Error with ReviewConsensusVariants by fgbio
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Entering edit mode
15 months ago
dyg2 • 0

I keep getting an error when trying to use the fgbio ReviewConsensusVariants command:

Exception in thread "main" java.util.NoSuchElementException
    at scala.collection.immutable.BitmapIndexedMapNode.apply(HashMap.scala:569)
    at scala.collection.immutable.BitmapIndexedMapNode.apply(HashMap.scala:567)
    at scala.collection.immutable.BitmapIndexedMapNode.apply(HashMap.scala:567)
    at scala.collection.immutable.HashMap.apply(HashMap.scala:132)
    at com.fulcrumgenomics.umi.ReviewConsensusVariants.$anonfun$generateDetailsFile$13(ReviewConsensusVariants.scala:255)
    at com.fulcrumgenomics.umi.ReviewConsensusVariants.$anonfun$generateDetailsFile$13$adapted(ReviewConsensusVariants.scala:251)
    at scala.collection.immutable.List.foreach(List.scala:312)
    at com.fulcrumgenomics.umi.ReviewConsensusVariants.$anonfun$generateDetailsFile$4(ReviewConsensusVariants.scala:251)
    at com.fulcrumgenomics.umi.ReviewConsensusVariants.$anonfun$generateDetailsFile$4$adapted(ReviewConsensusVariants.scala:234)
    at scala.collection.IterableOnceOps.foreach(IterableOnce.scala:576)
    at scala.collection.IterableOnceOps.foreach$(IterableOnce.scala:574)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1196)
    at com.fulcrumgenomics.umi.ReviewConsensusVariants.generateDetailsFile(ReviewConsensusVariants.scala:234)
    at com.fulcrumgenomics.umi.ReviewConsensusVariants.execute(ReviewConsensusVariants.scala:204)
    at com.fulcrumgenomics.cmdline.FgBioMain.makeItSo(FgBioMain.scala:110)
    at com.fulcrumgenomics.cmdline.FgBioMain.makeItSoAndExit(FgBioMain.scala:86)
    at com.fulcrumgenomics.cmdline.FgBioMain$.main(FgBioMain.scala:50)
    at com.fulcrumgenomics.cmdline.FgBioMain.main(FgBioMain.scala)

I perform the following steps prior to execuing ReviewConsensusVariants:

  1. Create an unmapped bam from PE reads (picard FastqToSam)
  2. Downsample (picard DownsampleSam)
  3. Extract fastqs from downsampled bam (picard SamToFastq)
  4. Align to reference (bwa mem)
  5. Merge the aligned and unaligned bams (picard MergeBamAlignment)
  6. AnnotateBamWithUMIs (fgbio)
  7. Sort annotated bam by query name (picard)
  8. SetMateInformation (fgbio)
  9. GroupReadsByUmi (fgbio)
  10. CallMolecularConsensus (fgbio)
  11. Extract fastqs from the consensus bam (picard SamToFastq)
  12. Realign the consensus fastq to reference (bwa mem)
  13. Merge the unaligned and aligned consensus bams (picard MergeBamAlignment)
  14. Sort the merged consensus bam by coordinate (picard)
  15. FilterConsensusReads (fgbio)
  16. Coordinate-sort (picard) and index (samtools) the filtered consensus bam and UMI-grouped bam
  17. ReviewConsensusVariants

Final note: the last command does produce a list of variant-supporting reads, but it's usually truncated after 1-5 positions (probably matching the first time a missing element is encountered [see the error above]). Any advice would be greatly appreciated. The reads that are output do make sense for the positions that they cover in terms of variant frequencies. It's just that the program terminates prematurely.

next-gen software error fgbio UMI • 420 views
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