Crossposting from an issue on Wigits/hmftools github in case anyone has solutions here: Hi all, I am having trouble processing one sample (WGS ~100x T, 40x N). Esvee raises an error "failed to process junction": Command output:

...
  16:11:33.339 [DEBUG] deleting 25 candidate BAMs
  16:11:33.520 [INFO ] 22482263 records written to BAM
  16:11:33.521 [DEBUG] writing sorted BAM: esvee/PANX_1341_Lv_M.esvee.prep.bam
  16:12:00.532 [DEBUG] writing sorted BAM: esvee/PANX_1341_Ly_R.esvee.prep.bam
  16:12:08.262 [INFO ] Esvee prep complete, mins(30.158)
  16:12:08.298 [DEBUG] processing tumor prep bam(s): [esvee/PANX_1341_Lv_M.esvee.prep.bam]
  16:12:08.298 [DEBUG] processing reference prep bam(s): [esvee/PANX_1341_Ly_R.esvee.prep.bam]
  16:12:08.344 [INFO ] writing to output directory(esvee/)
  16:12:08.365 [INFO ] fragment length bounds(min=151 max=779)
  16:12:11.166 [INFO ] loaded 461154 junctions, types(split=454597 discordant=6557 indel=13833 hotspot=3) from file: esvee/PANX_1341_Lv_M.esvee.prep.junction.tsv
  16:12:14.849 [DEBUG] primary assembly splits 269998 junction groups across 40 threads
  16:12:19.754 [WARN ] assembly(junc(chr1:2678382:-1) coords(extLen=37 refLen=134 refBasePos=2678515 len=171 juncIndex=37) support(38) mismatches(8)) excluding long remote region(chr1:2659634-2671618 reads(117) counts(mate=0 supp=0 disc=117) softClipMapQual(0))
  16:12:33.212 [DEBUG] processed 10000 junction groups, remaining(259998)
  16:12:37.415 [ERROR] failed to process junction(chr19:1161907:-1) with 249 reads

Command error:

...
  16:12:11.166 [INFO ] loaded 461154 junctions, types(split=454597 discordant=6557 indel=13833 hotspot=3) from file: esvee/PANX_1341_Lv_M.esvee.prep.junction.tsv
  16:12:14.849 [DEBUG] primary assembly splits 269998 junction groups across 40 threads
  16:12:19.754 [WARN ] assembly(junc(chr1:2678382:-1) coords(extLen=37 refLen=134 refBasePos=2678515 len=171 juncIndex=37) support(38) mismatches(8)) excluding long remote region(chr1:2659634-2671618 reads(117) counts(mate=0 supp=0 disc=117) softClipMapQual(0))
  16:12:33.212 [DEBUG] processed 10000 junction groups, remaining(259998)
  16:12:37.415 [ERROR] failed to process junction(chr19:1161907:-1) with 249 reads
  java.lang.ArrayIndexOutOfBoundsException: Index 61 out of bounds for length 61
  	at com.hartwig.hmftools.esvee.assembly.ExtReadParseState.currentBase(ExtReadParseState.java:76)
  	at com.hartwig.hmftools.esvee.assembly.ExtensionSeqBuilder.buildSequence(ExtensionSeqBuilder.java:263)
  	at com.hartwig.hmftools.esvee.assembly.ExtensionSeqBuilder.<init>(ExtensionSeqBuilder.java:131)
  	at com.hartwig.hmftools.esvee.assembly.JunctionAssembler.processJunction(JunctionAssembler.java:125)
  	at com.hartwig.hmftools.esvee.assembly.JunctionGroupAssembler.processJunctionGroup(JunctionGroupAssembler.java:186)
  	at com.hartwig.hmftools.esvee.assembly.JunctionGroupAssembler.run(JunctionGroupAssembler.java:113)

Any clues as to where to look at? Let me know if you need i.e. the esvee prep bam files or slices. This is ESVEE v1.2 on Oncoanalyser v2.3. I have run >100 samples in that cohort, this is the only one that fails. Thanks! Jose

On it José 🙂

Thanks Rayan! I shared it with you over email 👍