Comments (4)
mmterpstra
commented on July 22, 2024
1
After some additional analysises It seems to happen at about ~114 times the minus strand and the plus strand is differently affected by reporting ambiguous alignments that are not likely to change the mapping position:
$ diff <(bedtools bamtobed -i <(samtools view -Su .../bedtrimmed.tmp.sam) | perl -wpe 'BEGIN{our @slast;}; my @s=split("\t",$_); $_ = "" if(defined($s[0]) && defined($s[5]) && $s[0] eq $slast[0] && $s[1] == $slast[1] && $s[2] == $slast[2] && $s[3] eq $slast[3] && $s[5] eq $slast[5] );@slast=@s;') <(bedtools bamtobed -i <(samtools view -Su .../.bedtrimmed.tmp.sam))
Use of uninitialized value in string eq at -e line 1, <> line 1.
10300a10301
> 12 6646172 6646382 M01997:246:000000000-ANBW6_NNNNNN:1:2103:14983:7946 0 -
21169a21171
> 1 115256594 115258758 M01997:246:000000000-ANBW6_NNNNNN:1:2103:27010:12001 0 -
25317a25320
> 19 3054191 3057701 M01997:246:000000000-ANBW6_NNNNNN:1:2103:14433:13500 1 -
27721a27725
> 8 128751256 128752737 M01997:246:000000000-ANBW6_NNNNNN:1:2103:6939:14355 0 -
31295a31300
> 19 3054191 3057700 M01997:246:000000000-ANBW6_NNNNNN:1:2103:20841:15645 1 -
73194a73200
> 12 6646170 6646369 M01997:246:000000000-ANBW6_NNNNNN:1:2104:12265:9450 0 -
88170a88177
> 12 6646173 6646494 M01997:246:000000000-ANBW6_NNNNNN:1:2104:14486:14331 1 -
95448a95456
> 19 3054191 3057701 M01997:246:000000000-ANBW6_NNNNNN:1:2104:14377:16768 1 -
96240a96249
> 12 6646121 6647271 M01997:246:000000000-ANBW6_NNNNNN:1:2104:10838:17029 1 -
136005a136015
> 5 162864619 162866322 M01997:246:000000000-ANBW6_NNNNNN:1:2102:21327:8746 1 +
151528a151539
> 12 6645755 6646107 M01997:246:000000000-ANBW6_NNNNNN:1:2102:16911:14081 1 -
153412a153424
> 12 6644001 6646281 M01997:246:000000000-ANBW6_NNNNNN:1:2102:12756:14688 1 -
190371a190384
> 6 159205758 159206470 M01997:246:000000000-ANBW6_NNNNNN:1:2109:12416:5647 1 -
198723a198737
> 8 128748805 128750538 M01997:246:000000000-ANBW6_NNNNNN:1:2109:14697:8958 0 -
201794a201809
> 12 6646169 6646382 M01997:246:000000000-ANBW6_NNNNNN:1:2109:11829:10017 1 -
208993a209009
> 8 128751256 128752737 M01997:246:000000000-ANBW6_NNNNNN:1:2109:17006:12473 0 -
209062a209079
> 9 18123 18480 M01997:246:000000000-ANBW6_NNNNNN:1:2109:15663:12493 1 -
279590a279608
> 6 159210402 159239255 M01997:246:000000000-ANBW6_NNNNNN:1:1105:17107:14323 1 -
288379a288398
> 6 159190975 159192290 M01997:246:000000000-ANBW6_NNNNNN:1:1105:12336:16878 1 -
296722a296742
> 12 6645756 6646116 M01997:246:000000000-ANBW6_NNNNNN:1:1105:15230:19305 1 -
298072a298093
> 12 6645751 6646097 M01997:246:000000000-ANBW6_NNNNNN:1:1105:6804:19716 0 -
310947a310969
> 12 6646170 6646369 M01997:246:000000000-ANBW6_NNNNNN:1:1105:7034:24285 0 -
330873a330896
> 19 17973834 17974120 M01997:246:000000000-ANBW6_NNNNNN:1:1106:7533:8101 1 -
352296a352320
> 12 6646123 6647270 M01997:246:000000000-ANBW6_NNNNNN:1:1106:12968:14734 1 -
365448a365473
> 6 159190973 159191927 M01997:246:000000000-ANBW6_NNNNNN:1:1106:12025:18574 1 -
389720a389746
> 12 6646121 6647271 M01997:246:000000000-ANBW6_NNNNNN:1:1106:15457:28176 1 -
403088a403115
> 12 6646121 6647270 M01997:246:000000000-ANBW6_NNNNNN:1:1103:19825:8096 1 -
430253a430281
> 8 38275850 38277160 M01997:246:000000000-ANBW6_NNNNNN:1:1103:10363:16310 1 -
435834a435863
> 8 38275861 38277171 M01997:246:000000000-ANBW6_NNNNNN:1:1103:10772:17907 1 -
439020a439050
> 12 6646121 6647272 M01997:246:000000000-ANBW6_NNNNNN:1:1103:19412:18859 1 -
443529a443560
> 8 38275748 38277058 M01997:246:000000000-ANBW6_NNNNNN:1:1103:9010:20235 1 -
449287a449319
> 12 6646170 6646363 M01997:246:000000000-ANBW6_NNNNNN:1:1103:11030:22069 0 -
451497a451530
> 8 38275855 38277165 M01997:246:000000000-ANBW6_NNNNNN:1:1103:8364:22845 1 +
459836a459870
> 8 38275819 38277129 M01997:246:000000000-ANBW6_NNNNNN:1:1103:13649:26433 1 +
$## Actual SAM records here: ##############
$ grep -P 'M01997:246:000000000-ANBW6_NNNNNN:1:2102:21327:8746|M01997:246:000000000-ANBW6_NNNNNN:1:1103:8364:22845|M01997:246:000000000-ANBW6_NNNNNN:1:1103:13649:26433|M01997:246:000000000-ANBW6_NNNNNN:1:1104:12331:8208' -n --color=always /path/to/SAMPLE-2_S2_L001_R1_001.fq.gz.bedtrimmed.tmp.sam
