.sam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -s 1 -O sam - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a_regex.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b_regex.sam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/merge.tag.1.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/merge.tag.2.bam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/merge.tag.3.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/merge.tag.4.bam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge --no-PG -O SAM - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge --no-PG -O SAM -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/merge/merge.bed - /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/merge.bed.1.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/merge.bed.2.bam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -@ 2 -s 1 -O sam - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_c.sam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -@ 2 -s 1 -O sam - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.bam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_c.bam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -@ 2 -s 1 -O sam -b /tmp/guix-build-samtools-1.12.drv-0/blteToso5e - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -@ 2 -s 1 -O sam - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.bam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -@ 2 -r -s 1 -O sam - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_c.sam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -@ 2 -cp -s 1 -O sam - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b.sam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -@ 2 -s 1 -O sam - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a_regex.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_b_regex.sam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/merge.tag.1.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/merge.tag.2.bam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/merge.tag.3.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/merge.tag.4.bam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -@ 2 --no-PG -O SAM - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -@ 2 --no-PG -O SAM -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/merge/merge.bed - /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/merge.bed.1.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/merge.bed.2.bam .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/sortout .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -f /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/sortout.bam .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -o /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/sorttmp .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -m 10M /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -n -m 10M /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -t RG -m 10M /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -n -t RG -m 10M /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -t AS -m 10M /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -t FI -m 10M /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -@ 2 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/sortout .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -@ 2 -f /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/sortout.bam .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -@ 2 -o /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/sorttmp .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -@ 2 -m 10M /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -@ 2 -n -m 10M /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -@ 2 -t RG -m 10M /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -@ 2 -n -t RG -m 10M /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -@ 2 -t AS -m 10M /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -@ 2 -t FI -m 10M /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_collate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools collate --output-fmt=sam -O /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_d.sam .. ok test_collate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools collate -o /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/collate1.tmp.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_d.sam .. ok test_collate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools collate -o /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/collate2.tmp.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_d.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/collate2.tmp .. ok test_collate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools collate --output-fmt=sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_d.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/collate3.tmp .. ok test_collate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools collate --output-fmt=sam -f /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/fast_collate.sam -o /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/1_fast_collate.sam .. ok test_collate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools collate --output-fmt=sam -f -r 4 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/fast_collate.sam -o /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools collate -@ 2 --output-fmt=sam -O /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_d.sam .. ok test_collate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools collate -@ 2 -o /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/collate1.tmp.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_d.sam .. ok test_collate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools collate -@ 2 -o /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/collate2.tmp.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_d.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/collate2.tmp .. ok test_collate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools collate -@ 2 --output-fmt=sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_d.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/collate3.tmp .. ok test_collate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools collate -@ 2 --output-fmt=sam -f /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/fast_collate.sam -o /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/1_fast_collate.sam .. ok test_collate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools collate -@ 2 --output-fmt=sam -f -r 4 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/fast_collate.sam -o /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -O sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -O sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -O sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -O sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -cO sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/5_ct.sam - .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -cO sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -O sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -O sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -@ 2 -O sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -@ 2 -O sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -@ 2 -O sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -@ 2 -O sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -@ 2 -cO sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/5_ct.sam - .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -@ 2 -cO sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -@ 2 -O sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -@ 2 -O sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/fixmate/8_isize_overflow_64bit.sam - .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools calmd -uAr /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/mpileup.1.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/mpileup.ref.fa .. ok /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools calmd -@ 2 -uAr /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/mpileup.1.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/mpileup.ref.fa .. ok test_idxstat: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools idxstats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.bam .. ok test_idxstat: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools idxstats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.cram .. ok test_idxstat: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools idxstats /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/test_input_1_a.sam .. ok test_quickcheck: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools quickcheck /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools quickcheck /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools quickcheck /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools quickcheck /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools quickcheck /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools quickcheck /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools quickcheck /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools quickcheck /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools quickcheck /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools quickcheck /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools quickcheck -v /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/1.quickcheck.badeof.bam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/2.quickcheck.badheader.bam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/3.quickcheck.ok.bam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/4.quickcheck.ok.bam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/5.quickcheck.scramble30.truncated.cram /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/6.quickcheck.cram21.ok.cram /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/7.quickcheck.cram30.ok.cram /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/8.quickcheck.cram21.truncated.cram /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/9.quickcheck.cram30.truncated.cram /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools quickcheck -uv /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools reheader /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/reheader/hdr.