Source: pbbam Version: 0.18.0+dfsg-1 X-Debbugs-CC: debian...@lists.debian.org User: debian...@lists.debian.org Usertags: regression
Dear maintainers, With a recent upload of pbbam the autopkgtest of pbbam fails in testing when that autopkgtest is run with the binary packages of pbbam from unstable. It passes when run with only packages from testing. I copied some of the output at the bottom of this report. Currently this regression is contributing to the delay of the migration to testing [1]. Can you please investigate the situation and fix it? If needed, please change the bug's severity. More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation Paul [1] https://qa.debian.org/excuses.php?package=pbbam https://ci.debian.net/data/autopkgtest/testing/amd64/p/pbbam/954327/log.gz tests/src/cram/pbbamify.deb.t: failed --- tests/src/cram/pbbamify.deb.t +++ tests/src/cram/pbbamify.deb.t.err @@ -90,42 +90,12 @@ Test on a dataset, input contains alignments from all subread sets. $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-all.bam $DATADIR/pbbamify/synthetic-ref-1.fa | samtools view -h - [Warning] No records found for query 'synthetic_movie_1/10/0_100'. Skipping. - [Warning] Sequence 'synthetic_movie_1/1/0_100' (length 90) is not of the same length as the PacBio BAM sequence (length 100)! Skipping. - [Warning] Found 1 alignments without a seq field which were not converted (most likely secondary alignments). - [INFO] Done processing 25 alignments in 0 min. - @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc) - @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc) - @RG\tID:67e06f58\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=100-862-200;SEQUENCINGKIT=101-093-700;BASECALLERVERSION=5.0.0.5049;FRAMERATEHZ=80.000000\tPU:synthetic_movie_3\tPM:SEQUEL (esc) - @RG\tID:7a515ee0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_2\tPM:SEQUEL (esc) - @RG\tID:8d2370c0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_1\tPM:SEQUEL (esc) - @PG\tID:Handmade\tPN:Handmade (esc) - @PG\tID:baz2bam\tPN:baz2bam\tVN:5.0.0.5552\tCL:/opt/pacbio/ppa-5.0.0/bin/baz2bam /data/pb/synthetic_movie_1.baz -o /data/pb/synthetic_movie_1 --metadata /data/pb/.synthetic_movie_1.metadata.xml -j 12 -b 12 --progress --silent --minSubLength 50 --minSnr 3.750000 --adapters /data/pb/synthetic_movie_1.adapters.fasta (esc) - @PG\tID:bazFormat\tPN:bazformat\tVN:1.3.0 (esc) - @PG\tID:bazwriter\tPN:bazwriter\tVN:5.0.0.5552 (esc) - @PG\tID:ccs-3.0.0\tPN:ccs\tVN:3.0.0\tDS:Generate circular consensus sequences (ccs) from subreads.\tCL:ccs (esc) - synthetic_movie_1/1/0_100\t0\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t254\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tZE:f:1\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/2/0_101\t0\tsynthetic_ref_1\t23\t60\t8=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I7=\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t23\t60\t8=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I7=\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/3/0_100\t4\t*\t0\t255\t*\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:3\tRG:Z:8d2370c0 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t30\t60\t8S1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I1=6S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_2/1000001/0_100\t16\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000001/0_100\t272\tsynthetic_ref_1\t23\t254\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000001/0_100\t272\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tZE:f:1\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000001/0_100\t272\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000001/0_100\t272\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000002/0_101\t16\tsynthetic_ref_1\t23\t60\t8=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I7=\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000002 (esc) - 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synthetic_movie_2/1000002/0_101\t272\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000002 (esc) - synthetic_movie_2/1000002/0_101\t272\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000002 (esc) - synthetic_movie_3/3000001/ccs\t0\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tRG:Z:67e06f58\tnp:i:6\trq:f:0.993687\trs:B:i,8,1,0,0,0,0\tsn:B:f,6.21632,11.7596,4.35394,8.45458\tza:f:nan\tzm:i:3000001\tzs:B:f,nan,nan,nan,nan,nan,nan,-inf,nan,nan (esc) + + ERROR: Exactly two positional arguments must be specified. + + [W::sam_read1] Parse error at line 1 + [main_samview] truncated file. + [1] No-args: tests/src/cram/pbmerge_dataset.deb.t: passed # Ran 8 tests, 0 skipped, 1 failed. make: *** [debian/rules:33: override_dh_auto_test] Error 1 autopkgtest [17:59:53]: test command1: -----------------------] autopkgtest [17:59:53]: test command1: - - - - - - - - - - results - - - - - - - - - - command1 FAIL non-zero exit status 2 autopkgtest [17:59:54]: test command1: - - - - - - - - - - stderr - - - - - - - - - - dirname: missing operand Try 'dirname --help' for more information. make: *** [debian/rules:33: override_dh_auto_test] Error 1
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