CallMolecularConsensusReads Error java.lang.ArrayIndexOutOfBoundsException

I have a mapped BAM with UMIs on which I’ve already run the following commands without error: bwa mem; AnnotateBamWithUmis; SortBam; SetMateInformation; and GroupReadsByUmi.

I’m now attempting to run the following CallMolecularConsensusReadsCommand: fgbio --tmp-dir=./fgbio_tmp CallMolecularConsensusReads -1 41 -i ./groupby_umi.bam -o ./call_consensus.bam -M 2 2> ./call_consensus.log

However the task keeps failing, with the log file showing the error:

Time for last 2,000,000:  242s.  Last read position: */*
[2019/09/18 03:17:53 | CallMolecularConsensusReads | Info] processed    12,500,000 records.  Elapsed time: 00:04:05s.  Time for last 500,000:   12s.  Last read position: chr8:143,563,991
[2019/09/18 03:18:03 | CallMolecularConsensusReads | Info] processed    13,000,000 records.  Elapsed time: 00:04:16s.  Time for last 500,000:   10s.  Last read position: chr9:99,386,947
[2019/09/18 03:18:04 | FgBioMain | Info] CallMolecularConsensusReads failed. Elapsed time: 4.32 minutes.
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
    at com.fulcrumgenomics.umi.UmiConsensusCaller.$anonfun$toSourceRead$1(UmiConsensusCaller.scala:210)
    at com.fulcrumgenomics.commons.CommonsDef.forloop(CommonsDef.scala:210)
    at com.fulcrumgenomics.umi.UmiConsensusCaller.toSourceRead(UmiConsensusCaller.scala:209)
    at com.fulcrumgenomics.umi.UmiConsensusCaller.toSourceRead$(UmiConsensusCaller.scala:195)
    at com.fulcrumgenomics.umi.VanillaUmiConsensusCaller.toSourceRead(VanillaUmiConsensusCaller.scala:102)
    at com.fulcrumgenomics.umi.VanillaUmiConsensusCaller.$anonfun$consensusFromSamRecords$1(VanillaUmiConsensusCaller.scala:152)
    at scala.collection.immutable.Stream.flatMap(Stream.scala:486)
    at scala.collection.immutable.Stream.$anonfun$flatMap$1(Stream.scala:494)
    at scala.collection.immutable.Stream.$anonfun$append$1(Stream.scala:252)
    at scala.collection.immutable.Stream$Cons.tail(Stream.scala:1169)
    at scala.collection.immutable.Stream$Cons.tail(Stream.scala:1159)
    at scala.collection.immutable.Stream.length(Stream.scala:309)
    at scala.collection.SeqLike.sorted(SeqLike.scala:635)
    at scala.collection.SeqLike.sorted$(SeqLike.scala:634)
    at scala.collection.AbstractSeq.sorted(Seq.scala:41)
    at scala.collection.SeqLike.sortBy(SeqLike.scala:621)
    at scala.collection.SeqLike.sortBy$(SeqLike.scala:621)
    at scala.collection.AbstractSeq.sortBy(Seq.scala:41)
    at com.fulcrumgenomics.umi.UmiConsensusCaller.filterToMostCommonAlignment(UmiConsensusCaller.scala:290)
    at com.fulcrumgenomics.umi.UmiConsensusCaller.filterToMostCommonAlignment$(UmiConsensusCaller.scala:286)
    at com.fulcrumgenomics.umi.VanillaUmiConsensusCaller.filterToMostCommonAlignment(VanillaUmiConsensusCaller.scala:102)
    at com.fulcrumgenomics.umi.VanillaUmiConsensusCaller.consensusFromSamRecords(VanillaUmiConsensusCaller.scala:153)
    at com.fulcrumgenomics.umi.VanillaUmiConsensusCaller.consensusSamRecordsFromSamRecords(VanillaUmiConsensusCaller.scala:133)
    at com.fulcrumgenomics.umi.UmiConsensusCaller.consensusReadsFromSamRecords(UmiConsensusCaller.scala:248)
    at com.fulcrumgenomics.umi.UmiConsensusCaller.consensusReadsFromSamRecords$(UmiConsensusCaller.scala:246)
    at com.fulcrumgenomics.umi.VanillaUmiConsensusCaller.consensusReadsFromSamRecords(VanillaUmiConsensusCaller.scala:102)
    at com.fulcrumgenomics.umi.ConsensusCallingIterator.advance(ConsensusCallingIterator.scala:78)
    at com.fulcrumgenomics.umi.ConsensusCallingIterator.hasNext(ConsensusCallingIterator.scala:50)
    at scala.collection.Iterator.foreach(Iterator.scala:929)
    at scala.collection.Iterator.foreach$(Iterator.scala:929)
    at com.fulcrumgenomics.umi.ConsensusCallingIterator.foreach(ConsensusCallingIterator.scala:41)
    at com.fulcrumgenomics.Writer.write(Writer.scala:37)
    at com.fulcrumgenomics.Writer.write$(Writer.scala:37)
    at com.fulcrumgenomics.bam.api.SamWriter.write(SamWriter.scala:101)
    at com.fulcrumgenomics.Writer.$plus$plus$eq(Writer.scala:47)
    at com.fulcrumgenomics.Writer.$plus$plus$eq$(Writer.scala:46)
    at com.fulcrumgenomics.bam.api.SamWriter.$plus$plus$eq(SamWriter.scala:101)
    at com.fulcrumgenomics.umi.CallMolecularConsensusReads.execute(CallMolecularConsensusReads.scala:165)
    at com.fulcrumgenomics.cmdline.FgBioMain.makeItSo(FgBioMain.scala:99)
    at com.fulcrumgenomics.cmdline.FgBioMain.makeItSoAndExit(FgBioMain.scala:80)
    at com.fulcrumgenomics.cmdline.FgBioMain$.main(FgBioMain.scala:48)
    at com.fulcrumgenomics.cmdline.FgBioMain.main(FgBioMain.scala)

Any advice on what might be causing the error would be greatly appreciated

[jst43]

@lbaxter21 I think I either read the bam file into python to look for a malformed read, or I used pysam to catch the read. It was just a quick script so I’m afraid I don’t have the code I used.

[lbaxter21]

thanks - in the meantime I managed to identify that one of my fastq files had been incompletely downloaded, (using a unix one-liner: for i in ls *.gz; do echo $(gzcat ${i} | wc -l)/4|bc; done — so that was what was causing the outofrange error in my case.I was surprised that bwa hadn’t complained about a truncated input file or a mismatch between the number of reads in R1 and R2.  Annoying this slipped through and caused a problem later in the pipeline, but serves as a useful reminder for me to sanity-check input data properly!Thanks for your quick reply,L On Monday, 24 February 2020, 16:42:25 GMT, Joe Sneath Thompson [e-mail] wrote:

@lbaxter21 I think I either read the bam file into python to look for a malformed read, or I used pysam to catch the read. It was just a quick script so I’m afraid I don’t have the code I used.

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