141800:M01997:246:000000000-ANBW6_NNNNNN:1:2102:21327:8746 0 5 162864620 1 52M100N39M1452N60M * 0 0 CCCTGATCAGGGCCGAGTTGTCTCGGCGGCGCTGCCGAGGCCTCCACCCGGGGAGGGTGGTTACCGCTGAGGAGCTGCAGTCTCTGTCAAGATGATAGAGGTACTGACAACAACTGACTCTCAGAAACTGCTACACCAGCTGAATGCCCTG AA1A?BFFFD111EECEGFDE1A3B0AE??AEEEEFGGGCGG1B/>BEECCGGE???</B/FGFBC/CCCHGFCGFH1F1F1<FGF?FH1F1FF1FH1FHHGC1GHGFFGGG.CCGFHHBGFB::0;/CCFHFHCCGHHAGG0FGGB0CFF AS:i:-5 ZS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:49A101 YT:Z:UU XS:A:+ NH:i:2
141801:M01997:246:000000000-ANBW6_NNNNNN:1:2102:21327:8746 256 5 162864620 1 51M100N40M1452N60M * 0 0 CCCTGATCAGGGCCGAGTTGTCTCGGCGGCGCTGCCGAGGCCTCCACCCGGGGAGGGTGGTTACCGCTGAGGAGCTGCAGTCTCTGTCAAGATGATAGAGGTACTGACAACAACTGACTCTCAGAAACTGCTACACCAGCTGAATGCCCTG AA1A?BFFFD111EECEGFDE1A3B0AE??AEEEEFGGGCGG1B/>BEECCGGE???</B/FGFBC/CCCHGFCGFH1F1F1<FGF?FH1F1FF1FH1FHHGC1GHGFFGGG.CCGFHHBGFB::0;/CCFHFHCCGHHAGG0FGGB0CFF AS:i:-5 ZS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:49A101 YT:Z:UU XS:A:+ NH:i:2
471175:M01997:246:000000000-ANBW6_NNNNNN:1:1103:8364:22845 0 8 38275856 1 35M1159N116M * 0 0 CCCAGAGTTCATGGATGCACTGGAGTCAGCAGACACTGTTACCTGTCTGCGCAGAGGGATGCTCTTGGCCAGCTTGTGCACAGCCATCTGGCTGTGGAAGTCACTCTTCTTGGTACCACTCTTCATCTTGTAGACGATGACCGACCCCACC BBBBBBBDFFFBGCFFBFGGGGHHHHHHFHHHHFHHHGHGHHGHHHHHHGGCEGFHEFGF1FFGHHFHHHHHGHHHHBEFGGFFHGHHHGBHHFFGFHHFFHHFHHGHHHHHFFHHHBHHHHHFDGHHHFHHGHFGCFAGFH@BCGGGGGD AS:i:0 ZS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:151 YT:Z:UU NH:i:2
471176:M01997:246:000000000-ANBW6_NNNNNN:1:1103:8364:22845 256 8 38275856 1 36M1159N115M * 0 0 CCCAGAGTTCATGGATGCACTGGAGTCAGCAGACACTGTTACCTGTCTGCGCAGAGGGATGCTCTTGGCCAGCTTGTGCACAGCCATCTGGCTGTGGAAGTCACTCTTCTTGGTACCACTCTTCATCTTGTAGACGATGACCGACCCCACC BBBBBBBDFFFBGCFFBFGGGGHHHHHHFHHHHFHHHGHGHHGHHHHHHGGCEGFHEFGF1FFGHHFHHHHHGHHHHBEFGGFFHGHHHGBHHFFGFHHFFHHFHHGHHHHHFFHHHBHHHHHFDGHHHFHHGHFGCFAGFH@BCGGGGGD AS:i:0 ZS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:151 YT:Z:UU NH:i:2
479872:M01997:246:000000000-ANBW6_NNNNNN:1:1103:13649:26433 0 8 38275820 1 72M1159N79M * 0 0 CCTGGAGGAGAGCCGTGATGGTCGAACCAGAAGAACCCCAGAGTTCATGGATGCACTGGAGTCGGCAGACACTGTTACCTGTCTGCGCAGAGGGATGCTCTTGGCCAGCTTGTGCACAGCCATCTGGCTGTGGAAGTCACTCTTCTTGGTA AA1A?F1?AA1AGGGE0FGFFGBEEGG?CFFFHFHGHEGEGAGHHHH2AFHB1BGGBGHBA1FA/E/EFCGGGEEFFGFFBBFFGHC/ECE/C/?0>GB1G1E1GFGECCGFFG1>FGGHHGFH1F1GHFGGFGEGFFDHHGHHFFFHG1D AS:i:-15 ZS:i:-15 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:0A20C41A87 YT:Z:UU NH:i:2
479873:M01997:246:000000000-ANBW6_NNNNNN:1:1103:13649:26433 256 8 38275820 1 71M1159N80M * 0 0 CCTGGAGGAGAGCCGTGATGGTCGAACCAGAAGAACCCCAGAGTTCATGGATGCACTGGAGTCGGCAGACACTGTTACCTGTCTGCGCAGAGGGATGCTCTTGGCCAGCTTGTGCACAGCCATCTGGCTGTGGAAGTCACTCTTCTTGGTA AA1A?F1?AA1AGGGE0FGFFGBEEGG?CFFFHFHGHEGEGAGHHHH2AFHB1BGGBGHBA1FA/E/EFCGGGEEFFGFFBBFFGHC/ECE/C/?0>GB1G1E1GFGECCGFFG1>FGGHHGFH1F1GHFGGFGEGFFDHHGHHFFFHG1D AS:i:-15 ZS:i:-15 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:0A20C41A87 YT:Z:UU NH:i:2
496047:M01997:246:000000000-ANBW6_NNNNNN:1:1104:12331:8208 0 8 38275856 1 36M1159N115M * 0 0 CCCAGAGTTCATGGATGCACTGGAGTCAGCGGACACTGTTACCTGTCTGCGCAGAGGGATGCTCTTGGCCAGCTTGTGCACAGCCATCTGGCTGTGGAAGTCACTCTTCTTGGTACCACTCTTCATCTTGTAGACGATGACCGACCCCACC AAAA1>11BD@3FA1AAFDGGGCHHHHGFHGC0EEFHHHBFBFFGHGGHH/EEEEHGCAFGGH1FFG1CGEEC1FGFEFGHEGGHHHHDBGHG/BFGF10B1BFFFHG1GHEGFHBFHHHHGHFHFF>FH1FGFF/@AFG1F<<CCCGCGG AS:i:-5 ZS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:30A120 YT:Z:UU NH:i:2
496048:M01997:246:000000000-ANBW6_NNNNNN:1:1104:12331:8208 256 8 38275856 1 35M1159N116M * 0 0 CCCAGAGTTCATGGATGCACTGGAGTCAGCGGACACTGTTACCTGTCTGCGCAGAGGGATGCTCTTGGCCAGCTTGTGCACAGCCATCTGGCTGTGGAAGTCACTCTTCTTGGTACCACTCTTCATCTTGTAGACGATGACCGACCCCACC AAAA1>11BD@3FA1AAFDGGGCHHHHGFHGC0EEFHHHBFBFFGHGGHH/EEEEHGCAFGGH1FFG1CGEEC1FGFEFGHEGGHHHHDBGHG/BFGF10B1BFFFHG1GHEGFHBFHHHHGHFHFF>FH1FGFF/@AFG1F<<CCCGCGG AS:i:-5 ZS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:30A120 YT:Z:UU NH:i:2
