System.ArgumentOutOfRangeException: Index was out of range

[Gerde89]

Dear all, I meet an error while running canvas Tumor-normal-enrichment, could you please help me ? The CMD:

Canvas Tumor-normal-enrichment -b HCC2218C_S1.bam --normal-bam=HCC2218BL_S1.bam --reference=kmer.fa --manifest=NexteraRapidCapture_Exome_TargetedRegions_v1.2Used.txt -g hg19 -n HCC2218C -f filter13.bed -o result --sample-b-allele-vcf=HCC2218BL_S1.vcf --custom-parameters=CanvasBin,-m=TruncatedDynamicRange

  All the files are download from demo data.
  The error messages:

ERROR: Canvas workflow error: System.ArgumentOutOfRangeException: Index was out of range. Must be non-negative and less than the size of the collection.
Parameter name: index
   at System.ThrowHelper.ThrowArgumentOutOfRange_IndexException()
   at Canvas.CanvasRunner.GetIntermediateBinnedFilesByBamPath(GenomeMetadata genomeInfo, Boolean isPairedEnd, List`1 sampleIds, IDirectoryLocation tempFolder, String canvasReferencePath, String canvasBedPath, List`1 bamPaths, StringBuilder commandLine, String tempManifestPath)
   at Canvas.CanvasRunner.InvokeCanvasBin35Mers(CanvasCallset callset, String canvasReferencePath, String canvasBedPath, String ploidyVcfPath)
   at Isas.Framework.Checkpointing.Internals.SerializingCheckpointRunner.<>c__DisplayClass8_0`1.<RunCheckpoint>b__0(Checkpoint checkpoint)
   at Isas.Framework.Checkpointing.Internals.CoreCheckpointRunner.RunCheckpoint[TResult](String name, Func`2 run)
   at Canvas.CanvasRunner.<CallSampleInternal>d__36.MoveNext()
--- End of stack trace from previous location where exception was thrown ---
   at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
   at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task)
   at Canvas.CanvasRunner.CallSample(CanvasCallset callset)
   at Canvas.ModeLauncher.Launch()

  Thanks a lot !
  PS: the version of Canvas is 1.32.0.918

Best, Gerde

[wongjessica93]

Did you ever figure this out? I am running into the same issue

[eroller]

see https://github.com/Illumina/canvas/issues/62

[wongjessica93]

Thanks Eric! Switching to v1.11.0 ran successfully. I am wondering if you have any recommended tools for visualizing Canvas CNV results as the vcf file formatting is slightly different than ones used for tools such as CNVkit, etc?

[eroller]

You should be able to load the VCF file in IGV. Unfortunately we have introduced visualization files only in the newest versions of Canvas which does not support the Enrichment workflows. Typically we use the coverage and b-allele information for visualization of CNVs (along with the actual CNV calls from the VCF). You can extract this data from the .partitioned file and the VFResults.txt.gz files.