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.tmp.bam | /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools reheader /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/reheader/hdr.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.tmp.v21.cram | /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools reheader /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/reheader/hdr.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.tmp.v30.cram | /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools reheader --in-place /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/reheader/hdr.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.tmp.v21.cram && /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -h --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools reheader --in-place /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/reheader/hdr.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.tmp.v30.cram && /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -h --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.tmp.bam | /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/dat/view.001.tmp.v30.cram | /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools addreplacerg -O sam -m overwrite_all /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/addrprg/1_fixup.sam .. ok test_addrprg: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools addreplacerg -O sam -m orphan_only /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools addreplacerg -O sam -R '1#9' /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/addrprg/1_fixup.sam .. ok test_addrprg: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/addrprg/1_fixup.sam .. ok test_addrprg: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools addreplacerg -@ 2 -O sam -m overwrite_all /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/addrprg/1_fixup.sam .. ok test_addrprg: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools addreplacerg -@ 2 -O sam -m orphan_only /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools addreplacerg -@ 2 -O sam -R '1#9' /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/addrprg/1_fixup.sam .. ok test_addrprg: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/addrprg/1_fixup.sam .. ok test_addrprg: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/addrprg/4_fixup_norg.sam .. ok test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/5_markdup.sam - .. ok test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -O sam -r --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/6_remove_dups.sam - .. ok test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -S -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/8_optical_dup.sam - .. ok test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -@ 2 -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -@ 2 -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -@ 2 -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -@ 2 -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -@ 2 -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/5_markdup.sam - .. ok test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -@ 2 -O sam -r --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/6_remove_dups.sam - .. ok test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -@ 2 -S -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/8_optical_dup.sam - .. ok test_markdup: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/markdup/9_optical_dup_qcfail.sam - .. ok test_bedcov: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools bedcov /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bedcov/bedcov.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bedcov/bedcov.bam .. ok test_bedcov: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools bedcov -j /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bedcov/bedcov.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bedcov/bedcov.bam .. ok test_bedcov: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools bedcov -g512 -G2048 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bedcov/bedcov_gG.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/bedcov/bedcov.bam .. ok test_split: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools split --output-fmt sam -u /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/split/split.tmp.unk.sam -f /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/split/split.tmp.%!.%. /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/split/split.sam .. ok test_split: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools split -@ 2 --output-fmt sam -u /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/split/split.tmp.unk.sam -f /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/split/split.tmp.%!.%. /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/split/split.sam .. ok test_large_positions: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -h --no-PG /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/longref.sam.gz .. ok test_large_positions: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -h --no-PG /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools view -h --no-PG -L /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/large_pos/test.bed /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/longref.sam.gz .. ok test_large_positions: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -O sam --no-PG -m 10M /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/large_pos/longref_name.sam .. ok test_large_positions: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools merge -O sam --no-PG - /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/large_pos/longref.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/large_pos/longref2.sam .. ok test_large_positions: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools depth /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/large_pos/longref.sam .. ok test_large_positions: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools depth -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/large_pos/test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/large_pos/longref.sam .. ok test_large_positions: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/guix-build-samtools-1.12.drv-0/RNgR7B8tdT/longref.sam.gz .. ok test_large_positions: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools fixmate -O sam --no-PG - - | /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip --no-PG --output-fmt=sam -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconstats: /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/samtools ampliconstats -@ 2 -t 50 -d 1,20,100 /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/ac_test.bed /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_hard_clipped.expected.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_soft_clipped.expected.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/1_soft_clipped_strand.expected.sam /tmp/guix-build-samtools-1.12.drv-0/samtools-1.12/test/ampliconclip/2_both_clipped.expected.sam | egrep -v 'Samtools version|Command line' .. ok Number of tests: total .. 727 passed .. 696 failed .. 0 expected failure .. 31 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="gawk" ./regression.sh mpileup.reg === Testing mpileup.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 163 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="gawk" ./regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 47 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS phase `check' succeeded after 86.3 seconds starting phase `install' mkdir -p -m 755 /gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12/bin /gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12/bin /gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12/share/man/man1 install -p samtools /gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12/bin install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12/share/man/man1 phase `install' succeeded after 0.1 seconds starting phase `install-headers' phase `install-headers' succeeded after 0.0 seconds starting phase `install-library' phase `install-library' succeeded after 0.0 seconds starting phase `patch-shebangs' phase `patch-shebangs' succeeded after 0.0 seconds starting phase `strip' stripping binaries in "/gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12/lib" with "strip" and flags ("--strip-unneeded" "--enable-deterministic-archives") stripping binaries in "/gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12/bin" with "strip" and flags ("--strip-unneeded" "--enable-deterministic-archives") phase `strip' succeeded after 0.1 seconds starting phase `validate-runpath' validating RUNPATH of 0 binaries in "/gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12/lib"... validating RUNPATH of 7 binaries in "/gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12/bin"... phase `validate-runpath' succeeded after 0.0 seconds starting phase `validate-documentation-location' phase `validate-documentation-location' succeeded after 0.0 seconds starting phase `delete-info-dir-file' phase `delete-info-dir-file' succeeded after 0.0 seconds starting phase `patch-dot-desktop-files' phase `patch-dot-desktop-files' succeeded after 0.0 seconds starting phase `make-dynamic-linker-cache' created '/gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12/etc/ld.so.cache' from 19 library search path entries phase `make-dynamic-linker-cache' succeeded after 0.3 seconds starting phase `install-license-files' installing 1 license files from '.' phase `install-license-files' succeeded after 0.0 seconds starting phase `reset-gzip-timestamps' phase `reset-gzip-timestamps' succeeded after 0.0 seconds starting phase `compress-documentation' compressing documentation in '/gnu/store/g9zw99j774r3kdv6xhpgapv0c3i52hwl-samtools-1.12/share/man' with "gzip" and flags ("--best" "--no-name") phase `compress-documentation' succeeded after 0.0 seconds