Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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an error?I use pilon to polish my ONT—data assembly genome. Then I got the line: Exception in thread "main" java.lang.IllegalStateException: Inappropriate call if not paired read.so what can I do next.my bam file has some error? #164
contig_1 1038 ins . G
contig_1 1100 snp G T
contig_1 2635 del C .
contig_1 3551 snp G A
contig_1 3605 snp C T
contig_1 3632 snp C T
contig_1 6249 snp G C
contig_1 6523 del G .
contig_1 7683 snp G A
contig_1 7774 del G .
contig_1 7781 del A .
contig_1 7854 del C .
contig_1 12079 snp A G
contig_1 12525 snp T C
contig_1 12619 snp T C
contig_1 12668 snp G C
contig_1 12692 snp G A
contig_1 12695 snp G A
contig_1 12707 snp C T
contig_1 12758 snp C T
contig_1 12773 snp G A
contig_1 17594 snp G C
contig_1 17636 snp C G
contig_1 17651 snp G A
contig_1 19716 snp C T
contig_1 21719 snp G T
contig_1 21767 snp G C
contig_1 21875 del G .
contig_1 22059 snp C T
contig_1 22077 snp G C
contig_1 23313 snp G A
contig_1 23406 snp G A
contig_1 24166 snp A G
contig_1 24172 snp C A
contig_1 24178 snp G A
contig_1 24184 snp G A
contig_1 24250 snp A C
contig_1 24274 snp G A
contig_1 24307 snp G A
contig_1 24466 snp G T
contig_1 24487 del T .
contig_1 24494 snp A T
contig_1 24509 snp C A
contig_1 24515 snp G A
contig_1 24530 snp A G
contig_1 24593 snp A C
contig_1 24644 snp G A
contig_1 27022 snp C G
contig_1 27140 snp C G
contig_1 27179 snp G A
contig_1 27457 snp G C
contig_1 27475 snp C A
contig_1 27578 snp G C
contig_1 27587 snp G A
contig_1 27605 snp C T
contig_1 27611 snp C G
contig_1 27623 snp C T
contig_1 27677 snp C G
contig_1 27695 snp G A
contig_1 27701 snp C T
contig_1 27711 snp T A
contig_1 27736 snp G T
contig_1 27743 snp G A
contig_1 29947 snp G C
contig_1 29959 snp G A
contig_1 29962 snp G A
contig_1 30020 snp C T
contig_1 30037 snp G C
contig_1 30040 snp A G
contig_1 30077 snp C T
contig_1 30092 del CCG .
contig_1 31342 snp A G
contig_1 31374 snp G T
contig_1 31379 del T .
contig_1 31383 del T .
contig_1 31393 del C .
contig_1 31415 snp T C
contig_1 31430 snp G A
contig_1 34010 del C .
contig_1 34022 snp C T
contig_1 37035 snp T C
contig_1 37038 snp C G
contig_1 37056 snp C T
contig_1 37065 snp A G
contig_1 37068 snp T C
contig_1 37086 snp G T
contig_1 45616 snp A G
contig_1 45622 snp C T
contig_1 45628 snp C T
contig_1 45631 snp C T
contig_1 45706 snp T C
contig_1 47672 snp G A
contig_1 48432 snp G A
contig_1 48459 snp G A
contig_1 48516 snp T G
contig_1 49156 snp T C
contig_1 49216 snp G A
contig_1 49246 snp A G
contig_1 49252 snp C T
contig_1 49273 snp C T
contig_1 49279 snp G T
contig_1 49285 snp A G
contig_1 49345 snp C T
contig_1 49366 snp C T
contig_1 57952 snp G A
contig_1 59700 snp C T
contig_1 59742 snp C T
contig_1 61619 snp C T
contig_1 61649 snp C T
contig_1 61994 snp T C
contig_1 64020 snp G A
contig_1 64137 snp C T
contig_1 64287 snp C T
contig_1 64536 snp C T
contig_1 64668 del C .
