Tumor-normal-enrichment Mode for Version 1.25 and up

[ghost]

I'm trying to run Tumor-normal-enrichment mode on some samples, but I'm getting several errors even with the sample data in the README:

~/Canvas-1.25/Canvas Tumor-normal-enrichment -b HCC2218C_S1.bam --normal-bam HCC2218BL_S1.bam --manifest NexteraRapidCapture_Exome_TargetedRegions_v1.2Used.txt -o output -r hg19/kmer.fa -g hg19/genome_dir/ -f hg19/filter13.bed --sample-b-allele-vcf HCC2218BL_S1.vcf -n HCC_samples

One of the errors I'm getting on both my samples and the example in the README is:

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 ploidyBedPath)
   at Isas.Framework.Checkpointing.SerializingCheckpointRunner.<>c__DisplayClass7_0`1.<RunCheckpoint>b__0(Checkpoint checkpoint)
   at Isas.Framework.Checkpointing.CoreCheckpointRunner.RunCheckpoint[TResult](String name, Func`2 run)
   at Canvas.CanvasRunner.<CallSampleInternal>d__33.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.<>c__DisplayClass5_0.<Launch>b__0(FrameworkServices frameworkServices)
2017-09-03T21:12:52,ERROR: Exception from tracked tasks encountered in checkpointer dispose: System.AggregateException: One or more errors occurred. (dotnet returned error code 134

---Failed command:
/usr/bin/dotnet /home/ec2-user/Canvas-1.25/CanvasSNV.dll  -c 1 -v /home/ec2-user/canvas_tn/HCC_test/HCC2218BL_S1.vcf -b /home/ec2-user/canvas_tn/HCC_test/HCC2218C_S1.bam -o /home/ec2-user/canvas_tn/HCC_test/output/TempCNV_HCC_samples/1-HCC_samples.SNV.txt.gz --isSomatic

With only the README samples, I'm also getting several Unhandled Exception: System.ArgumentException: Error: Chromosome name '1' does not match bam file at '/home/ec2-user/canv as_tn/HCC_test/HCC2218C_S1.bam' errors, but that's not occurring with my samples, so it's probably just an issue with the formatting of the HCC2218 VCF.

The example in the README is for version 1.3.4, which is very outdated. Can you please update the README with a working Tumor-normal-enrichment example for 1.25 and up?

Thank you,

Raymon

[jlac]

I'm encountering exactly the same error. Any resolution to this?

[eroller]

Sorry for this error. T/N enrichment workflow has not had any improvements since version 1.11.0 so if you can run that version with mono that should give you the same results. We have been focusing on whole genome sequencing workflows (especially Small Pedigree) so this has not been a high priority.

[BenoitFiset]

Hi Eric,

Is version 1.11.0 still the one to use for T/N enrichment or fixes are made in the newest version ?

Thanks,

B.

[eroller]

It is still 1.11.0. We don't have any plans to update the T/N Enrichment mode.