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Canvas - Copy number variant (CNV) calling from DNA sequencing data
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Small Pedigree Workflow canvaserror: missing libpng #111

Closed clairepalles closed 5 years ago

clairepalles commented 5 years ago

I am trying to run the smallpedigree-WGS workflow in CANVAS using four whole genomes from a family (father and children). The CANVAS log ends with: Running checkpoint 06: Variant calling, Checkpoint 05 CanvasPartition complete..... Launching process for job CanvasPedigreeCaller: Job CanvasPedigreeCaller duration: 00:02:41.6. However the CANVASError file shows:

2019-01-16T23:53:24+00:00,ERROR: Job CanvasPedigreeCaller failed with exit code 255. Job logs: Logging/CanvasPedigreeCaller.stdout Logging/CanvasPedigreeCaller.stderr Job error log has more that 20 lines.Please consult the log for the full content. First 35 lines: --- End of inner exception stack trace --- at System.Threading.Tasks.Task1.GetResultCore(Boolean waitCompletionNotification) at Isas.ClassicBioinfoTools.KentUtils.BedGraphToBigWigConverter.Convert(IFileLocation sourceFile, GenomeMetadata genomeMetadata, IDirectoryLocation outputDirectory) at CanvasPedigreeCaller.Visualization.CoverageBigWigWriter.Write(IReadOnlyList1 segments, IDirectoryLocation output, Double normalizationFactor) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasPedigreeCaller\Visualization\CoverageBigWigWriter.cs:line 37 at CanvasPedigreeCaller.CanvasPedigreeCaller.CallVariants(List1 variantFrequencyFiles, List1 segmentFiles, IFileLocation outVcfFile, String ploidyBedPath, String referenceFolder, List1 sampleNames, String commonCnvsBedPath, List1 sampleTypes) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasPedigreeCaller\CanvasPedigreeCaller.cs:line 148 at CanvasPedigreeCaller.Program.<>cDisplayClass2_0.b12(IWorkDoer workDoer) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasPedigreeCaller\Program.cs:line 191 at Isas.Framework.WorkManagement.JobLaunching.JobLauncherFactory.RunWithJobLauncher(ILogger logger, ISettings settings, IDirectoryLocation loggingDir, Action1 logCommand, CancellationToken cancellationToken, Action1 function) at Isas.Framework.WorkManagement.JobLaunching.JobLauncherFactory.RunWithJobLauncher(ILogger logger, ISettings settings, IDirectoryLocation analysisFolder, CancellationToken cancellationToken, Action1 function) at Isas.Framework.WorkManagement.ResourceManagement.WorkResourceManagerFactory.RunWithResourceManager(ILogger logger, ISettings settings, CancellationToken cancellationToken, Action1 function) at Isas.Framework.WorkManagement.WorkDoerFactory.RunWithWorkDoer(ILogger logger, ISettings settings, IDirectoryLocation analysisFolder, CancellationTokenSource cancellationTokenSource, Action1 function) at CanvasPedigreeCaller.Program.Run(String[] args) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasPedigreeCaller\Program.cs:line 193 at CanvasPedigreeCaller.Program.Main(String[] args) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasPedigreeCaller\Program.cs:line 39 ---> (Inner Exception #0) Isas.Framework.WorkManagement.JobFailedException: Job bedGraphToBigWig-coverage.bedgraph.1 failed with exit code 127 at