contig_1 64696 snp C T
contig_1 66737 snp C T
contig_1 66977 snp C T
contig_1 67004 snp G A
contig_1 67223 snp C T
contig_1 67238 snp C T
contig_1 91036 snp C T
contig_1 94331 snp G A
contig_1 100784 snp G A
contig_1 101937 snp G A
contig_1 101946 snp G A
contig_1 102264 snp G A
contig_1 102270 snp C T
contig_1 102287 snp G T
contig_1 102339 snp G C
contig_1 102875 snp T C
contig_1 102887 snp G C
contig_1 102908 snp C T
contig_1 102936 snp C T
contig_1 106386 snp G A
contig_1 108236 snp G A
contig_1 108254 snp C T
contig_1 108278 snp G A
contig_1 108287 snp A G
contig_1 108332 snp G A
contig_1 108352 snp G A
contig_1 108595 snp G A
contig_1 108619 snp C T
contig_1 109117 snp G A
contig_1 109168 snp G C
contig_1 109198 snp G A
contig_1 109300 snp A C
contig_1 109339 snp G A
contig_1 109393 snp A G
contig_1 113734 snp C G
contig_1 114662 snp T C
contig_1 115928 ins . C
contig_1 115954 snp A G
contig_1 117152 snp G A
contig_1 118025 snp G C
contig_1 118031 snp G C
contig_1 118034 snp G T
contig_1 118139 snp T G
contig_1 118386 snp G C
contig_1 118431 snp G A
contig_1 119028 snp G A
contig_1 119082 snp T C
contig_1 119103 snp C A
contig_1 119112 snp C T
contig_1 119458 snp G A
contig_1 119461 snp G A
contig_1 122749 snp C T
contig_1 123393 del A .
contig_1 123412 del T .
contig_1 123414 snp G C
contig_1 123456 snp C T
contig_1 123460 snp C T
contig_1 123465 snp C T
contig_1 123483 snp C G
contig_1 124550 snp C A
contig_1 124661 snp C T
contig_1 124664 del G .
contig_1 124719 snp G A
contig_1 124734 snp C G
contig_1 125412 snp C G
contig_1 128515 snp G A
contig_1 128517 snp C T
contig_1 128564 snp A C
contig_1 128566 snp C T
contig_1 129128 amb G C
contig_1 129154 snp G A
contig_1 130315 snp G A
contig_1 130325 snp A G
contig_1 134020 snp T C
contig_1 134123 snp C A
contig_1 134129 snp C T
contig_1 134971 snp C G
contig_1 135013 snp T G
contig_1 135040 snp T C
contig_1 137373 snp C T
contig_1 141830 snp A G
contig_1 145645 snp T G
contig_1 145658 snp C T
contig_1 145953 snp G A
contig_1 146456 snp G C
contig_1 146489 snp C T
contig_1 146492 snp C T
contig_1 146531 snp C T
contig_1 146690 snp G A
contig_1 147401 snp C G
contig_1 147692 snp C T
contig_1 148310 snp C T
contig_1 149255 snp C T
contig_1 151270 snp G A
contig_1 151824 snp C G
contig_1 171877 del A .
contig_1 171887 del G .
contig_1 172638 snp T G
contig_1 172645 snp G C
contig_1 172663 snp G A
contig_1 172895 snp C A
contig_1 172910 del C .
contig_1 172923 del C .
contig_1 172942 snp G A
contig_1 172996 del C .
contig_1 173016 snp T G
contig_1 173030 del CA .
contig_1 173035 ins . CA
contig_1 173039 snp G T
contig_1 173045 del C .
contig_1 173076 snp C G
contig_1 173079 snp C G
contig_1 173111 snp C A
contig_1 173133 snp G A
contig_1 173169 snp G C
contig_1 173177 snp T C
contig_1 173178 snp C T
contig_1 173184 del G .
