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Why am I get this error when running Mutect2.wdl with orientation_bias_mixture_model_filter enabled

The code:
I locally ran Mutect2.wdl with mutect2.exome.inputs.json, from: GATK github repo, changed "Mutect2.run_orientation_bias_filter": "False" to "Mutect2.run_orientation_bias_filter": "True".

The error:
`[2019-08-27 13:20:12,84] [error] WorkflowManagerActor Workflow 50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a failed (during ExecutingWorkflowState): Job Mutect2.M2:49:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /media/volume2/gatk4-somatic-snvs-indels/m2_v36/ob_fiter/cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/execution/stderr.
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/tmp.2ab6d0ca
10:10:14.946 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
10:10:16.985 INFO GetSampleName - ------------------------------------------------------------
10:10:16.986 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.1.2.0
10:10:16.986 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/
10:10:16.986 INFO GetSampleName - Executing as [email protected] on Linux v3.10.0-957.21.3.el7.x86_64 amd64
10:10:16.986 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_191-8u191-b12-0ubuntu0.16.04.1-b12
10:10:16.986 INFO GetSampleName - Start Date/Time: August 27, 2019 10:10:14 AM UTC
10:10:16.986 INFO GetSampleName - ------------------------------------------------------------
10:10:16.986 INFO GetSampleName - ------------------------------------------------------------
10:10:16.987 INFO GetSampleName - HTSJDK Version: 2.19.0
10:10:16.987 INFO GetSampleName - Picard Version: 2.19.0
10:10:16.987 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:10:16.987 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:10:16.987 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:10:16.987 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:10:16.987 INFO GetSampleName - Deflater: IntelDeflater
10:10:16.987 INFO GetSampleName - Inflater: IntelInflater
10:10:16.987 INFO GetSampleName - GCS max retries/reopens: 20
10:10:16.987 INFO GetSampleName - Requester pays: disabled
10:10:16.988 WARN GetSampleName -

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Warning: GetSampleName is a BETA tool and is not yet ready for use in production

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

10:10:16.988 INFO GetSampleName - Initializing engine
WARNING: BAM index file /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143.bai is older than BAM /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143.bam
10:10:18.623 INFO GetSampleName - Done initializing engine
10:10:18.633 INFO ProgressMeter - Starting traversal
10:10:18.633 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
10:10:18.634 INFO ProgressMeter - unmapped 0.0 0 NaN
10:10:18.634 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
10:10:18.634 INFO GetSampleName - Shutting down engine
[August 27, 2019 10:10:18 AM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1758986240
Using GATK jar /root/gatk.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 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/Homo_sapiens_assembly19.fasta -I /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143.bam -O tumor_name.txt -encode
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/tmp.2ab6d0ca
10:10:30.213 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
10:10:32.643 INFO GetSampleName - ------------------------------------------------------------
10:10:32.644 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.1.2.0
10:10:32.644 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/
10:10:32.644 INFO GetSampleName - Executing as [email protected] on Linux v3.10.0-957.21.3.el7.x86_64 amd64
10:10:32.644 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_191-8u191-b12-0ubuntu0.16.04.1-b12
10:10:32.645 INFO GetSampleName - Start Date/Time: August 27, 2019 10:10:30 AM UTC
10:10:32.645 INFO GetSampleName - ------------------------------------------------------------
10:10:32.645 INFO GetSampleName - ------------------------------------------------------------
10:10:32.645 INFO GetSampleName - HTSJDK Version: 2.19.0
10:10:32.645 INFO GetSampleName - Picard Version: 2.19.0
10:10:32.645 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:10:32.645 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:10:32.645 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:10:32.646 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:10:32.646 INFO GetSampleName - Deflater: IntelDeflater
10:10:32.679 INFO GetSampleName - Inflater: IntelInflater
10:10:32.679 INFO GetSampleName - GCS max retries/reopens: 20
10:10:32.679 INFO GetSampleName - Requester pays: disabled
10:10:32.680 WARN GetSampleName -

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Warning: GetSampleName is a BETA tool and is not yet ready for use in production

