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Error in generating DetermineGermlineContigPloidy

sridhar_28sridhar_28 bangaloreMember
Hi Team,
I trying to generate CNV from GATK pipeline.
Process intervals and collect read counts are done when i am running Determine germlinecontig ploidy i am getting this error.

Errors in detail

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 -jar /home/ec2-user/data/gatk_cnv/gatk-4.1.4.0/gatk-package-4.1.4.0-local.jar DetermineGermlineContigPloidy --contig-ploidy-priors ploidy_model/interval_ploidy_new.txt --interval-merging-rule OVERLAPPING_ONLY -L preprocessed_intervals.interval_list -I ESI_17.tsv -I ES_msc.tsv --exclude-intervals exclude_intervals.bed --output esi_ploidy --output-prefix esi_cnvploidy --verbosity DEBUG
.................................................
................................................
04:46:53.856 INFO DetermineGermlineContigPloidy - Aggregating read-count file ESI_17.tsv (1 / 2)
04:46:57.935 INFO DetermineGermlineContigPloidy - Shutting down engine
[October 22, 2019 4:46:57 AM UTC] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 0.60 minutes.
Runtime.totalMemory()=3437232128
java.lang.IllegalArgumentException: Intervals for read-count file ESI_17.tsv do not contain all specified intervals.
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:725)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.writeSamplesByCoveragePerContig(DetermineGermlineContigPloidy.java:374)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.doWork(DetermineGermlineContigPloidy.java:285)
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:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)

Please help me in fixing the bug.

Thank you

Answers

  • sleeslee Member, Broadie, Dev ✭✭✭

    @sridhar_28 It looks like you are trying to exclude intervals using --exclude-intervals exclude_intervals.bed. From the tool documentation:

    It is possible to run the tool over a subset of all intervals present in the input count files, which can be specified by -L; this can be used to pass a filtered interval list produced by FilterIntervals to mask intervals from modeling. Intervals may also be blacklisted using -XL. The specified intervals that result from resolving -L/-XL inputs must be exactly present in all of the input count files.

    You should ensure that this is satisfied. If not, you may need to edit your exclude_intervals.bedfile accordingly; alternatively, you could blacklist these intervals from the outset during the PreprocessIntervals step (which would result in counts not being collected at all in the excluded regions).

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