Notice I would not call these types of alignment wrong in the informative case although you might want too look at it.
from hisat2.
infphilo
commented on July 22, 2024
Hi @mmterpstra,
I fixed one issue that you mentioned in your first thread, where HISAT2 reports duplicate alignments for those being soft-clipped. The fix is available in the master branch, if you'd like to give it a try.
Thanks again for brining this to my attention!
Daehwan
from hisat2.
mmterpstra
commented on July 22, 2024
This script enables to detect both errors(this issue).
https://github.com/mmterpstra/pipeline-util/blob/master/bin/refineSam.pl.
Will output warnings when the next read has same alignment start, name,
chromosome and end in the input and omits printing the output (for both
type of reads mentioned earlyer on this issue). For the old issue ill make
a run with picard sam validator tool.
from hisat2.
mmterpstra
commented on July 22, 2024
Looks like it gets better, didn't test in detail:
125 vs 177 duplicate alignments with equal chr-start-stop in 5.7m reads. I think this will fix the main issue in the first post.
For the rest possible solutions are alignment to:
Annotation, splice-donor/acceptor sequence (GU---intron---AG ) , nearest to transcript start (left aligned to transcript).
somebody@somewhere:~ ml hisat2/454b21f-foss-2016a
somebody@somewhere:~ hisat2 -x /ftp.broadinstitute.org/bundle/2.8/b37//hisat2/2.0.3-beta-goolf-1.7.20/human_g1k_v37_decoy -U sample_1.fq.gz -S /dev/stdout --threads 1| perl /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl - 1>/dev/null
Commandline: /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl -
lastr:ARRAY(0x1b080a0);r:ARRAY(0x1b081a8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 280457.
lastr:ARRAY(0x1af8d90);r:ARRAY(0x1b08010) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 453804.
lastr:ARRAY(0x19527e0);r:ARRAY(0x1b07ff8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 487067.
lastr:ARRAY(0x1b07ce0);r:ARRAY(0x1b07fe0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 500503.
lastr:ARRAY(0x1b08238);r:ARRAY(0x1b08190) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 514473.
lastr:ARRAY(0x1b07f20);r:ARRAY(0x1b08160) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 593679.
lastr:ARRAY(0x1b08340);r:ARRAY(0x1b07f38) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 888524.
lastr:ARRAY(0x1b082f8);r:ARRAY(0x1aeb3a0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1030568.
lastr:ARRAY(0x1b08250);r:ARRAY(0x1b081f0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1061731.
lastr:ARRAY(0x1b08448);r:ARRAY(0x1b08160) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1061733.
lastr:ARRAY(0x1b08370);r:ARRAY(0x1aea920) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1068467.
lastr:ARRAY(0x1b08130);r:ARRAY(0x1b082b0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1079802.
lastr:ARRAY(0x1b08070);r:ARRAY(0x1b080e8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1079804.
lastr:ARRAY(0x1b082e0);r:ARRAY(0x1b08448) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1522130.
lastr:ARRAY(0x1b08388);r:ARRAY(0x1aea920) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1586421.
lastr:ARRAY(0x1b080d0);r:ARRAY(0x1b07f68) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1630550.
lastr:ARRAY(0x1b07fb0);r:ARRAY(0x1b083d0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1630552.
lastr:ARRAY(0x1b07fb0);r:ARRAY(0x1b08298) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1945224.
lastr:ARRAY(0x1b07f38);r:ARRAY(0x1946708) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1952399.
lastr:ARRAY(0x1b085f8);r:ARRAY(0x1b08148) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1993778.
lastr:ARRAY(0x19527e0);r:ARRAY(0x1b08010) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2013499.
lastr:ARRAY(0x1af9318);r:ARRAY(0x1b08610) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2077404.
lastr:ARRAY(0x1b08058);r:ARRAY(0x1b07e18) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2144171.
