I'm trying to run Mutect2 with mitochondrial mode and ERC BP_RESOLUTION and then FilterMutectCalls. I don't know if it's just not possible to do so, but it seems to work ok for about 90% of my files, but for the others I get an error (below).

Is this a bug or am I doing something wrong?

Thanks for your advice and assistance,

Larry.

 

GATK version: 4.1.7.0

Command: 

First I ran: Mutect2 then FilterMutectCalls 

gatk Mutect2         --java-options "-Xmx22G -Djava.io.tmpdir=/nobackup/lnsingh/MTRNA/tmp"         --disable-read-filter MappingQualityReadFilter         --disable-read-filter MappingQualityNotZeroReadFilter         --disable-read-filter MappingQualityAvailableReadFilter         --mitochondria-mode true --callable-depth 25         -R /nobackup/lnsingh/MTRNA/lib/rCRS.fa         -I /nobackup/lnsingh/MTRNA/out/COVSUBJ_0121_1_N_HA_filtered.humanspliced.bam         -L MT         -ERC BP_RESOLUTION         -O /nobackup/lnsingh/MTRNA/out/COVSUBJ_0121_1_N_HA_filtered.humanspliced.gvcf.gz

gatk FilterMutectCalls         --java-options "-Xmx22G -Djava.io.tmpdir=/nobackup/lnsingh/MTRNA/tmp"         --disable-read-filter MappingQualityReadFilter         --disable-read-filter MappingQualityNotZeroReadFilter         --disable-read-filter MappingQualityAvailableReadFilter         --mitochondria-mode true         -R /nobackup/lnsingh/MTRNA/lib/rCRS.fa         -V /nobackup/lnsingh/MTRNA/out/COVSUBJ_0121_1_N_HA_filtered.humanspliced.gvcf.gz         -L MT         -O /nobackup/lnsingh/MTRNA/out/COVSUBJ_0121_1_N_HA_filtered.humanspliced.filtered.gvcf.gz

Log:

Running: gatk Mutect2         --java-options "-Xmx22G -Djava.io.tmpdir=/nobackup/lnsingh/MTRNA/tmp"         --disable-read-filter MappingQualityReadFilter         --disable-read-filter MappingQualityNotZeroReadFilter         --disable-read-filter MappingQualityAvailableReadFilter         --mitochondria-mode true --callable-depth 25         -R /nobackup/lnsingh/MTRNA/lib/rCRS.fa         -I /nobackup/lnsingh/MTRNA/out/COVSUBJ_0121_1_N_HA_filtered.humanspliced.bam         -L MT         -ERC BP_RESOLUTION         -O /nobackup/lnsingh/MTRNA/out/COVSUBJ_0121_1_N_HA_filtered.humanspliced.gvcf.gz

Using GATK jar /nobackupp16/swbuild/hsp/COVID19/anaconda3/envs/COVIRT_GATK/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-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 -Xmx22G -Djava.io.tmpdir=/nobackup/lnsingh/MTRNA/tmp -jar /nobackupp16/swbuild/hsp/COVID19/anaconda3/envs/COVIRT_GATK/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar Mutect2 --disable-read-filter MappingQualityReadFilter --disable-read-filter MappingQualityNotZeroReadFilter --disable-read-filter MappingQualityAvailableReadFilter --mitochondria-mode true --callable-depth 25 -R /nobackup/lnsingh/MTRNA/lib/rCRS.fa -I /nobackup/lnsingh/MTRNA/out/COVSUBJ_0121_1_N_HA_filtered.humanspliced.bam -L MT -ERC BP_RESOLUTION -O /nobackup/lnsingh/MTRNA/out/COVSUBJ_0121_1_N_HA_filtered.humanspliced.gvcf.gz

07:12:55.253 WARN  GATKReadFilterPluginDescriptor - Values were supplied for (MappingQualityReadFilter) that is also disabled

07:12:55.307 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/nobackupp16/swbuild/hsp/COVID19/anaconda3/envs/COVIRT_GATK/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

Sep 20, 2020 7:12:55 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

INFO: Failed to detect whether we are running on Google Compute Engine.