contig_1 173186 snp G C
contig_1 173187 snp C T
contig_1 173190 snp C T
contig_1 173203 snp T G
contig_1 173212 snp G T
contig_1 173338 snp G C
contig_1 177457 snp C T
contig_1 177487 snp G C
contig_1 177499 snp C T
contig_1 177502 snp C T
contig_1 177511 snp C T
contig_1 177520 snp G T
contig_1 177553 snp G A
contig_1 177613 snp C T
contig_1 182476 snp G A
contig_1 182479 snp C G
contig_1 182875 snp C T
contig_1 183052 snp C A
contig_1 183080 snp G A
contig_1 183088 snp G A
contig_1 190138 snp T C
contig_1 192473 snp C T
contig_1 192477 snp C T
contig_1 192493 snp A G
contig_1 210067 snp G A
contig_1 210290 snp G A
contig_1 210419 snp C T
contig_1 210428 snp C T
contig_1 210652 snp C T
contig_1 210723 snp G T
contig_1 211218 snp C A
contig_1 236270 snp G A
contig_1 237383 del A .
contig_1 245238 del C .
contig_1 246211 snp A G
contig_1 246220 snp C T
contig_1 249506 snp T C
contig_1 249521 snp C A
contig_1 249563 snp C A
contig_1 251155 snp G A
contig_1 251167 snp C T
contig_1 251212 snp G T
contig_1 251218 snp G C
contig_1 251224 snp G T
contig_1 251260 snp G A
contig_1 251278 snp C G
contig_1 251294 del T .
contig_1 251297 snp C T
contig_1 251304 snp C T
contig_1 251342 snp T G
contig_1 251345 snp G A
contig_1 251373 snp C T
contig_1 251375 ins . G
contig_1 251378 del TG .
contig_1 251406 snp G A
contig_1 252346 snp A G
contig_1 260490 snp C T
contig_1 268845 snp T C
contig_1 268884 ins . G
contig_1 268889 snp C G
contig_1 268892 snp C T
contig_1 268900 snp A G
contig_1 268901 snp T C
contig_1 274640 snp G C
contig_1 274644 snp C T
contig_1 274650 snp T C
contig_1 277944 snp T C
contig_1 277953 snp T A
contig_1 277956 snp C T
contig_1 277977 snp A C
contig_1 278019 snp T A
contig_1 285310 snp T G
contig_1 285316 snp G A
contig_1 285319 snp G A
contig_1 285337 snp G T
contig_1 285355 snp C T
contig_1 285745 snp T G
contig_1 285746 snp A C
contig_1 285747 snp T C
Confirmed 22828 of 302494 bases (7.55%)
Corrected 282 snps; 1 ambiguous bases; corrected 7 small insertions totaling 8 bases, 31 small de letions totaling 36 bases
Large collapsed region: contig_1:17502-27810 size 10309
Large collapsed region: contig_1:56779-67336 size 10558
Large collapsed region: contig_1:112360-125533 size 13174
Large collapsed region: contig_1:176853-194296 size 17444
Attempting to fix local continuity breaks
fixBreak: contig_1:2761-24200
Exception in thread "main" java.lang.IllegalStateException: Inappropriate call if not paired read
at htsjdk.samtools.SAMRecord.requireReadPaired(SAMRecord.java:892)
at htsjdk.samtools.SAMRecord.getFirstOfPairFlag(SAMRecord.java:950)
at org.broadinstitute.pilon.BamFile$MateMap.addRead(BamFile.scala:236)
at org.broadinstitute.pilon.BamFile$MateMap.$anonfun$addReads$1(BamFile.scala:232)
at org.broadinstitute.pilon.BamFile$MateMap.$anonfun$addReads$1$adapted(BamFile.scala:232 )
at scala.collection.immutable.List.foreach(List.scala:333)
at org.broadinstitute.pilon.BamFile$MateMap.addReads(BamFile.scala:232)
at org.broadinstitute.pilon.BamFile$MateMap.(BamFile.scala:230)
at org.broadinstitute.pilon.BamFile.recruitFlankReads(BamFile.scala:351)