lastr:ARRAY(0x1b08220);r:ARRAY(0x19528b8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2159655.
lastr:ARRAY(0x1b08100);r:ARRAY(0x1b084a8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2196942.
lastr:ARRAY(0x1aba028);r:ARRAY(0x1b08238) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2250917.
lastr:ARRAY(0x1b08550);r:ARRAY(0x1aeb370) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2285402.
lastr:ARRAY(0x1a32448);r:ARRAY(0x1946858) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2289969.
lastr:ARRAY(0x1b08118);r:ARRAY(0x1b08220) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2306528.
lastr:ARRAY(0x1b08130);r:ARRAY(0x1b08628) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2327194.
lastr:ARRAY(0x1b08628);r:ARRAY(0x1b08148) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2343931.
lastr:ARRAY(0x1b08400);r:ARRAY(0x1aba028) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2368921.
lastr:ARRAY(0x1b085e0);r:ARRAY(0x1b07f80) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2409390.
lastr:ARRAY(0x1b07f80);r:ARRAY(0x1b08430) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2438449.
lastr:ARRAY(0x1b08508);r:ARRAY(0x1b081d8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2446716.
lastr:ARRAY(0x1b08250);r:ARRAY(0x1b08178) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2483052.
lastr:ARRAY(0x1aba028);r:ARRAY(0x1b082e0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2537629.
lastr:ARRAY(0x1b07ff8);r:ARRAY(0x1b08070) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2542591.
lastr:ARRAY(0x1b07ed8);r:ARRAY(0x1b08220) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2552231.
lastr:ARRAY(0x1b080d0);r:ARRAY(0x1b07fc8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2574626.
lastr:ARRAY(0x1b08358);r:ARRAY(0x1b085b0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2663888.
lastr:ARRAY(0x1b08280);r:ARRAY(0x1b07f38) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2663894.
lastr:ARRAY(0x1b08040);r:ARRAY(0x1b08610) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2797178.
lastr:ARRAY(0x1b08190);r:ARRAY(0x1b08088) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2818949.
lastr:ARRAY(0x1b08178);r:ARRAY(0x1b08370) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2826268.
lastr:ARRAY(0x1b081d8);r:ARRAY(0x1b07fb0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2928467.
lastr:ARRAY(0x19467b0);r:ARRAY(0x1b07f38) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2945062.
lastr:ARRAY(0x1b082e0);r:ARRAY(0x1b08370) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2982874.
lastr:ARRAY(0x1b08598);r:ARRAY(0x1b084f0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2992761.
lastr:ARRAY(0x1b08370);r:ARRAY(0x1af8d90) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3014109.
lastr:ARRAY(0x1b084c0);r:ARRAY(0x1af92d0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3112247.
lastr:ARRAY(0x1af92d0);r:ARRAY(0x1b08148) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3112248.
lastr:ARRAY(0x1b08148);r:ARRAY(0x1b080e8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3132665.
lastr:ARRAY(0x1946720);r:ARRAY(0x1b080a0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3132668.
lastr:ARRAY(0x1af9228);r:ARRAY(0x19467c8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3164945.
lastr:ARRAY(0x1b08628);r:ARRAY(0x1b07ff8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3276990.
lastr:ARRAY(0x1b08430);r:ARRAY(0x1b084a8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3309075.
lastr:ARRAY(0x1b07f98);r:ARRAY(0x1b07f08) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3325412.
lastr:ARRAY(0x1b08568);r:ARRAY(0x1946858) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3362159.
lastr:ARRAY(0x1b07f50);r:ARRAY(0x1b07ed8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3446345.
lastr:ARRAY(0x1b08070);r:ARRAY(0x1b08118) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3513123.
lastr:ARRAY(0x1b08490);r:ARRAY(0x1af8d60) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3612289.
lastr:ARRAY(0x1a32448);r:ARRAY(0x1946858) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3649196.
lastr:ARRAY(0x1b081f0);r:ARRAY(0x1946840) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3723396.
lastr:ARRAY(0x1b086a0);r:ARRAY(0x1b081c0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3765436.
lastr:ARRAY(0x1b07f98);r:ARRAY(0x1a322b0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3782250.
lastr:ARRAY(0x1b08148);r:ARRAY(0x1b07f20) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3782252.
lastr:ARRAY(0x1b08358);r:ARRAY(0x1b085c8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3963839.
lastr:ARRAY(0x1b086b8);r:ARRAY(0x1b08088) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3983639.
lastr:ARRAY(0x1946840);r:ARRAY(0x1b086d0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3988193.
lastr:ARRAY(0x1b081f0);r:ARRAY(0x1b08070) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4020490.
lastr:ARRAY(0x1b084f0);r:ARRAY(0x19467c8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4069693.
lastr:ARRAY(0x1b08088);r:ARRAY(0x1af8d90) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4103794.
lastr:ARRAY(0x1b07e18);r:ARRAY(0x19527e0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4113700.
lastr:ARRAY(0x1b07f08);r:ARRAY(0x1b086d0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4187128.
lastr:ARRAY(0x1b08418);r:ARRAY(0x1b07ed8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4206925.
lastr:ARRAY(0x1946720);r:ARRAY(0x1b08070) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4276655.
lastr:ARRAY(0x1946858);r:ARRAY(0x1a322b0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4316045.
lastr:ARRAY(0x1b08118);r:ARRAY(0x1b08010) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4361724.
lastr:ARRAY(0x1b084a8);r:ARRAY(0x1af92d0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4437798.
lastr:ARRAY(0x1b084a8);r:ARRAY(0x1b08658) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4473459.
lastr:ARRAY(0x1af92d0);r:ARRAY(0x1af92somewhere28) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4492022.
lastr:ARRAY(0x1af9318);r:ARRAY(0x1b08280) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4550417.
lastr:ARRAY(0x1b08460);r:ARRAY(0x1952870) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4625179.
