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Problem with DenoiseReadCounts

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Sara Franzelli

Hello,

I'm following this tutorial: Tutorial#11682, after following the Germline CNV (gCNV) workflow tutorial, to plot my results. The third step gives me the following error

REQUIRED for all errors and issues:
a) GATK version used: 4.1.2.0

b) Exact command used:

gatk --java-options "-Xmx4g -XX:ParallelGCThreads=1" DenoiseReadCounts -I /work/common/gatk_test/gatk/test3/CP00040571.counts.hdf5 --count-panel-of-normals cnvponC.pon.hdf5 --standardized-copy-ratios CP00040571_clean.standardizedCR.tsv --denoised-copy-ratios CP00040571_clean.denoisedCR.tsv


c) Entire program log:

Using GATK jar /opt/miniconda2/envs/gatk4/share/gatk4-4.1.2.0-1/gatk-package-4.1.2.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4g -XX:ParallelGCThreads=1 -jar /opt/miniconda2/envs/gatk4/share/gatk4-4.1.2.0-1/gatk-package-4.1.2.0-local.jar DenoiseReadCounts -I /work/common/gatk_test/gatk/test3/CP00040571.counts.hdf5 --count-panel-of-normals cnvponC.pon.hdf5 --standardized-copy-ratios CP00040571_clean.standardizedCR.tsv --denoised-copy-ratios CP00040571_clean.denoisedCR.tsv
12:22:58.331 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/miniconda2/envs/gatk4/share/gatk4-4.1.2.0-1/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Oct 17, 2023 12:23:00 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
12:23:00.081 INFO  DenoiseReadCounts - ------------------------------------------------------------
12:23:00.081 INFO  DenoiseReadCounts - The Genome Analysis Toolkit (GATK) v4.1.2.0
12:23:00.082 INFO  DenoiseReadCounts - For support and documentation go to https://software.broadinstitute.org/gatk/
12:23:00.082 INFO  DenoiseReadCounts - Executing as sara.franzelli@vmngs8.aosp.biodec.com on Linux v5.10.0-13-amd64 amd64
12:23:00.082 INFO  DenoiseReadCounts - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12
12:23:00.082 INFO  DenoiseReadCounts - Start Date/Time: October 17, 2023 12:22:58 PM CEST
12:23:00.082 INFO  DenoiseReadCounts - ------------------------------------------------------------
12:23:00.082 INFO  DenoiseReadCounts - ------------------------------------------------------------
12:23:00.084 INFO  DenoiseReadCounts - HTSJDK Version: 2.19.0
12:23:00.084 INFO  DenoiseReadCounts - Picard Version: 2.19.0
12:23:00.084 INFO  DenoiseReadCounts - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:23:00.084 INFO  DenoiseReadCounts - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:23:00.084 INFO  DenoiseReadCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:23:00.084 INFO  DenoiseReadCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:23:00.084 INFO  DenoiseReadCounts - Deflater: IntelDeflater
12:23:00.085 INFO  DenoiseReadCounts - Inflater: IntelInflater
12:23:00.085 INFO  DenoiseReadCounts - GCS max retries/reopens: 20
12:23:00.085 INFO  DenoiseReadCounts - Requester pays: disabled
12:23:00.085 INFO  DenoiseReadCounts - Initializing engine
12:23:00.085 INFO  DenoiseReadCounts - Done initializing engine
log4j:WARN No appenders could be found for logger (org.broadinstitute.hdf5.HDF5Library).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
12:23:00.124 INFO  DenoiseReadCounts - Reading read-counts file (/work/common/gatk_test/gatk/test3/CP00040571.counts.hdf5)...
HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
  #000: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5D.c line 358 in H5Dopen2(): not found
    major: Dataset
    minor: Object not found
  #001: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Gloc.c line 430 in H5G_loc_find(): can't find object
    major: Symbol table
    minor: Object not found
  #002: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
    major: Symbol table
    minor: Object not found
  #003: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Gtraverse.c line 755 in H5G_traverse_real(): component not found
    major: Symbol table
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
  #000: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5D.c line 358 in H5Dopen2(): not found
    major: Dataset
    minor: Object not found
  #001: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Gloc.c line 430 in H5G_loc_find(): can't find object
    major: Symbol table
    minor: Object not found
  #002: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
    major: Symbol table
    minor: Object not found
  #003: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Gtraverse.c line 755 in H5G_traverse_real(): component not found
    major: Symbol table
    minor: Object not found
12:23:00.862 INFO  SVDDenoisingUtils - Validating sample intervals against original intervals used to build panel of normals...
12:23:01.506 INFO  SVDDenoisingUtils - Preprocessing and standardizing sample read counts...
12:23:01.556 INFO  SVDDenoisingUtils - Preprocessing read counts...
12:23:01.556 INFO  SVDDenoisingUtils - Transforming read counts to fractional coverage...
12:23:01.605 INFO  SVDDenoisingUtils - Subsetting sample intervals to post-filter panel intervals...
12:23:02.411 INFO  SVDDenoisingUtils - Dividing by interval medians from the panel of normals...
12:23:02.447 INFO  SVDDenoisingUtils - Sample read counts preprocessed.
12:23:02.447 INFO  SVDDenoisingUtils - Standardizing read counts...
12:23:02.447 INFO  SVDDenoisingUtils - Dividing by sample medians and transforming to log2 space...
12:23:02.677 INFO  SVDDenoisingUtils - Subtracting sample median...
12:23:02.749 INFO  SVDDenoisingUtils - Sample read counts standardized.
12:23:02.749 WARN  SVDDenoisingUtils - A zero number of eigensamples was specified or no eigensamples were available to perform denoising; denoised copy ratios will be identical to the standardized copy ratios...
12:23:02.749 INFO  SVDDenoisingUtils - Sample denoised.
12:23:02.752 INFO  DenoiseReadCounts - Shutting down engine
[October 17, 2023 12:23:02 PM CEST] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=2478309376
java.lang.IllegalArgumentException: Non-finite log2 copy ratio is not allowed.
        at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:724)
        at org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio.<init>(CopyRatio.java:14)
        at org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisedCopyRatioResult.lambda$new$0(SVDDenoisedCopyRatioResult.java:43)
        at java.util.stream.IntPipeline$4$1.accept(IntPipeline.java:250)
        at java.util.stream.Streams$RangeIntSpliterator.forEachRemaining(Streams.java:110)
        at java.util.Spliterator$OfInt.forEachRemaining(Spliterator.java:693)
        at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
        at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
        at org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisedCopyRatioResult.<init>(SVDDenoisedCopyRatioResult.java:44)
        at org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisingUtils.denoise(SVDDenoisingUtils.java:142)
        at org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals.denoise(SVDReadCountPanelOfNormals.java:88)
        at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:200)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
        at org.broadinstitute.hellbender.Main.main(Main.java:291) 

