Not generating denoisedLimit4.png with PlotModeledSegments

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Hanyin Wang

• September 10, 2021 07:23

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.1.8.1

b) Exact command used: 

gatk PlotModeledSegments \
    --denoised-copy-ratios {input.denoisedCR} \
    --allelic-counts {input.hets} \
    --segments {input.segments} \
    --sequence-dictionary {config[reference_dict]} \
    --minimum-contig-length 46709983 \
    --output {params.outputdir} \
    --output-prefix {params.outputprefix}

c) Entire error log: no error message, but here is the log:

"""

01:56:16.587 INFO PlotDenoisedCopyRatios - ------------------------------------------------------------
01:56:16.588 INFO PlotDenoisedCopyRatios - The Genome Analysis Toolkit (GATK) v4.1.8.1
01:56:16.588 INFO PlotDenoisedCopyRatios - For support and documentation go to https://software.broadinstitute.org/gatk/
01:56:16.588 INFO PlotDenoisedCopyRatios - Executing as ******
01:56:16.588 INFO PlotDenoisedCopyRatios - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_272-b10
01:56:16.588 INFO PlotDenoisedCopyRatios - Start Date/Time: September 10, 2021 1:56:16 AM CDT
01:56:16.588 INFO PlotDenoisedCopyRatios - ------------------------------------------------------------
01:56:16.588 INFO PlotDenoisedCopyRatios - ------------------------------------------------------------
01:56:16.589 INFO PlotDenoisedCopyRatios - HTSJDK Version: 2.23.0
01:56:16.589 INFO PlotDenoisedCopyRatios - Picard Version: 2.22.8
01:56:16.589 INFO PlotDenoisedCopyRatios - HTSJDK Defaults.COMPRESSION_LEVEL : 2
01:56:16.589 INFO PlotDenoisedCopyRatios - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
01:56:16.589 INFO PlotDenoisedCopyRatios - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
01:56:16.589 INFO PlotDenoisedCopyRatios - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
01:56:16.589 INFO PlotDenoisedCopyRatios - Deflater: IntelDeflater
01:56:16.590 INFO PlotDenoisedCopyRatios - Inflater: IntelInflater
01:56:16.590 INFO PlotDenoisedCopyRatios - GCS max retries/reopens: 20
01:56:16.590 INFO PlotDenoisedCopyRatios - Requester pays: disabled
01:56:16.590 INFO PlotDenoisedCopyRatios - Initializing engine
01:56:16.590 INFO PlotDenoisedCopyRatios - Done initializing engine
01:56:16.591 INFO PlotDenoisedCopyRatios - Reading and validating input files...
01:56:17.554 INFO PlotDenoisedCopyRatios - Contigs above length threshold: {chr1=249250621, chr2=243199373, chr3=198022430, chr4=191154276, chr5=180915260, chr6=171115067, chr7=159138663, chr8=146364022, chr9=141213431, chr10=135534747, chr11=135006516, chr12=133851895, chr13=115169878, chr14=107349540, chr15=102531392, chr16=90354753, chr17=81195210, chr18=78077248, chr19=59128983, chr20=63025520, chr21=48129895, chr22=51304566, chrX=155270560, chrY=59373566}
01:56:17.748 INFO PlotDenoisedCopyRatios - Writing plots to *****
01:56:20.067 INFO PlotDenoisedCopyRatios - PlotDenoisedCopyRatios complete.
01:56:20.068 INFO PlotDenoisedCopyRatios - Shutting down engine
[September 10, 2021 1:56:20 AM CDT] org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatios done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=2246049792
"""

If not an error, choose a category for your question(REQUIRED):
c) Why do I NOT seeing denoisedLimit4.png generated from PlotModeledSegments?

Hello, I am running CNV pipeline using GATK. With above commend everything went well except it did not generate "denoisedLimit4.png" as expected from latest tutorial (Tutorial#11682). I did get the rest 5 files including "denoised.png". The rest of CNV pipeline is also working well.

Many thanks.

Hanyin

0

• 

  Pamela Bretscher

  • September 10, 2021 13:20

  Hi Hanyin Wang,

  Thank you for writing in to the forum. Are you seeing any issue with the output of PlotModeledSegments? I see your command for PlotModeledSegments but your output of PlotDenoisedCopyRatios. Could you post the command that you ran for PlotDenoisedCopyRatios given that you are experiencing an issue with the output from this tool?

  Kind regards,

  Pamela

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• 

  Hanyin Wang

  • September 10, 2021 14:34

  Thanks for the kind reply Pamela!

  I am so sorry I meant to say the issue is with PlotDenoisedCopyRatios. No issue with PlotModeledSegments. Would be happy to change the question if there's a way.

  Here's my command for PlotDenoisedCopyRatios:

  gatk PlotDenoisedCopyRatios \
      --standardized-copy-ratios {input.standardized} \
      --denoised-copy-ratios {input.denoised} \
      --sequence-dictionary {config[reference_dict]} \
      --minimum-contig-length {config[min_contig_len]} \
      --output {params.outputdir} \
      --output-prefix {params.outputprefix} 

  Best,

  Hanyin

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• 

  Pamela Bretscher

  • September 10, 2021 15:27

  Hi Hanyin Wang,

  Thank you for sharing the command and no worries about changing the question! The somatic CNV pipeline is actually out of date so PlotDenoisedCopyRatios works a little bit differently now. The denoisedLimit4.png file is no longer generated and the denoised.png file automatically restricts the copy ratio to a value of 4, which you should see reflected in this file. If you would like to change the default max copy ratio, you can specify --maximum-copy-ratio when running the tool. I hope this clarifies the results you are getting, please let me know if you have any additional questions.

  Kind regards,

  Pamela

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• 

  Hanyin Wang

  • September 11, 2021 02:23

  This is tremendously helpful! Thank you so much Pamela.

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