Isas.Framework.WorkManagement.JobLaunching.BasicJobLauncher.RunSystemProcessCheckExitAsync(JobInfo job, Action1 stdoutCallback, Action1 stderrCallback) at Isas.Framework.WorkManagement.JobLaunching.RuntimeTrackingJobLauncher.LaunchJobAsync(JobInfo jobInfo, Action1 stdoutCallback, Action1 stderrCallback) at Isas.Framework.WorkManagement.IJobLauncherExtensions.LaunchJob(IJobLauncher jobLauncher, JobInfo jobInfo, Action1 stdoutCallback, Action`1 stderrCallback) at Isas.ClassicBioinfoTools.KentUtils.BedGraphToBigWigConverter.<>cDisplayClass6_0.b0(WorkResources resources, IJobLauncher jobLauncher) at Isas.Framework.WorkManagement.ResourceManagement.ThreadedWorkResourceManager.<>cDisplayClass11_01.<RunWithResources>b__3(WorkResources resources) --- End of stack trace from previous location where exception was thrown --- at Isas.Framework.WorkManagement.ResourceManagement.ThreadedWorkResourceManager.<RunWithResources>b__11_1[T](Task1 resourceRequestTask, Task1 functionTask)<--- 2019-01-16T23:53:28+00:00,ERROR: Canvas workflow error: Isas.Framework.WorkManagement.JobFailedException: Job CanvasPedigreeCaller failed with exit code 255 at Isas.Framework.WorkManagement.JobLaunching.BasicJobLauncher.RunSystemProcessCheckExitAsync(JobInfo job, Action1 stdoutCallback, Action1 stderrCallback) at Isas.Framework.WorkManagement.JobLaunching.RuntimeTrackingJobLauncher.LaunchJobAsync(JobInfo jobInfo, Action1 stdoutCallback, Action1 stderrCallback) at Isas.Framework.WorkManagement.IJobLauncherExtensions.LaunchJob(IJobLauncher jobLauncher, JobInfo jobInfo, Action1 stdoutCallback, Action`1 stderrCallback) at Isas.Framework.WorkManagement.IWorkDoerJobExtensions.<>cDisplayClass0_01.<DoWork>b__0(WorkResources sr, IJobLauncher jobLauncher) at Isas.Framework.WorkManagement.ResourceManagement.ThreadedWorkResourceManager.<>c__DisplayClass11_01.b3(WorkResources resources) --- End of stack trace from previous location where exception was thrown --- at Isas.Framework.WorkManagement.ResourceManagement.ThreadedWorkResourceManager.b11_1[T](Task1 resourceRequestTask, Task1 functionTask) at Isas.Framework.WorkManagement.AsTaskExtensions.Await[T](Task1 task) at Canvas.CanvasRunner.RunSmallPedigreeCalling(List1 partitionedPaths, SmallPedigreeCallset callsets) at Isas.Framework.Checkpointing.Legacy.LegacyCheckpointRunner.<>cDisplayClass0_0.b0() at Isas.Framework.Checkpointing.Internals.SerializingCheckpointRunner.<>cDisplayClass8_0`1.b0(Checkpoint checkpoint) at Isas.Framework.Checkpointing.Internals.CoreCheckpointRunner.RunCheckpoint[TResult](String name, Func`2 run) at Isas.Framework.Checkpointing.Legacy.LegacyCheckpointRunner.RunCheckpoint(ICheckpointRunner runner, String name, Action a) at Canvas.CanvasRunner.CallSampleInternal(SmallPedigreeCallset callset) at Canvas.CanvasRunner.CallPedigree(SmallPedigreeCallset callset) at Canvas.ModeLauncher.Launch() I am really at a loss as to how to fix this error as I dont understand the error message. Are you able to take a look and advise?
These are my command line arguments: Command-line arguments: SmallPedigree-WGS --bam=S1.bam --bam=S2.bam --bam=S3bam --bam=S4.bam --sample-b-allele-vcf=variants.vcf.gz -o SmallPedigree-WGS-results -r Sequence/WholeGenomeFasta/kmer.fa -g Sequence/WholeGenomeFasta/ -f Sequence/WholeGenomeFasta/filter13.bed