at org.broadinstitute.pilon.GapFiller.$anonfun$recruitReadsFromBams$1(GapFiller.scala:367 )
at org.broadinstitute.pilon.GapFiller.$anonfun$recruitReadsFromBams$1$adapted(GapFiller.s cala:366)
at scala.collection.immutable.List.foreach(List.scala:333)
at org.broadinstitute.pilon.GapFiller.recruitReadsFromBams(GapFiller.scala:366)
at org.broadinstitute.pilon.GapFiller.recruitReadsOfType(GapFiller.scala:375)
at org.broadinstitute.pilon.GapFiller.recruitFrags(GapFiller.scala:379)
at org.broadinstitute.pilon.GapFiller.recruitLocalReads(GapFiller.scala:394)
at org.broadinstitute.pilon.GapFiller.recruitReads(GapFiller.scala:401)
at org.broadinstitute.pilon.GapFiller.assembleAcrossBreak(GapFiller.scala:54)
at org.broadinstitute.pilon.GapFiller.fixBreak(GapFiller.scala:46)
at org.broadinstitute.pilon.GenomeRegion.$anonfun$identifyAndFixIssues$6(GenomeRegion.sca la:401)
at org.broadinstitute.pilon.GenomeRegion.$anonfun$identifyAndFixIssues$6$adapted(GenomeRe gion.scala:399)
at scala.collection.immutable.List.foreach(List.scala:333)
at org.broadinstitute.pilon.GenomeRegion.identifyAndFixIssues(GenomeRegion.scala:399)
at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$4(GenomeFile.scala:113)
at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$4$adapted(GenomeFile.scala :102)
at scala.collection.immutable.List.foreach(List.scala:333)
at org.broadinstitute.pilon.GenomeFile.processRegions(GenomeFile.scala:102)
at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:111)
at org.broadinstitute.pilon.Pilon.main(Pilon.scala)
/public2/home/lhd1/ONT-data/zpz2rd/hebing_zpz/minimapasb.sort.bam: 18026073 reads, 0 filtered, 14 918576 mapped, 45156 proper, 440 stray, Unpaired 100% 149+/-8, max 443 Processing contig_1:1-302494 frags /public2/home/lhd1/ONT-data/zpz2rd/hebing_zpz/minimapasb.sort.bam: ...100000...200000...300 000coverage 2 Total Reads: 5577, Coverage: 2, minDepth: 10 Frag coverage mean=2.276061673950558, median=18.0
IdentifyIssues: contig_1:1-302494
size=302494 medianCoverage=18.0 meanCoverage=2.276260024992231
LowCoverage n=202 bases=240076
HighCN n=191 bases=60802
pctBadOverall: 29827 688555 4
Break? n=18 bases=230265
Clip? n=25 bases=261
CollapsedRepeat? n=188 bases=60683
contig_1 1038 ins . G contig_1 1100 snp G T contig_1 2635 del C . contig_1 3551 snp G A contig_1 3605 snp C T contig_1 3632 snp C T contig_1 6249 snp G C contig_1 6523 del G . contig_1 7683 snp G A contig_1 7774 del G . contig_1 7781 del A . contig_1 7854 del C . contig_1 12079 snp A G contig_1 12525 snp T C contig_1 12619 snp T C contig_1 12668 snp G C contig_1 12692 snp G A contig_1 12695 snp G A contig_1 12707 snp C T contig_1 12758 snp C T contig_1 12773 snp G A contig_1 17594 snp G C contig_1 17636 snp C G contig_1 17651 snp G A contig_1 19716 snp C T contig_1 21719 snp G T contig_1 21767 snp G C contig_1 21875 del G . contig_1 22059 snp C T contig_1 22077 snp G C contig_1 23313 snp G A contig_1 23406 snp G A contig_1 24166 snp A G contig_1 24172 snp C A contig_1 24178 snp G A contig_1 24184 snp G A contig_1 24250 snp A C contig_1 24274 