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

10:10:32.680 INFO GetSampleName - Initializing engine
WARNING: BAM index file /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143_normal.bai is older than BAM /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143_normal.bam
10:10:33.900 INFO GetSampleName - Done initializing engine
10:10:33.930 INFO ProgressMeter - Starting traversal
10:10:33.930 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
10:10:33.931 INFO ProgressMeter - unmapped 0.0 0 NaN
10:10:33.931 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
10:10:33.931 INFO GetSampleName - Shutting down engine
[August 27, 2019 10:10:33 AM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=2057830400
Using GATK jar /root/gatk.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 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/Homo_sapiens_assembly19.fasta -I /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143_normal.bam -O normal_name.txt -encode
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/tmp.2ab6d0ca
10:10:48.541 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
10:10:50.332 INFO Mutect2 - ------------------------------------------------------------
10:10:50.332 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.1.2.0
10:10:50.332 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
10:10:50.332 INFO Mutect2 - Executing as [email protected] on Linux v3.10.0-957.21.3.el7.x86_64 amd64
10:10:50.332 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_191-8u191-b12-0ubuntu0.16.04.1-b12
10:10:50.333 INFO Mutect2 - Start Date/Time: August 27, 2019 10:10:48 AM UTC
10:10:50.333 INFO Mutect2 - ------------------------------------------------------------
10:10:50.333 INFO Mutect2 - ------------------------------------------------------------
10:10:50.333 INFO Mutect2 - HTSJDK Version: 2.19.0
10:10:50.333 INFO Mutect2 - Picard Version: 2.19.0
10:10:50.333 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:10:50.333 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:10:50.333 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:10:50.334 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:10:50.334 INFO Mutect2 - Deflater: IntelDeflater
10:10:50.337 INFO Mutect2 - Inflater: IntelInflater
10:10:50.337 INFO Mutect2 - GCS max retries/reopens: 20
10:10:50.337 INFO Mutect2 - Requester pays: disabled
10:10:50.337 INFO Mutect2 - Initializing engine
WARNING: BAM index file /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143.bai is older than BAM /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143.bam
WARNING: BAM index file /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143_normal.bai is older than BAM /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143_normal.bam
10:10:52.002 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/Mutect2-exome-panel.vcf
10:10:52.263 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/af-only-gnomad.raw.sites.vcf
10:10:55.503 INFO IntervalArgumentCollection - Processing 897413 bp from intervals
10:10:55.556 WARN IndexUtils - Feature file "/cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/af-only-gnomad.raw.sites.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
10:11:02.089 WARN IndexUtils - Index file /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/af-only-gnomad.raw.sites.vcf.idx is out of date (index older than input file). Use IndexFeatureFile to make a new index.
10:11:02.141 INFO Mutect2 - Done initializing engine
10:11:02.321 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
10:11:02.347 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
10:11:02.445 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
10:11:02.445 INFO IntelPairHmm - Available threads: 24
10:11:02.445 INFO IntelPairHmm - Requested threads: 4
10:11:02.445 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
10:11:02.784 INFO ProgressMeter - Starting traversal
10:11:02.785 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
10:11:16.920 INFO ProgressMeter - X:83352758 0.2 20 84.9
10:11:32.628 INFO ProgressMeter - X:83724032 0.5 50 100.5
10:11:43.547 INFO ProgressMeter - X:84502558 0.7 70 103.0
10:11:54.258 INFO ProgressMeter - X:84569415 0.9 90 104.9
10:12:12.839 INFO ProgressMeter - X:85213804 1.2 110 94.2
10:12:22.921 INFO ProgressMeter - X:91132345 1.3 160 119.8
10:12:33.331 INFO ProgressMeter - X:99887464 1.5 250 165.7
10:12:43.657 INFO ProgressMeter - X:100382071 1.7 350 208.2
10:12:53.794 INFO ProgressMeter - X:100630082 1.9 420 227.0
10:13:04.133 INFO ProgressMeter - X:101857308 2.0 540 267.0
10:13:14.287 INFO ProgressMeter - X:103495183 2.2 670 305.7
10:13:24.811 INFO ProgressMeter - X:106486350 2.4 850 359.1
10:13:35.332 INFO ProgressMeter - X:107834743 2.5 1010 397.3
10:13:48.051 INFO ProgressMeter - X:109697099 2.8 1130 410.2
10:13:58.520 INFO ProgressMeter - X:115582571 2.9 1330 454.1
10:14:09.002 INFO ProgressMeter - X:117907800 3.1 1440 464.0
10:14:20.555 INFO ProgressMeter - X:118675277 3.3 1510 458.1
10:14:30.556 INFO ProgressMeter - X:119048632 3.5 1580 456.3
10:14:40.693 INFO ProgressMeter - X:119760303 3.6 1680 462.6
10:14:51.309 INFO ProgressMeter - X:123019741 3.8 1800 472.6
10:15:01.778 INFO ProgressMeter - X:128652291 4.0 1930 484.5
10:15:11.874 INFO ProgressMeter - X:129173065 4.2 2040 491.4
10:15:23.066 INFO ProgressMeter - X:130409716 4.3 2160 497.9
10:15:33.098 INFO ProgressMeter - X:133379680 4.5 2290 508.3
10:15:43.530 INFO ProgressMeter - X:135289112 4.7 2460 525.7
10:15:54.168 INFO ProgressMeter - X:135961553 4.9 2600 535.4
10:16:04.732 INFO ProgressMeter - X:142121802 5.0 2760 548.4
10:16:14.841 INFO ProgressMeter - X:150791353 5.2 2990 574.9
10:16:25.784 INFO ProgressMeter - X:152735857 5.4 3180 590.7
10:16:36.191 INFO ProgressMeter - X:153173150 5.6 3410 613.7
10:16:46.442 INFO ProgressMeter - X:153633692 5.7 3630 633.8
10:16:56.886 INFO ProgressMeter - X:154020339 5.9 3810 645.6
10:17:07.018 INFO ProgressMeter - Y:14885508 6.1 4180 688.6
10:17:08.768 INFO Mutect2 - 1300074 read(s) filtered by: (((((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonChimericOriginalAlignmentReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND ReadLengthReadFilter) AND GoodCigarReadFilter) AND WellformedReadFilter)
1300074 read(s) filtered by: ((((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonChimericOriginalAlignmentReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND ReadLengthReadFilter) AND GoodCigarReadFilter)
1300074 read(s) filtered by: (((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonChimericOriginalAlignmentReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND ReadLengthReadFilter)
1300074 read(s) filtered by: ((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonChimericOriginalAlignmentReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter)
1300074 read(s) filtered by: (((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonChimericOriginalAlignmentReadFilter)
1300074 read(s) filtered by: ((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter)
1135597 read(s) filtered by: (((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter)
520431 read(s) filtered by: ((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter)
520431 read(s) filtered by: (((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter)
520431 read(s) filtered by: ((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter)
520431 read(s) filtered by: (MappingQualityReadFilter AND MappingQualityAvailableReadFilter)
520431 read(s) filtered by: MappingQualityReadFilter
615166 read(s) filtered by: NotDuplicateReadFilter
164477 read(s) filtered by: PassesVendorQualityCheckReadFilter

