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Issue with running CNV germline workflows using "cnv_germline_cohort_workflow.wdl"

azzathaazzatha MakkahMember

Greetings GATK team,

I am trying to run CNV germline workflows using "cnv_germline_cohort_workflow.wdl". I'm using the examples provided in Github
However, after the step PostprocessGermlineCNVCalls I got the following error:

22:37:00.588 INFO  PostprocessGermlineCNVCalls - Shutting down engine
[October 7, 2019 10:37:00 PM UTC] org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls done. Elapsed time: 1.67 minutes.
Runtime.totalMemory()=2294808576
Exception in thread "Thread-1" htsjdk.samtools.util.RuntimeIOException: java.nio.file.DirectoryNotEmptyException: /cromwell-executions/CNVGermlineCohortWorkflow/208592f4-6e9d-403d-99bf-1066a8a82cd7/call-PostprocessGermlineCNVCalls/shard-0/tmp.c77022dd/gcnv-segmented-calls2725641956355372386/SAMPLE_0
        at htsjdk.samtools.util.IOUtil.recursiveDelete(IOUtil.java:1346)
        at org.broadinstitute.hellbender.utils.io.IOUtils.deleteRecursively(IOUtils.java:1061)
        at org.broadinstitute.hellbender.utils.io.DeleteRecursivelyOnExitPathHook.runHooks(DeleteRecursivelyOnExitPathHook.java:56)
        at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.file.DirectoryNotEmptyException: /cromwell-executions/CNVGermlineCohortWorkflow/208592f4-6e9d-403d-99bf-1066a8a82cd7/call-PostprocessGermlineCNVCalls/shard-0/tmp.c77022dd/gcnv-segmented-calls2725641956355372386/SAMPLE_0
        at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:242)
        at sun.nio.fs.AbstractFileSystemProvider.deleteIfExists(AbstractFileSystemProvider.java:108)
        at java.nio.file.Files.deleteIfExists(Files.java:1165)
        at htsjdk.samtools.util.IOUtil$3.postVisitDirectory(IOUtil.java:1338)
        at htsjdk.samtools.util.IOUtil$3.postVisitDirectory(IOUtil.java:1327)
        at java.nio.file.Files.walkFileTree(Files.java:2688)
        at java.nio.file.Files.walkFileTree(Files.java:2742)
        at htsjdk.samtools.util.IOUtil.recursiveDelete(IOUtil.java:1344)
        ... 3 more
Using GATK jar /cromwell-executions/CNVGermlineCohortWorkflow/208592f4-6e9d-403d-99bf-1066a8a82cd7/call-PostprocessGermlineCNVCalls/shard-0/inputs/-25482348/gatk-package-4.1.2.0-local.jar defined in environment variable GATK_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 -Xmx6000m -jar /cromwell-executions/CNVGermlineCohortWorkflow/208592f4-6e9d-403d-99bf-1066a8a82cd7/call-PostprocessGermlineCNVCalls/shard-0/inputs/-25482348/gatk-package-4.1.2.0-local.jar PostprocessGermlineCNVCalls --calls-shard-path CALLS_0 --model-shard-path MODEL_0 --allosomal-contig X --allosomal-contig Y --autosomal-ref-copy-number 2 --contig-ploidy-calls contig-ploidy-calls --sample-index 0 --output-genotyped-intervals genotyped-intervals-SM-74NEG_20xy-downsampled.vcf.gz --output-genotyped-segments genotyped-segments-SM-74NEG_20xy-downsampled.vcf.gz
/encrypted/genomics/nationalguard/new_cnv_azza/final_workflow/gatk/scripts/cnv_wdl/germline/workdir/CNVGermlineCohortWorkflow/208592f4-6e9d-403d-99bf-1066a8a82cd7/call-PostprocessGermlineCNVCalls/shard-0/execution/script: line 68: --output-denoised-copy-ratios: command not found

I've been struggling to understand why this is happening, and already investigated and tested many things, but I cannot seem to find an explanation. Any advice is really appreciated.

Looking forward to your answer,

Best Regards,
Azza.

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