Any advice would be gratefully accepted. I can see I have a multi sample CNV vcf. Am I ok to use the CNV calls in this even if the PedigreeCaller has failed?

Thanks in advance for any help!

eroller commented 5 years ago

If there is a CNV vcf created then that is the final output. To figure out the error could you show these files:

2019-01-16T23:53:24+00:00,ERROR: Job CanvasPedigreeCaller failed with exit code 255. Job logs: Logging/CanvasPedigreeCaller.stdout Logging/CanvasPedigreeCaller.stderr

The issue may be a problem with execute permissions for the bigwig tools. Make sure all the files in the Canvas binary release are executable: chmod +x -R /path/to/CanvasRelease

clairepalles commented 5 years ago

Thank you for the speedy reply. I think these are the important lines from the files you suggested looking at. I hadnt looked in the Logging folder, just at the CanvasLog.txt. This is more informative I see.

Logging/CanvasPedigreeCaller.stderr 2019-01-16T23:53:21+00:00,ERROR: Job bedGraphToBigWig-coverage.bedgraph.1 failed with exit code 127. Job logs: SmallPedigree-WGS-results/CanvasPedigreeCaller/Logging/bedGraphToBigWig-coverage.bedgraph.1.stdout SmallPedigree-WGS-results/CanvasPedigreeCaller/Logging/bedGraphToBigWig-coverage.bedgraph.1.stderr Job error message: Canvas-1.39.0.1598+master_x64/CanvasPedigreeCaller/bedGraphToBigWig: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory 2019-01-16T23:53:21+00:00,ERROR: Exception caught in WorkDoerFactory. Cancelling all jobs. Exception:

Logging/CanvasPedigreeCaller.stdout

2019-01-16T23:53:20+00:00,Launching process for job bedGraphToBigWig-coverage.bedgraph.1: bash -o pipefail -c " /castles/nr/projects/2017/pallesc-gwas-bo-oac/software/Canvas-1.39.0.1598+master_x64/CanvasPedigreeCaller/bedGraphToBigWig /castles/nr/projects/2017/pallesc-gwas-bo-oac/Claire/SI-NET/CANVAS/SmallPedigree-WGS-results/VisualizationTempG191927Y/coverage.bedgraph /castles/nr/projects/2017/pallesc-gwas-bo-oac/Claire/SI-NET/CANVAS/SmallPedigree-WGS-results/VisualizationTempG191927Y/BigWigConverter/chrom.sizes /castles/nr/projects/2017/pallesc-gwas-bo-oac/Claire/SI-NET/CANVAS/SmallPedigree-WGS-results/VisualizationTempG191927Y/BigWigConverter/coverage.bigwig " 2019-01-16T23:53:21+00:00,Job bedGraphToBigWig-coverage.bedgraph.1 duration: 00:00:00.0

So I need to install libpng12.so.0 to fix this?

Thanks

Claire

From: notifications@github.com [notifications@github.com] Sent: 17 January 2019 21:00 To: Illumina/canvas Cc: Claire Palles (Institute of Cancer and Genomic Sciences); Author Subject: Re: [Illumina/canvas] Small Pedigree Workflow canvaserror (#111)

If there is a CNV vcf created then that is the final output. To figure out the error could you show these files:

2019-01-16T23:53:24+00:00,ERROR: Job CanvasPedigreeCaller failed with exit code 255. Job logs: Logging/CanvasPedigreeCaller.stdout Logging/CanvasPedigreeCaller.stderr

The issue may be a problem with execute permissions for the bigwig tools. Make sure all the files in the Canvas binary release are executable: chmod +x -R /path/to/CanvasRelease

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Illumina/canvas/issues/111#issuecomment-455330138, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AoseTQUP3uThRld7xRrpuEMpDX9VWJkqks5vEORagaJpZM4aGsxH.

eroller commented 5 years ago

Yes, or there is another solution listed at the end of this issue: https://github.com/Illumina/canvas/issues/97

clairepalles commented 5 years ago

Thanks. I did already replace bedGraphToBigWig with a freshly downloaded one. I guess I need to look into what versions of libpng are on my system and update these.

I appreciate your time trouble shooting this!

Claire

From: notifications@github.com [notifications@github.com] Sent: 17 January 2019 21:53 To: Illumina/canvas Cc: Claire Palles (Institute of Cancer and Genomic Sciences); Author Subject: Re: [Illumina/canvas] Small Pedigree Workflow canvaserror (#111)

Yes, or there is another solution listed at the end of this issue: #97https://github.com/Illumina/canvas/issues/97

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Illumina/canvas/issues/111#issuecomment-455345728, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AoseTTxJIq_TMgSeyYNyqFv5DALx9rxhks5vEPC8gaJpZM4aGsxH.