10:17:08.768 INFO ProgressMeter - Y:59335502 6.1 4578 750.5
10:17:08.769 INFO ProgressMeter - Traversal complete. Processed 4578 total regions in 6.1 minutes.
10:17:11.549 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.092782131
10:17:11.549 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 8.986074343
10:17:11.550 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 2.80 sec
10:17:11.616 INFO Mutect2 - Shutting down engine
[August 27, 2019 10:17:11 AM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 6.39 minutes.
Runtime.totalMemory()=3034054656
Using GATK jar /root/gatk.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 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/Homo_sapiens_assembly19.fasta -I /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143.bam -tumor HCC1143 -I /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143_normal.bam -normal HCC1143_BL --germline-resource /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/af-only-gnomad.raw.sites.vcf -pon /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/Mutect2-exome-panel.vcf -L /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/1323905931/0049-scattered.interval_list -O output.vcf --f1r2-tar-gz f1r2.tar.gz
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/tmp.2ab6d0ca
10:17:28.341 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
10:17:30.717 INFO GetPileupSummaries - ------------------------------------------------------------
10:17:30.718 INFO GetPileupSummaries - The Genome Analysis Toolkit (GATK) v4.1.2.0
10:17:30.718 INFO GetPileupSummaries - For support and documentation go to https://software.broadinstitute.org/gatk/
10:17:30.718 INFO GetPileupSummaries - Executing as [email protected] on Linux v3.10.0-957.21.3.el7.x86_64 amd64
10:17:30.718 INFO GetPileupSummaries - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_191-8u191-b12-0ubuntu0.16.04.1-b12
10:17:30.718 INFO GetPileupSummaries - Start Date/Time: August 27, 2019 10:17:28 AM UTC
10:17:30.718 INFO GetPileupSummaries - ------------------------------------------------------------
10:17:30.718 INFO GetPileupSummaries - ------------------------------------------------------------
10:17:30.719 INFO GetPileupSummaries - HTSJDK Version: 2.19.0
10:17:30.719 INFO GetPileupSummaries - Picard Version: 2.19.0
10:17:30.719 INFO GetPileupSummaries - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:17:30.719 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:17:30.719 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:17:30.719 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:17:30.719 INFO GetPileupSummaries - Deflater: IntelDeflater
10:17:30.719 INFO GetPileupSummaries - Inflater: IntelInflater
10:17:30.720 INFO GetPileupSummaries - GCS max retries/reopens: 20
10:17:30.720 INFO GetPileupSummaries - Requester pays: disabled
10:17:30.720 WARN GetPileupSummaries -