snp G A contig_1 24307 snp G A contig_1 24466 snp G T contig_1 24487 del T . contig_1 24494 snp A T contig_1 24509 snp C A contig_1 24515 snp G A contig_1 24530 snp A G contig_1 24593 snp A C contig_1 24644 snp G A contig_1 27022 snp C G contig_1 27140 snp C G contig_1 27179 snp G A contig_1 27457 snp G C contig_1 27475 snp C A contig_1 27578 snp G C contig_1 27587 snp G A contig_1 27605 snp C T contig_1 27611 snp C G contig_1 27623 snp C T contig_1 27677 snp C G contig_1 27695 snp G A contig_1 27701 snp C T contig_1 27711 snp T A contig_1 27736 snp G T contig_1 27743 snp G A contig_1 29947 snp G C contig_1 29959 snp G A contig_1 29962 snp G A contig_1 30020 snp C T contig_1 30037 snp G C contig_1 30040 snp A G contig_1 30077 snp C T contig_1 30092 del CCG . contig_1 31342 snp A G contig_1 31374 snp G T contig_1 31379 del T . contig_1 31383 del T . contig_1 31393 del C . contig_1 31415 snp T C contig_1 31430 snp G A contig_1 34010 del C . contig_1 34022 snp C T contig_1 37035 snp T C contig_1 37038 snp C G contig_1 37056 snp C T contig_1 37065 snp A G contig_1 37068 snp T C contig_1 37086 snp G T contig_1 45616 snp A G contig_1 45622 snp C T contig_1 45628 snp C T contig_1 45631 snp C T contig_1 45706 snp T C contig_1 47672 snp G A contig_1 48432 snp G A contig_1 48459 snp G A contig_1 48516 snp T G contig_1 49156 snp T C contig_1 49216 snp G A contig_1 49246 snp A G contig_1 49252 snp C T contig_1 49273 snp C T contig_1 49279 snp G T contig_1 49285 snp A G contig_1 49345 snp C T contig_1 49366 snp C T contig_1 57952 snp G A contig_1 59700 snp C T contig_1 59742 snp C T contig_1 61619 snp C T contig_1 61649 snp C T contig_1 61994 snp T C contig_1 64020 snp G A contig_1 64137 snp C T contig_1 64287 snp C T contig_1 64536 snp C T contig_1 64668 del C . contig_1 64696 snp C T contig_1 66737 snp C T contig_1 66977 snp C T contig_1 67004 snp G A contig_1 67223 snp C T contig_1 67238 snp C T contig_1 91036 snp C T contig_1 94331 snp G A contig_1 100784 snp G A contig_1 101937 snp G A contig_1 101946 snp G A contig_1 102264 snp G A contig_1 102270 snp C T contig_1 102287 snp G T contig_1 102339 snp G C contig_1 102875 snp T C contig_1 102887 snp G C contig_1 102908 snp C T contig_1 102936 snp C T contig_1 106386 snp G A contig_1 108236 snp G A contig_1 108254 snp C T contig_1 108278 snp G A contig_1 108287 snp A G contig_1 108332 snp G A contig_1 108352 snp G A contig_1 108595 snp G A contig_1 108619 snp C T contig_1 109117 snp G A contig_1 109168 snp G C contig_1 109198 snp G A contig_1 109300 snp A C contig_1 109339 snp G A contig_1 109393 snp A G contig_1 113734 snp C G contig_1 114662 snp T C contig_1 115928 ins . C contig_1 115954 snp A G contig_1 117152 snp G A contig_1 118025 snp G C contig_1 118031 snp G C contig_1 118034 snp G T contig_1 118139 snp T G contig_1 118386 snp G C contig_1 118431 snp G A contig_1 119028 snp G A contig_1 119082 snp T C contig_1 119103 snp C A contig_1 119112 snp C T contig_1 119458 snp G A contig_1 119461 snp G A contig_1 122749 snp C T contig_1 123393 del A . contig_1 123412 del T . contig_1 123414 