Thank you for any help

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4 comments

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  • Avatar
    Gökalp Çelik

    Hi Sara Franzelli

    Can you clarify whether you trying to plot the results of a gCNV workflow or a Somatic CNV workflow?

     

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  • Avatar
    Wenhong Jiang

    I have similar problem while plotting the results of a Somatic CNV workflow.

    HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
      #000: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5D.c line 358 in H5Dopen2(): not found
        major: Dataset
        minor: Object not found
      #001: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Gloc.c line 430 in H5G_loc_find(): can't find object
        major: Symbol table
        minor: Object not found
      #002: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
        major: Symbol table
        minor: Object not found
      #003: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Gtraverse.c line 755 in H5G_traverse_real(): component not found
        major: Symbol table
        minor: Object not found
    HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
      #000: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5D.c line 358 in H5Dopen2(): not found
        major: Dataset
        minor: Object not found
      #001: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Gloc.c line 430 in H5G_loc_find(): can't find object
        major: Symbol table
        minor: Object not found
      #002: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
        major: Symbol table
        minor: Object not found
      #003: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Gtraverse.c line 755 in H5G_traverse_real(): component not found
        major: Symbol table
        minor: Object not found

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  • Avatar
    Gökalp Çelik

    Hi Wenhong Jiang

    You may be facing with a wrong file format or a corrupt file which results in this error. Can you check your hdf5 files with hdfview tool to see if the data is present. 

    https://www.hdfgroup.org/download-hdfview/

    Also your PoN and sample may not be compatible therefore you may be facing a similar issue.

    Regards. 

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  • Avatar
    ArdigenSupport

    Suggested Steps

    1. Check your sample count file (.counts.hdf5)

      • Re-run CollectReadCounts if needed, ensuring intervals are clean and consistent.

    2. Recreate the Panel of Normals

      • Use at least 15–30 high-quality normal samples.

      • Ensure all normals use the exact same interval list.

    3. Filter Low-Quality Intervals

      • Consider removing extremely low-coverage or noisy regions.

    4. Upgrade GATK (Optional but recommended)

      • You're using GATK v4.1.2.0, which is quite old.

      • A lot of bugs have been fixed in later versions (4.2+).

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