lastr:ARRAY(0x1b08040);r:ARRAY(0x1b07fe0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4652114.
lastr:ARRAY(0x1b08310);r:ARRAY(0x1b083a0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4688904.
lastr:ARRAY(0x1b08208);r:ARRAY(0x19467c8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4788181.
lastr:ARRAY(0x1b07f38);r:ARRAY(0x1b08088) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4946173.
lastr:ARRAY(0x1b08418);r:ARRAY(0x1b086a0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4950094.
lastr:ARRAY(0x1b07ed8);r:ARRAY(0x1b084d8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4964894.
lastr:ARRAY(0x1b08028);r:ARRAY(0x1af92d0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4970968.
lastr:ARRAY(0x1b086a0);r:ARRAY(0x1b07f50) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5062463.
lastr:ARRAY(0x1b080a0);r:ARRAY(0x1b08640) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5174208.
lastr:ARRAY(0x1b08070);r:ARRAY(0x1b08028) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5219719.
lastr:ARRAY(0x1b07f20);r:ARRAY(0x1b07ef0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5282560.
lastr:ARRAY(0x1b07de8);r:ARRAY(0x1b08400) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5363578.
lastr:ARRAY(0x1a32448);r:ARRAY(0x1b08700) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5552425.
lastr:ARRAY(0x1b07fe0);r:ARRAY(0x1b08028) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5585884.
lastr:ARRAY(0x1b08238);r:ARRAY(0x1b07fc8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5586227.
lastr:ARRAY(0x1b08400);r:ARRAY(0x1b084d8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5616145.
lastr:ARRAY(0x1b086e8);r:ARRAY(0x1b083b8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5616147.
lastr:ARRAY(0x1b07f38);r:ARRAY(0x1b07f68) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5623584.
lastr:ARRAY(0x1946858);r:ARRAY(0x1b08568) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5704318.
lastr:ARRAY(0x1b08310);r:ARRAY(0x1952858) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5721568.
lastr:ARRAY(0x1b08490);r:ARRAY(0x1b085f8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5788175.
lastr:ARRAY(0x1b083d0);r:ARRAY(0x1b08280) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5788177.
lastr:ARRAY(0x1b086e8);r:ARRAY(0x1b08688) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5834861.
lastr:ARRAY(0x1b08448);r:ARRAY(0x1b085c8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5837082.
lastr:ARRAY(0x19466f0);r:ARRAY(0x1b07e18) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5906502.
lastr:ARRAY(0x1b07f98);r:ARRAY(0x1b08028) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5918929.
lastr:ARRAY(0x1b07fb0);r:ARRAY(0x1b07de8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5920679.
lastr:ARRAY(0x1b08598);r:ARRAY(0x1b08190) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5937413.
lastr:ARRAY(0x1b08568);r:ARRAY(0x1b08100) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5976707.
lastr:ARRAY(0x1b07f08);r:ARRAY(0x1946ba0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5997462.
lastr:ARRAY(0x1b08010);r:ARRAY(0x1b08190) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5999574.
lastr:ARRAY(0x1b07f38);r:ARRAY(0x1b07d88) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6151326.
lastr:ARRAY(0x1b08148);r:ARRAY(0x1946858) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6152814.
lastr:ARRAY(0x1b07fc8);r:ARRAY(0x1b07d88) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6152816.
lastr:ARRAY(0x1b080e8);r:ARRAY(0x1b07ed8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6155060.
lastr:ARRAY(0x1b08508);r:ARRAY(0x1b08238) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6192229.
lastr:ARRAY(0x1b08388);r:ARRAY(0x1b07ef0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6196084.
lastr:ARRAY(0x1b081a8);r:ARRAY(0x1b08340) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6202864.
lastr:ARRAY(0x1b08538);r:ARRAY(0x1b07fb0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6233218.
lastr:ARRAY(0x1b083d0);r:ARRAY(0x1b08340) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6243804.
lastr:ARRAY(0x1a322b0);r:ARRAY(0x1af8d60) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6243806.
5658119 reads; of these:
5658119 (100.00%) were unpaired; of these:
945515 (16.71%) aligned 0 times
2386835 (42.18%) aligned exactly 1 time
2325769 (41.10%) aligned >1 times
83.29% overall alignment rate
somebody@somewhere:~ ml hisat2/2.0.3-beta-foss-2016a
The following have been reloaded with a version change:
1) hisat2/454b21f-foss-2016a => hisat2/2.0.3-beta-foss-2016a
somebody@somewhere:~ hisat2 -x /ftp.broadinstitute.org/bundle/2.8/b37//hisat2/2.0.3-beta-goolf-1.7.20/human_g1k_v37_decoy -U sample_1.fq.gz -S /dev/stdout --threads 1| perl /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl - 1>/dev/null
Commandline: /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl -
lastr:ARRAY(0x13b9308);r:ARRAY(0x11f77e8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 9707.
lastr:ARRAY(0x13b9200);r:ARRAY(0x13b9218) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 59836.
lastr:ARRAY(0x13b8ff0);r:ARRAY(0x11f7710) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 140864.
lastr:ARRAY(0x13b9290);r:ARRAY(0x13b94b8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 174639.
lastr:ARRAY(0x13b94b8);r:ARRAY(0x139c3c0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 204859.
lastr:ARRAY(0x13a9d90);r:ARRAY(0x13b90b0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 260221.
lastr:ARRAY(0x13b8fd8);r:ARRAY(0x12038d0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 339807.
lastr:ARRAY(0x13b9518);r:ARRAY(0x13b91d0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 360706.
lastr:ARRAY(0x13b8df8);r:ARRAY(0x11f7878) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 394008.
lastr:ARRAY(0x13b92d8);r:ARRAY(0x13b9098) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 453547.
lastr:ARRAY(0x1203888);r:ARRAY(0x13b9200) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 486691.