snp G C contig_1 123456 snp C T contig_1 123460 snp C T contig_1 123465 snp C T contig_1 123483 snp C G contig_1 124550 snp C A contig_1 124661 snp C T contig_1 124664 del G . contig_1 124719 snp G A contig_1 124734 snp C G contig_1 125412 snp C G contig_1 128515 snp G A contig_1 128517 snp C T contig_1 128564 snp A C contig_1 128566 snp C T contig_1 129128 amb G C contig_1 129154 snp G A contig_1 130315 snp G A contig_1 130325 snp A G contig_1 134020 snp T C contig_1 134123 snp C A contig_1 134129 snp C T contig_1 134971 snp C G contig_1 135013 snp T G contig_1 135040 snp T C contig_1 137373 snp C T contig_1 141830 snp A G contig_1 145645 snp T G contig_1 145658 snp C T contig_1 145953 snp G A contig_1 146456 snp G C contig_1 146489 snp C T contig_1 146492 snp C T contig_1 146531 snp C T contig_1 146690 snp G A contig_1 147401 snp C G contig_1 147692 snp C T contig_1 148310 snp C T contig_1 149255 snp C T contig_1 151270 snp G A contig_1 151824 snp C G contig_1 171877 del A . contig_1 171887 del G . contig_1 172638 snp T G contig_1 172645 snp G C contig_1 172663 snp G A contig_1 172895 snp C A contig_1 172910 del C . contig_1 172923 del C . contig_1 172942 snp G A contig_1 172996 del C . contig_1 173016 snp T G contig_1 173030 del CA . contig_1 173035 ins . CA contig_1 173039 snp G T contig_1 173045 del C . contig_1 173076 snp C G contig_1 173079 snp C G contig_1 173111 snp C A contig_1 173133 snp G A contig_1 173169 snp G C contig_1 173177 snp T C contig_1 173178 snp C T contig_1 173184 del G . contig_1 173186 snp G C contig_1 173187 snp C T contig_1 173190 snp C T contig_1 173203 snp T G contig_1 173212 snp G T contig_1 173338 snp G C contig_1 177457 snp C T contig_1 177487 snp G C contig_1 177499 snp C T contig_1 177502 snp C T contig_1 177511 snp C T contig_1 177520 snp G T contig_1 177553 snp G A contig_1 177613 snp C T contig_1 182476 snp G A contig_1 182479 snp C G contig_1 182875 snp C T contig_1 183052 snp C A contig_1 183080 snp G A contig_1 183088 snp G A contig_1 190138 snp T C contig_1 192473 snp C T contig_1 192477 snp C T contig_1 192493 snp A G contig_1 210067 snp G A contig_1 210290 snp G A contig_1 210419 snp C T contig_1 210428 snp C T contig_1 210652 snp C T contig_1 210723 snp G T contig_1 211218 snp C A contig_1 236270 snp G A contig_1 237383 del A . contig_1 245238 del C . contig_1 246211 snp A G contig_1 246220 snp C T contig_1 249506 snp T C contig_1 249521 snp C A contig_1 249563 snp C A contig_1 251155 snp G A contig_1 251167 snp C T contig_1 251212 snp G T contig_1 251218 snp G C contig_1 251224 snp G T contig_1 251260 snp G A contig_1 251278 snp C G contig_1 251294 del T . contig_1 251297 snp C T contig_1 251304 snp C T contig_1 251342 snp T G contig_1 251345 snp G A contig_1 251373 snp C T contig_1 251375 ins . G contig_1 251378 del TG . contig_1 251406 snp G A contig_1 252346 snp A G contig_1 260490 snp C T contig_1 268845 snp T C contig_1 268884 ins . G contig_1 268889 snp C G contig_1 268892 snp C T contig_1 268900 snp A G contig_1 268901 snp T C contig_1 274640 snp G C contig_1 274644 snp C T