FilterMutectCalls "Duplicate key" error

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Bug Report

Affected tool(s) or class(es)

FilterMutectCalls

Affected version(s)

gatk-4.1.9.0

Description

When I was running FilterMutectCalls with one of my samples, I got an error as "Duplicate key".

14:50:59.201 INFO FilterMutectCalls - ------------------------------------------------------------ 14:50:59.202 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.1.9.0 14:50:59.202 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/ 14:50:59.203 INFO FilterMutectCalls - Executing as mparment@her2-w110 on Linux v5.7.7-1.el7.elrepo.x86_64 amd64 14:50:59.203 INFO FilterMutectCalls - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_31-b13 14:50:59.203 INFO FilterMutectCalls - Start Date/Time: December 12, 2020 2:50:57 PM CET 14:50:59.203 INFO FilterMutectCalls - ------------------------------------------------------------ 14:50:59.203 INFO FilterMutectCalls - ------------------------------------------------------------ 14:50:59.204 INFO FilterMutectCalls - HTSJDK Version: 2.23.0 14:50:59.204 INFO FilterMutectCalls - Picard Version: 2.23.3 14:50:59.204 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2 14:50:59.204 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 14:50:59.204 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 14:50:59.205 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 14:50:59.205 INFO FilterMutectCalls - Deflater: IntelDeflater 14:50:59.205 INFO FilterMutectCalls - Inflater: IntelInflater 14:50:59.205 INFO FilterMutectCalls - GCS max retries/reopens: 20 14:50:59.205 INFO FilterMutectCalls - Requester pays: disabled 14:50:59.205 INFO FilterMutectCalls - Initializing engine 14:51:00.692 INFO FeatureManager - Using codec VCFCodec to read file file:///workdir/mparment/data/process/A2683/PTC2_unfiltered.vcf.gz 14:51:01.406 INFO FilterMutectCalls - Done initializing engine 14:51:02.360 INFO FilterMutectCalls - Shutting down engine [December 12, 2020 2:51:02 PM CET] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.07 minutes. Runtime.totalMemory()=2385510400 java.lang.IllegalStateException: Duplicate key 7.395307178412063E-4 at java.util.stream.Collectors.lambda$throwingMerger$138(Collectors.java:133) at java.util.stream.Collectors$$Lambda$67/403388441.apply(Unknown Source) at java.util.HashMap.merge(HashMap.java:1245) at java.util.stream.Collectors.lambda$toMap$196(Collectors.java:1320) at java.util.stream.Collectors$$Lambda$69/854719230.accept(Unknown Source) at java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:512) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:502) 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.walkers.mutect.filtering.ContaminationFilter.(ContaminationFilter.java:26) at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.buildFiltersList(Mutect2FilteringEngine.java:290) at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.(Mutect2FilteringEngine.java:60) at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls.onTraversalStart(FilterMutectCalls.java:138) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1047) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211) 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) srun: error: her2-w110: task 0: Exited with exit code 3

Steps to reproduce

cd /software/gatk-4.1.9.0

srun ./gatk FilterMutectCalls -R /CECI/proj/iribhm/tc_phylogeny/genome/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -V /workdir/mparment/data/process/A2683/PTC2_unfiltered.vcf.gz --tumor-segmentation /workdir/mparment/data/process/A2683/PTC2_N3_S2_PTC2_T1_segments.table --tumor-segmentation /workdir/mparment/data/process/A2683/PTC2_N3_S2_PTC2_T2_S1_segments.table --tumor-segmentation /workdir/mparment/data/process/A2683/PTC2_N3_S2_PTC2_T2_S3_segments.table --tumor-segmentation /workdir/mparment/data/process/A2683/PTC2_N3_S2_PTC2_T2_S5_segments.table --tumor-segmentation /workdir/mparment/data/process/A2683/PTC2_N3_S2_PTC2_T3_segments.table --tumor-segmentation /workdir/mparment/data/process/A2683/PTC2_N3_S2_PTC2_T4_segments.table --tumor-segmentation /workdir/mparment/data/process/A2683/PTC2_N3_S4_PTC2_T1_segments.table --tumor-segmentation /workdir/mparment/data/process/A2683/PTC2_N3_S4_PTC2_T2_S1_segments.table --tumor-segmentation /workdir/mparment/data/process/A2683/PTC2_N3_S4_PTC2_T2_S3_segments.table --tumor-segmentation /workdir/mparment/data/process/A2683/PTC2_N3_S4_PTC2_T2_S5_segments.table --tumor-segmentation /workdir/mparment/data/process/A2683/PTC2_N3_S4_PTC2_T3_segments.table --tumor-segmentation /workdir/mparment/data/process/A2683/PTC2_N3_S4_PTC2_T4_segments.table --contamination-table /workdir/mparment/data/process/A2683/PTC2_N3_S2_PTC2_T1_contamination.table --contamination-table /workdir/mparment/data/process/A2683/PTC2_N3_S2_PTC2_T2_S1_contamination.table --contamination-table /workdir/mparment/data/process/A2683/PTC2_N3_S2_PTC2_T2_S3_contamination.table --contamination-table /workdir/mparment/data/process/A2683/PTC2_N3_S2_PTC2_T2_S5_contamination.table --contamination-table /workdir/mparment/data/process/A2683/PTC2_N3_S2_PTC2_T3_contamination.table --contamination-table /workdir/mparment/data/process/A2683/PTC2_N3_S2_PTC2_T4_contamination.table --contamination-table /workdir/mparment/data/process/A2683/PTC2_N3_S4_PTC2_T1_contamination.table --contamination-table /workdir/mparment/data/process/A2683/PTC2_N3_S4_PTC2_T2_S1_contamination.table --contamination-table /workdir/mparment/data/process/A2683/PTC2_N3_S4_PTC2_T2_S3_contamination.table --contamination-table /workdir/mparment/data/process/A2683/PTC2_N3_S4_PTC2_T2_S5_contamination.table --contamination-table /workdir/mparment/data/process/A2683/PTC2_N3_S4_PTC2_T3_contamination.table --contamination-table /workdir/mparment/data/process/A2683/PTC2_N3_S4_PTC2_T4_contamination.table -ob-priors /workdir/mparment/data/process/A2683/PTC2_read-orientation-model.tar.gz -O /workdir/mparment/data/process/A2683/PTC2_filtered.vcf.gz

Actual behavior

It look like this error: https://github.com/broadinstitute/gatk/issues/3018. I followed GATK's good practice rules and I use Mutect2 in "multisample" mode.

broadinstitute / gatk