lastr:ARRAY(0x13b9110);r:ARRAY(0x13b93e0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 500053.
lastr:ARRAY(0x13b9308);r:ARRAY(0x13b8f60) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 513994.
lastr:ARRAY(0x13b92c0);r:ARRAY(0x13b9380) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 523368.
lastr:ARRAY(0x13b90c8);r:ARRAY(0x139c3f0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 563294.
lastr:ARRAY(0x12038d0);r:ARRAY(0x13b8f00) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 575529.
lastr:ARRAY(0x13aa318);r:ARRAY(0x13b9368) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 659553.
lastr:ARRAY(0x13b9458);r:ARRAY(0x13b90c8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 799695.
lastr:ARRAY(0x12038d0);r:ARRAY(0x11f7728) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 886392.
lastr:ARRAY(0x13b9098);r:ARRAY(0x13b9218) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 891437.
lastr:ARRAY(0x13b8ff0);r:ARRAY(0x13b9230) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 933001.
lastr:ARRAY(0x13b92d8);r:ARRAY(0x13b8d98) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1029367.
lastr:ARRAY(0x13b9440);r:ARRAY(0x13571e0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1051869.
lastr:ARRAY(0x13b9260);r:ARRAY(0x13b9110) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1058888.
lastr:ARRAY(0x13b91a0);r:ARRAY(0x13b9248) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1058890.
lastr:ARRAY(0x13b9338);r:ARRAY(0x12e3498) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1065611.
lastr:ARRAY(0x13b9440);r:ARRAY(0x13b95c0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1076945.
lastr:ARRAY(0x13b90e0);r:ARRAY(0x11f7710) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1076947.
lastr:ARRAY(0x13b9290);r:ARRAY(0x11f77e8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1086793.
lastr:ARRAY(0x13b8d98);r:ARRAY(0x13b8f78) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1088057.
lastr:ARRAY(0x13b8fa8);r:ARRAY(0x13b9470) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1115802.
lastr:ARRAY(0x13b9368);r:ARRAY(0x13b8f60) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1143305.
lastr:ARRAY(0x13b9338);r:ARRAY(0x13b8df8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1174206.
lastr:ARRAY(0x13b9398);r:ARRAY(0x13b92a8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1236713.
lastr:ARRAY(0x13b9158);r:ARRAY(0x13b93c8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1258085.
lastr:ARRAY(0x13b9098);r:ARRAY(0x13b8f18) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1294452.
lastr:ARRAY(0x13b9008);r:ARRAY(0x13b8fc0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1296708.
lastr:ARRAY(0x13b95d8);r:ARRAY(0x13b9008) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1310831.
lastr:ARRAY(0x12038e8);r:ARRAY(0x13b9560) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1341269.
lastr:ARRAY(0x11f7bc0);r:ARRAY(0x13b9350) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1368711.
lastr:ARRAY(0x13b8f30);r:ARRAY(0x13b92c0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1369314.
lastr:ARRAY(0x13b9170);r:ARRAY(0x13b9380) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1444336.
lastr:ARRAY(0x13b9290);r:ARRAY(0x13b8e28) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1480805.
lastr:ARRAY(0x13b9248);r:ARRAY(0x13b91b8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1517338.
lastr:ARRAY(0x13b9500);r:ARRAY(0x13b90b0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1519638.
lastr:ARRAY(0x139b970);r:ARRAY(0x13b9440) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1526304.
lastr:ARRAY(0x13b9368);r:ARRAY(0x13b8fd8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1547331.
lastr:ARRAY(0x13b9488);r:ARRAY(0x13b9350) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1565687.
lastr:ARRAY(0x13b9218);r:ARRAY(0x13b94d0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1581329.
lastr:ARRAY(0x13b91d0);r:ARRAY(0x13b9170) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1582882.
lastr:ARRAY(0x13b90b0);r:ARRAY(0x13b95a8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1625339.
lastr:ARRAY(0x13b9158);r:ARRAY(0x11f76f8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1625341.
lastr:ARRAY(0x13b8d50);r:ARRAY(0x13b9548) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1719960.
lastr:ARRAY(0x13a9d90);r:ARRAY(0x13b95d8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1722201.
lastr:ARRAY(0x13b91e8);r:ARRAY(0x13b8f30) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1835629.
lastr:ARRAY(0x13b94e8);r:ARRAY(0x13b9368) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1917513.
lastr:ARRAY(0x11f7878);r:ARRAY(0x13b9200) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 1974678.
lastr:ARRAY(0x13aa228);r:ARRAY(0x13b9428) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2006675.
lastr:ARRAY(0x13b8d98);r:ARRAY(0x13aa2d0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2049828.
lastr:ARRAY(0x13b9578);r:ARRAY(0x12e3498) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2057030.
lastr:ARRAY(0x13b9050);r:ARRAY(0x13b92f0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2062430.
lastr:ARRAY(0x13b9410);r:ARRAY(0x13b90f8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2167804.
lastr:ARRAY(0x13b9440);r:ARRAY(0x13b93f8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2173891.
lastr:ARRAY(0x13b9338);r:ARRAY(0x11f7728) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2223499.
lastr:ARRAY(0x13b91e8);r:ARRAY(0x1203738) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2247280.
lastr:ARRAY(0x13b91e8);r:ARRAY(0x12038e8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2248900.
lastr:ARRAY(0x13b9020);r:ARRAY(0x13b94b8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2397390.
lastr:ARRAY(0x13b90e0);r:ARRAY(0x11f7848) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2542942.
lastr:ARRAY(0x11f7848);r:ARRAY(0x13b8f48) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2677001.
lastr:ARRAY(0x13b8cf0);r:ARRAY(0x13b94e8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2779851.
lastr:ARRAY(0x13b90c8);r:ARRAY(0x13b93c8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2909300.
lastr:ARRAY(0x13b8f30);r:ARRAY(0x13aa228) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2964779.