contig_1 274650 snp T C contig_1 277944 snp T C contig_1 277953 snp T A contig_1 277956 snp C T contig_1 277977 snp A C contig_1 278019 snp T A contig_1 285310 snp T G contig_1 285316 snp G A contig_1 285319 snp G A contig_1 285337 snp G T contig_1 285355 snp C T contig_1 285745 snp T G contig_1 285746 snp A C contig_1 285747 snp T C Confirmed 22828 of 302494 bases (7.55%) Corrected 282 snps; 1 ambiguous bases; corrected 7 small insertions totaling 8 bases, 31 small de letions totaling 36 bases Large collapsed region: contig_1:17502-27810 size 10309 Large collapsed region: contig_1:56779-67336 size 10558 Large collapsed region: contig_1:112360-125533 size 13174 Large collapsed region: contig_1:176853-194296 size 17444
Attempting to fix local continuity breaks
fixBreak: contig_1:2761-24200
Exception in thread "main" java.lang.IllegalStateException: Inappropriate call if not paired read at htsjdk.samtools.SAMRecord.requireReadPaired(SAMRecord.java:892) at htsjdk.samtools.SAMRecord.getFirstOfPairFlag(SAMRecord.java:950) at org.broadinstitute.pilon.BamFile$MateMap.addRead(BamFile.scala:236) at org.broadinstitute.pilon.BamFile$MateMap.$anonfun$addReads$1(BamFile.scala:232) at org.broadinstitute.pilon.BamFile$MateMap.$anonfun$addReads$1$adapted(BamFile.scala:232 ) at scala.collection.immutable.List.foreach(List.scala:333) at org.broadinstitute.pilon.BamFile$MateMap.addReads(BamFile.scala:232) at org.broadinstitute.pilon.BamFile$MateMap.(BamFile.scala:230)
at org.broadinstitute.pilon.BamFile.recruitFlankReads(BamFile.scala:351)
at org.broadinstitute.pilon.GapFiller.$anonfun$recruitReadsFromBams$1(GapFiller.scala:367 )
at org.broadinstitute.pilon.GapFiller.$anonfun$recruitReadsFromBams$1$adapted(GapFiller.s cala:366)
at scala.collection.immutable.List.foreach(List.scala:333)
at org.broadinstitute.pilon.GapFiller.recruitReadsFromBams(GapFiller.scala:366)
at org.broadinstitute.pilon.GapFiller.recruitReadsOfType(GapFiller.scala:375)
at org.broadinstitute.pilon.GapFiller.recruitFrags(GapFiller.scala:379)
at org.broadinstitute.pilon.GapFiller.recruitLocalReads(GapFiller.scala:394)
at org.broadinstitute.pilon.GapFiller.recruitReads(GapFiller.scala:401)
at org.broadinstitute.pilon.GapFiller.assembleAcrossBreak(GapFiller.scala:54)
at org.broadinstitute.pilon.GapFiller.fixBreak(GapFiller.scala:46)
at org.broadinstitute.pilon.GenomeRegion.$anonfun$identifyAndFixIssues$6(GenomeRegion.sca la:401)
at org.broadinstitute.pilon.GenomeRegion.$anonfun$identifyAndFixIssues$6$adapted(GenomeRe gion.scala:399)
at scala.collection.immutable.List.foreach(List.scala:333)
at org.broadinstitute.pilon.GenomeRegion.identifyAndFixIssues(GenomeRegion.scala:399)
at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$4(GenomeFile.scala:113)
at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$4$adapted(GenomeFile.scala :102)
at scala.collection.immutable.List.foreach(List.scala:333)
at org.broadinstitute.pilon.GenomeFile.processRegions(GenomeFile.scala:102)
at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:111)
at org.broadinstitute.pilon.Pilon.main(Pilon.scala)