No output from sex chromosomes

[alvaralmstedt]

Hi!

I'm a bit confused about my output. I'm getting CNV calls in all chromosomes except X & Y using my current pipeline as described here (both in CNV.vcf.gz CNV.CoverageAndVariantFrequency.txt):

Issue 97

I suspect that the problem is the vcfs im using for the --ploidy-vcf flag. I am currently using the "placeholder" vcf described in this issue (only changing chrY to Y etc.):

Issue 89

I am doing this because when I try to use the normal vcf (the same one I'm using for the --sample-b-allele-vcf flag) I get the following crash:

2018-11-21T11:49:34+01:00,ERROR: Job A2_SVs.recode.partitioned failed with exit code 134. Job logs:
        /tmp/canvas_on_sentieon/scripttest15/Logging/A2_SVs.recode.partitioned.stdout
        /tmp/canvas_on_sentieon/scripttest15/Logging/A2_SVs.recode.partitioned.stderr
Job error message:
Unhandled Exception: System.Collections.Generic.KeyNotFoundException: The given key was not present in the dictionary.
   at System.ThrowHelper.ThrowKeyNotFoundException()
   at System.Collections.Generic.Dictionary`2.get_Item(TKey key)
   at CanvasCommon.PloidyInfo.LoadPloidyFromVcfFile(String vcfPath, Int32 sampleIndex) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasCommon\PloidyInfo.cs:line 146
   at CanvasPartition.CanvasPartition.Main(String[] args) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasPartition\CanvasPartition.cs:line 112
2018-11-21T11:49:34+01:00,ERROR: Canvas workflow error: Isas.Framework.WorkManagement.JobFailedException: Job A2_SVs.recode.partitioned failed with exit code 134
   at Isas.Framework.WorkManagement.JobLaunching.BasicJobLauncher.<RunSystemProcessCheckExitAsync>d__7.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 Isas.Framework.WorkManagement.JobLaunching.RuntimeTrackingJobLauncher.<LaunchJobAsync>d__6.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 Isas.Framework.WorkManagement.IJobLauncherExtensions.LaunchJob(IJobLauncher jobLauncher, JobInfo jobInfo, Action`1 stdoutCallback, Action`1 stderrCallback)
   at Isas.Framework.WorkManagement.IWorkDoerJobExtensions.<>c__DisplayClass0_0`1.<DoWork>b__0(WorkResources sr, IJobLauncher jobLauncher)
   at Isas.Framework.WorkManagement.ResourceManagement.ThreadedWorkResourceManager.<>c__DisplayClass11_0`1.<RunWithResources>b__3(WorkResources resources)
--- 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 Isas.Framework.WorkManagement.ResourceManagement.ThreadedWorkResourceManager.<<RunWithResources>b__11_1>d`1.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 Isas.Framework.WorkManagement.AsTaskExtensions.Await[T](Task`1 task)
   at Canvas.CanvasRunner.InvokeCanvasPartition(CanvasCallset callset, IFileLocation cleanedPath, String canvasBedPath, IFileLocation canvasSnvPath, 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__38.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()

Does the --ploidy-vcf need to be formatted in some special way like the GT flag be replaced by CN? Although i suspect that getting no calls in the sex chromosomes using the placeholder vcfs is not indeded behaviour either way.

Thankful for any assistance!

[alvaralmstedt]

Solved.
The issue was that the GenomeSize.xml I had generated for my hs37d5 reference had "Unknown" for all of the chromosomes in the "type" field. It worked after I changed 1..22 to "Autosome" as well as X and Y to "Allosome".