lastr:ARRAY(0x13b9428);r:ARRAY(0x139c3c0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2971208.
lastr:ARRAY(0x13b8ee8);r:ARRAY(0x13b95d8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2973255.
lastr:ARRAY(0x13b9068);r:ARRAY(0x13b92f0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 2985926.
lastr:ARRAY(0x13b8d50);r:ARRAY(0x13aa228) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3019398.
lastr:ARRAY(0x139c3c0);r:ARRAY(0x13b9260) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3035640.
lastr:ARRAY(0x13b93f8);r:ARRAY(0x139b970) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3102015.
lastr:ARRAY(0x139b970);r:ARRAY(0x13b92a8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3102016.
lastr:ARRAY(0x13b96f8);r:ARRAY(0x13b9560) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3122361.
lastr:ARRAY(0x13b8ff0);r:ARRAY(0x13b9320) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3122364.
lastr:ARRAY(0x13b9710);r:ARRAY(0x13b9218) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3164822.
lastr:ARRAY(0x11f7848);r:ARRAY(0x13b9218) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3219977.
lastr:ARRAY(0x11f77e8);r:ARRAY(0x13b91b8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3228047.
lastr:ARRAY(0x13b91d0);r:ARRAY(0x12038e8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3314898.
lastr:ARRAY(0x13b9068);r:ARRAY(0x13b90f8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3397887.
lastr:ARRAY(0x13b8d50);r:ARRAY(0x11f7728) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3443492.
lastr:ARRAY(0x13b9080);r:ARRAY(0x13aa2d0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3462516.
lastr:ARRAY(0x13b9608);r:ARRAY(0x11f7860) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3466578.
lastr:ARRAY(0x139b970);r:ARRAY(0x13b9698) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3575083.
lastr:ARRAY(0x13b95d8);r:ARRAY(0x13a9d60) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3595117.
lastr:ARRAY(0x13b9440);r:ARRAY(0x13aa228) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3684248.
lastr:ARRAY(0x11f76f8);r:ARRAY(0x13b9608) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3723330.
lastr:ARRAY(0x13b92c0);r:ARRAY(0x13b9290) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3769057.
lastr:ARRAY(0x13b90e0);r:ARRAY(0x13b8f90) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3769059.
lastr:ARRAY(0x13b8cf0);r:ARRAY(0x13b9380) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3776401.
lastr:ARRAY(0x13b8f60);r:ARRAY(0x13b92c0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3776944.
lastr:ARRAY(0x13b9518);r:ARRAY(0x13b9560) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3795550.
lastr:ARRAY(0x13b9698);r:ARRAY(0x13b8f48) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3802087.
lastr:ARRAY(0x13b90f8);r:ARRAY(0x13b9080) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3832346.
lastr:ARRAY(0x1203738);r:ARRAY(0x13b95f0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3841012.
lastr:ARRAY(0x13b92c0);r:ARRAY(0x13b92a8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 3876653.
lastr:ARRAY(0x13b8fc0);r:ARRAY(0x13b94b8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4051654.
lastr:ARRAY(0x139c3f0);r:ARRAY(0x12038e8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4078514.
lastr:ARRAY(0x13b8f18);r:ARRAY(0x13571e0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4120752.
lastr:ARRAY(0x13b95f0);r:ARRAY(0x13b9620) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4153087.
lastr:ARRAY(0x13b9578);r:ARRAY(0x13b9200) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4189551.
lastr:ARRAY(0x13a9d60);r:ARRAY(0x13b9230) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4191081.
lastr:ARRAY(0x13b9230);r:ARRAY(0x13b9158) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4277537.
lastr:ARRAY(0x1203888);r:ARRAY(0x13b8f18) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4299238.
lastr:ARRAY(0x13b8f90);r:ARRAY(0x13b94d0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4343112.
lastr:ARRAY(0x139c3f0);r:ARRAY(0x13b9380) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4358652.
lastr:ARRAY(0x13b92f0);r:ARRAY(0x13b9530) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4426066.
lastr:ARRAY(0x13b8e28);r:ARRAY(0x13b8f48) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4511930.
lastr:ARRAY(0x13b95c0);r:ARRAY(0x13b9470) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4533928.
lastr:ARRAY(0x11f7728);r:ARRAY(0x13b94a0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4633220.
lastr:ARRAY(0x13b8fc0);r:ARRAY(0x13b8f30) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4643916.
lastr:ARRAY(0x11f77d0);r:ARRAY(0x13b92c0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4669680.
lastr:ARRAY(0x13b94a0);r:ARRAY(0x13b93c8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4680896.
lastr:ARRAY(0x13b8ee8);r:ARRAY(0x13b8fa8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4766006.
lastr:ARRAY(0x13b94d0);r:ARRAY(0x13b94b8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4883625.
lastr:ARRAY(0x13b8f48);r:ARRAY(0x13b9260) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4892828.
lastr:ARRAY(0x13b8f90);r:ARRAY(0x13b8d50) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4916937.
lastr:ARRAY(0x13b9590);r:ARRAY(0x13b8f90) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4925409.
lastr:ARRAY(0x12038d0);r:ARRAY(0x13aa318) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4928964.
lastr:ARRAY(0x11f7860);r:ARRAY(0x13b8f90) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4937052.
lastr:ARRAY(0x13b9020);r:ARRAY(0x13b9068) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4943744.
lastr:ARRAY(0x13b96c8);r:ARRAY(0x13b90c8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4949808.
lastr:ARRAY(0x11f7848);r:ARRAY(0x13b9080) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 4968418.
lastr:ARRAY(0x11f7860);r:ARRAY(0x13b8f18) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5151619.
lastr:ARRAY(0x13b94b8);r:ARRAY(0x13b8f30) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5194772.
lastr:ARRAY(0x13b9260);r:ARRAY(0x13b95a8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5196715.
