Running 260 WES samples through joint discovery and VQSR

Hi,

I am trying to process locally 260 WES gvcf through joint discovery wdl pipeline. I encountered an error at GenotypeGVCFs below which I am not sure how to proceed.

I have used all the default reference libraries and only modified the merge_count in the script to be 8144 so that my server resources won't be maxout fully in the ImportGVCFs step.

https://github.com/gatk-workflows/gatk4-germline-snps-indels/blob/master/joint-discovery-gatk4-local.wdl

23:17:43.992 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples
23:17:44.064 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples
23:17:46.334 INFO GenotypeGVCFs - Shutting down engine
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),30.197597194999727,Cpu time(s),28.791204838999864
[June 25, 2018 11:17:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 4.01 minutes.
Runtime.totalMemory()=5354029056
java.lang.IllegalArgumentException: log10LikelihoodsOfAC are bad 2.559797571100845E-21,NaN
at org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult.(AFCalculationResult.java:72)
at org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator.getLog10PNonRef(AlleleFrequencyCalculator.java:143)
at org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:255)
at org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:210)
at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.calculateGenotypes(GenotypeGVCFs.java:266)
at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.regenotypeVC(GenotypeGVCFs.java:222)
at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.apply(GenotypeGVCFs.java:201)
at org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:109)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.VariantWalkerBase.traverse(VariantWalkerBase.java:107)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:980)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Using GATK jar /gatk/build/libs/gatk-package-4.0.5.0-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 -Xmx5g -Xms5g -jar /gatk/build/libs/gatk-package-4.0.5.0-local.jar GenotypeGVCFs -R /cromwell-executions/JointGenotyping/3a733624-60a0-4e57-b7f5-7b7e99795738/call-GenotypeGVCFs/shard-25/inputs/data1/bill/pipeline/cromwell/hg38/Homo_sapiens_assembly38.fasta -O output.vcf.gz -D /cromwell-executions/JointGenotyping/3a733624-60a0-4e57-b7f5-7b7e99795738/call-GenotypeGVCFs/shard-25/inputs/data1/bill/pipeline/cromwell/hg38/Homo_sapiens_assembly38.dbsnp138.vcf -G StandardAnnotation --only-output-calls-starting-in-intervals --use-new-qual-calculator -V gendb://genomicsdb -L chrY:10821870-11717714

Tagged:

Issue · Github
by shlee

Issue Number
4975
State
closed
Last Updated
Assignee
Array
Closed By
droazen

Best Answers

Answers

  • mwleemwlee Member

    Hi Sheila,

    Yes, I am using 4.0.5.0 throughtout the analysis. I'll try to run with 4.0.4.0 to see if it worked. I tried with 1-10 sample for the flow with 4.0.5.0 and it worked, but failed with increase in samples. Any idea what this error is about?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @mwlee
    Hi,

    No, I am not sure. But, it seems to have popped up in 4.0.5.0. Can you confirm this works for all your samples in 4.0.4.0? I may need you to submit a bug report. Can you also try with 4.0.5.1 just to check?

    Thanks,
    Sheila

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @mwlee,

    I see from your command at the end that you may be using the new QUAL model.

    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 -Xmx5g -Xms5g -jar /gatk/build/libs/gatk-package-4.0.5.0-local.jar GenotypeGVCFs -R /cromwell-executions/JointGenotyping/3a733624-60a0-4e57-b7f5-7b7e99795738/call-GenotypeGVCFs/shard-25/inputs/data1/bill/pipeline/cromwell/hg38/Homo_sapiens_assembly38.fasta -O output.vcf.gz -D /cromwell-executions/JointGenotyping/3a733624-60a0-4e57-b7f5-7b7e99795738/call-GenotypeGVCFs/shard-25/inputs/data1/bill/pipeline/cromwell/hg38/Homo_sapiens_assembly38.dbsnp138.vcf -G StandardAnnotation --only-output-calls-starting-in-intervals \
    --use-new-qual-calculator \
    -V gendb://genomicsdb -L chrY:10821870-11717714
    

    Can you try WITHOUT the new qual (--use-new-qual-calculator)?

  • mwleemwlee Member

    Sorry for late reply.

    I confirm I don't see the issue with 4.0.4.0.

    I tried running without --use-new-qual-calculator and there is NO issue anymore. What does it do differently with both cromwell version?

  • mwleemwlee Member

    Thank you Shlee and Sheila for your help.

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