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Warning: GetPileupSummaries is a BETA tool and is not yet ready for use in production

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

10:17:30.720 INFO GetPileupSummaries - Initializing engine
WARNING: BAM index file /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143.bai is older than BAM /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143.bam
10:17:32.076 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/small_exac_common_3.vcf
10:17:32.439 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/small_exac_common_3.vcf
10:17:34.428 INFO IntervalArgumentCollection - Processing 412 bp from intervals
10:17:34.449 INFO GetPileupSummaries - Done initializing engine
10:17:34.460 INFO ProgressMeter - Starting traversal
10:17:34.460 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute
10:17:47.734 INFO GetPileupSummaries - 17080 read(s) filtered by: (((((((((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND MateOnSameContigOrNoMappedMateReadFilter) AND GoodCigarReadFilter) AND WellformedReadFilter)
17080 read(s) filtered by: ((((((((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND MateOnSameContigOrNoMappedMateReadFilter) AND GoodCigarReadFilter)
17080 read(s) filtered by: (((((((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND MateOnSameContigOrNoMappedMateReadFilter)
16981 read(s) filtered by: ((((((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter)
16981 read(s) filtered by: (((((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter)
14591 read(s) filtered by: ((((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter) AND NotDuplicateReadFilter)
2610 read(s) filtered by: (((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter)
2610 read(s) filtered by: ((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter)
2610 read(s) filtered by: (MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter)
2610 read(s) filtered by: MappingQualityNotZeroReadFilter
11981 read(s) filtered by: NotDuplicateReadFilter
2390 read(s) filtered by: PassesVendorQualityCheckReadFilter
99 read(s) filtered by: MateOnSameContigOrNoMappedMateReadFilter

10:17:47.734 INFO ProgressMeter - unmapped 0.2 401 1812.6
10:17:47.734 INFO ProgressMeter - Traversal complete. Processed 401 total loci in 0.2 minutes.
10:17:47.772 INFO GetPileupSummaries - Shutting down engine
[August 27, 2019 10:17:47 AM UTC] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed time: 0.33 minutes.
Runtime.totalMemory()=2065170432
Using GATK jar /root/gatk.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 -Xmx3000m -jar /root/gatk.jar GetPileupSummaries -R /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/Homo_sapiens_assembly19.fasta -I /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143.bam --interval-set-rule INTERSECTION -L /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/1323905931/0049-scattered.interval_list -V /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/small_exac_common_3.vcf -L /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/small_exac_common_3.vcf -O tumor-pileups.table
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/tmp.2ab6d0ca
Using GATK jar /root/gatk.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 -Xmx3000m -jar /root/gatk.jar GetPileupSummaries -R /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/Homo_sapiens_assembly19.fasta -I /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/HCC1143_normal.bam --interval-set-rule INTERSECTION -L /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/1323905931/0049-scattered.interval_list -V /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/small_exac_common_3.vcf -L /cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/inputs/-771983168/small_exac_common_3.vcf -O normal-pileups.table

[2019-08-27 13:20:12,84] [info] WorkflowManagerActor WorkflowActor-50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a is in a terminal state: WorkflowFailedState
[2019-08-27 13:20:55,10] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
`

Best Answer

Answers

  • Angry_PandaAngry_Panda Member
    Accepted Answer

    I have solved this by myself, via making new index file.

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Curious, did you see that it did work locally when it was set to false?
    Is what you copy and pasted here the same stderr that it says to check out:
    Check the content of stderr for potential additional information: /media/volume2/gatk4-somatic-snvs-indels/m2_v36/ob_fiter/cromwell-executions/Mutect2/50cca75d-1aeb-4ff8-80a2-4e3c3d35d01a/call-M2/shard-49/execution/stderr

  • @Tiffany_at_Broad , hi, sorry for my late reply. back to work from holiday. Yes, I index file. Also, actually, you need to change some input name in json file (if u use the same github repo offered wdl and json) Then it worked.

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