lastr:ARRAY(0x13b95a8);r:ARRAY(0x13b95c0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5197124.
lastr:ARRAY(0x13b8f18);r:ARRAY(0x13b92d8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5197126.
lastr:ARRAY(0x13b9158);r:ARRAY(0x139c3f0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5233685.
lastr:ARRAY(0x13b93f8);r:ARRAY(0x13b9368) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5291510.
lastr:ARRAY(0x13b96c8);r:ARRAY(0x13b8d98) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5292844.
lastr:ARRAY(0x13b9530);r:ARRAY(0x13b9590) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5384380.
lastr:ARRAY(0x13b90e0);r:ARRAY(0x13b8d50) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5590176.
lastr:ARRAY(0x13b91b8);r:ARRAY(0x11f7710) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5590178.
lastr:ARRAY(0x13b91b8);r:ARRAY(0x13b93b0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5597603.
lastr:ARRAY(0x13b9518);r:ARRAY(0x13b9158) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5615406.
lastr:ARRAY(0x13b9158);r:ARRAY(0x13b90e0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5615407.
lastr:ARRAY(0x13b8f78);r:ARRAY(0x13b9620) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5622993.
lastr:ARRAY(0x13b9380);r:ARRAY(0x13b8fc0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5640773.
lastr:ARRAY(0x13b95c0);r:ARRAY(0x13b9068) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5678288.
lastr:ARRAY(0x13b8ff0);r:ARRAY(0x13b92a8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5695531.
lastr:ARRAY(0x13b9458);r:ARRAY(0x13aa318) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5709693.
lastr:ARRAY(0x13b9560);r:ARRAY(0x13b96b0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5715600.
lastr:ARRAY(0x12038d0);r:ARRAY(0x13b9560) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5747212.
lastr:ARRAY(0x13b95a8);r:ARRAY(0x13b94a0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5761997.
lastr:ARRAY(0x13b95c0);r:ARRAY(0x13b94e8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5761999.
lastr:ARRAY(0x13b96f8);r:ARRAY(0x13b8d98) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5772780.
lastr:ARRAY(0x13b96f8);r:ARRAY(0x1203738) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5808633.
lastr:ARRAY(0x13b9068);r:ARRAY(0x13b92a8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5810859.
lastr:ARRAY(0x13b96c8);r:ARRAY(0x13b92f0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5841568.
lastr:ARRAY(0x13b96c8);r:ARRAY(0x13b9230) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5880188.
lastr:ARRAY(0x13b9530);r:ARRAY(0x13b95a8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5892606.
lastr:ARRAY(0x13b92a8);r:ARRAY(0x13b90c8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5894350.
lastr:ARRAY(0x13b9458);r:ARRAY(0x13b91b8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5901760.
lastr:ARRAY(0x13571e0);r:ARRAY(0x13b96e0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5906771.
lastr:ARRAY(0x12038d0);r:ARRAY(0x13b8f60) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5950301.
lastr:ARRAY(0x12f69c0);r:ARRAY(0x13b90f8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5957188.
lastr:ARRAY(0x13b90e0);r:ARRAY(0x13b8f78) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5973162.
lastr:ARRAY(0x13b9650);r:ARRAY(0x13b90f8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 5985501.
lastr:ARRAY(0x13b93b0);r:ARRAY(0x13b8fd8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6052589.
lastr:ARRAY(0x13b96e0);r:ARRAY(0x13b90c8) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6109381.
lastr:ARRAY(0x139c3c0);r:ARRAY(0x13b9590) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6126295.
lastr:ARRAY(0x13b9620);r:ARRAY(0x13b9008) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6126297.
lastr:ARRAY(0x13b9440);r:ARRAY(0x13b9530) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6128544.
lastr:ARRAY(0x13b9248);r:ARRAY(0x13b9158) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6169465.
lastr:ARRAY(0x13b96b0);r:ARRAY(0x13b8f00) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6176234.
lastr:ARRAY(0x13b8f48);r:ARRAY(0x13571e0) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6190002.
lastr:ARRAY(0x139b970);r:ARRAY(0x13b8f48) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6206524.
lastr:ARRAY(0x13b95c0);r:ARRAY(0x13b9350) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6217095.
lastr:ARRAY(0x13b95d8);r:ARRAY(0x13b9380) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6217097.
lastr:ARRAY(0x13b9458);r:ARRAY(0x11f7848) at /software/pipeline-util/0.2.3-foss-2016a-Perl-5.20.2-bare/bin/refineSam.pl line 46, <> line 6235887.
5658119 reads; of these:
5658119 (100.00%) were unpaired; of these:
942135 (16.65%) aligned 0 times
3393222 (59.97%) aligned exactly 1 time
1322762 (23.38%) aligned >1 times
83.35% overall alignment rate
from hisat2.
Related Issues (20)
- Align ATAC-seq with Hisat2?
- error minimum intron length with hisat2 v. 2.2.1
- Repeat mapping with different result
- Feature request: Add support for xz and zstd
- hisat2 hangs aligning axolotl reads HOT 1
- Output files(.snp, .haplotype) of hisat2_extract_snps_haplotypes_*.py are empty
- Please add the pbat option of hisat-3n
- A question about methylation information extraction
- Any plans to support Apple Silicon architecture?
- Installation Issue Error 1 - make HOT 1
- -np argument seemingly not working
- ERR): "fastq file.fastq" does not exist. Exiting now ...
- [Bug Report] hisat2-align exited with value 137, space complexity of hisat2
- hisat2 location does not exist
- Hisat-3N mapping quality
- hisat2-build index for circRNA-seq
- hisat2-build failed for Segmentation fault
- [Future request] hisat-3n table option to report conversions summarized to genomic feature or reads counts
- Issue with hisatgenotype HOT 1
- Mapping using different parameters --very-sensitive and default
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from hisat2.