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Canvas - Copy number variant (CNV) calling from DNA sequencing data
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System.Exception: Cannot calculate median of an empty SortedList. #56

Open fannyhartmann opened 7 years ago

fannyhartmann commented 7 years ago

Dear Development Team,

I could successfully run the demo with the HCC2218 dataset.

Unfortunately, when I run the workflow Germline-WGS with my own data (a non-model organism- diploid fungus), I had errors.

Here is my command line for the version 1.25:

dotnet ./1.25/Canvas.dll Germline-WGS --bam Run_Canvas/699.MvSl-1064-A1.marked.dupl.realigned.bam --sample-name=699 -r Run_Canvas/MvSl-1064-A1-R4kmer.fa -g Run_Canvas/WholeGenomeFasta --sample-b-allele-vcf Run_Canvas/699.MvSl-1064-A1.tagged.vcf --filter-bed Run_Canvas/filter.bed -o ./OutputCanvasrecentversion

Here is the error message: ---Last lines of stderr log file from /home/fannie/Bureau/OutputCanvasrecentversion/Logging/699_0.binned.stderr.txt: at CanvasBin.CanvasBin.CalculateSingleSampleBinSize(CanvasBinParameters parameters, Dictionary2 possibleAlignments, Dictionary2 observedAlignments, Dictionary2 fragmentLengths, NexteraManifest manifest) at CanvasBin.CanvasBin.RunSingleSample(CanvasBinParameters parameters) at CanvasBin.CanvasBin.Run(CanvasBinParameters parameters) at CanvasBin.Program.Main(String[] args) at Isas.Framework.WorkManagement.JobManager.CheckExitCodes(List1 jobs, Boolean throwExceptionOnBadExitCode) at Isas.Framework.WorkManagement.JobManager.ProcessJobs(List1 jobs, Int32 maxNumThreads, Boolean redirectOutput, Boolean checkExitCodes, Boolean throwExceptionOnBadExitCode) at Isas.Framework.WorkManagement.LocalWorkManager.DoWorkParallelLocal(List1 tasks, TaskResourceRequirements taskRequirements, Int32 maximumThreads, Boolean checkReturnCode, Boolean redirectOutput, Boolean throwExceptionOnError) at Isas.Framework.WorkManagement.LocalWorkManager.DoWorkParallel(List1 tasks, TaskResourceRequirements taskRequirements, Int32 maxAttempts, Boolean throwExceptionOnError) at Canvas.CanvasRunner.BamToBinned(IDirectoryLocation tempFolder, Boolean isPairedEnd, List1 sampleIds, String canvasReferencePath, String canvasBedPath, List1 bamPaths, StringBuilder commandLine, Int32 binSize, Dictionary2 intermediateDataPathsByBam) at Canvas.CanvasRunner.InvokeCanvasBin35Mers(CanvasCallset callset, String canvasReferencePath, String canvasBedPath, String ploidyBedPath) at Isas.Framework.Checkpointing.SerializingCheckpointRunner.<>cDisplayClass7_01.<RunCheckpoint>b__0(Checkpoint checkpoint) at Isas.Framework.Checkpointing.CoreCheckpointRunner.RunCheckpoint[TResult](String name, Func2 run) at Canvas.CanvasRunner.d33.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.<>cDisplayClass5_0.b0(FrameworkServices frameworkServices) 2017-07-28T14:17:44,Max job memory (GB): 0,0 2017-07-28T14:17:44,Longest job runtime (Hours): 0,00 2017-07-28T14:17:44,Total execution time: 00:01:07.9 699_0.binned.stderr.txt 699_0.binned.stdout.txt

see attached error files

I will appreciate your help as I really would be interested in running Canvas. Thank you.

Best wishes,

Fanny

Soniazumalave commented 5 years ago

Hi there,

I am experiencing the same problem. Have you found any solution? Thank you in advance.

BR, Sonia

fannyhartmann commented 5 years ago

Hi Sonia,

I haven't found a solution, but I haven't investigate it further.

Best wishes, Fanny

Le mer. 23 janv. 2019 à 13:54, Sonia Zumalave notifications@github.com a écrit :

Hi there,

I am experiencing the same problem. Have you found any solution? Thank you in advance.

BR, Sonia

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eroller commented 5 years ago

Germline-WGS has been deprecated. Please try Small-Pedigree-WGS workflow. It supports a single sample analysis. Also, HCC2218 is a cancer sample so is not appropriate for germline analysis. Unless you are analyzing the matched normal sample only, you should use the Somatic-WGS workflow.