07:12:55.535 INFO  Mutect2 - ------------------------------------------------------------

07:12:55.536 INFO  Mutect2 - The Genome Analysis Toolkit (GATK) v4.1.7.0

07:12:55.536 INFO  Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/

07:12:55.537 INFO  Mutect2 - Executing as lnsingh@pfe26 on Linux v4.12.14-122.23.1.20200609-nasa amd64

07:12:55.537 INFO  Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12

07:12:55.537 INFO  Mutect2 - Start Date/Time: September 20, 2020 7:12:55 AM PDT

07:12:55.537 INFO  Mutect2 - ------------------------------------------------------------

07:12:55.537 INFO  Mutect2 - ------------------------------------------------------------

07:12:55.537 INFO  Mutect2 - HTSJDK Version: 2.21.2

07:12:55.537 INFO  Mutect2 - Picard Version: 2.21.9

07:12:55.537 INFO  Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2

07:12:55.538 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

07:12:55.538 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

07:12:55.538 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

07:12:55.538 INFO  Mutect2 - Deflater: IntelDeflater

07:12:55.538 INFO  Mutect2 - Inflater: IntelInflater

07:12:55.538 INFO  Mutect2 - GCS max retries/reopens: 20

07:12:55.538 INFO  Mutect2 - Requester pays: disabled

07:12:55.538 INFO  Mutect2 - Initializing engine

07:12:55.964 INFO  IntervalArgumentCollection - Processing 16569 bp from intervals

07:12:55.971 INFO  Mutect2 - Done initializing engine

07:12:55.991 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/nobackupp16/swbuild/hsp/COVID19/anaconda3/envs/COVIRT_GATK/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so

07:12:55.999 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/nobackupp16/swbuild/hsp/COVID19/anaconda3/envs/COVIRT_GATK/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so

07:12:56.075 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM

07:12:56.075 INFO  IntelPairHmm - Available threads: 32

07:12:56.075 INFO  IntelPairHmm - Requested threads: 4

07:12:56.076 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation

07:12:56.089 WARN  Mutect2 - Note that the Mutect2 reference confidence mode is in BETA -- the likelihoods model and output format are subject to change in subsequent versions.

07:12:56.120 INFO  ProgressMeter - Starting traversal

07:12:56.121 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute

07:14:52.795 INFO  ProgressMeter -              MT:4306              1.9                    20             10.3

07:19:29.730 INFO  ProgressMeter -              MT:6746              6.6                    30              4.6

07:22:29.660 INFO  ProgressMeter -              MT:9150              9.6                    40              4.2

07:26:48.703 INFO  ProgressMeter -             MT:11639             13.9                    50              3.6

07:31:35.781 INFO  ProgressMeter -             MT:14148             18.7                    60              3.2

07:33:10.915 INFO  Mutect2 - 0 read(s) filtered by: MappedReadFilter

0 read(s) filtered by: NotSecondaryAlignmentReadFilter

0 read(s) filtered by: NotDuplicateReadFilter

0 read(s) filtered by: PassesVendorQualityCheckReadFilter

0 read(s) filtered by: NonChimericOriginalAlignmentReadFilter

0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter

0 read(s) filtered by: ReadLengthReadFilter

0 read(s) filtered by: GoodCigarReadFilter

0 read(s) filtered by: WellformedReadFilter

0 total reads filtered

07:33:10.917 INFO  ProgressMeter -             MT:14148             20.2                    68              3.4

07:33:10.918 INFO  ProgressMeter - Traversal complete. Processed 68 total regions in 20.2 minutes.

07:33:11.021 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.8959607420000001

07:33:11.023 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 786.91934956

07:33:11.024 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 84.56 sec

07:33:11.025 INFO  Mutect2 - Shutting down engine

[September 20, 2020 7:33:11 AM PDT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 20.26 minutes.

Runtime.totalMemory()=1294991360

Tool returned:

SUCCESS

Running: gatk FilterMutectCalls         --java-options "-Xmx22G -Djava.io.tmpdir=/nobackup/lnsingh/MTRNA/tmp"         --disable-read-filter MappingQualityReadFilter         --disable-read-filter MappingQualityNotZeroReadFilter         --disable-read-filter MappingQualityAvailableReadFilter         --mitochondria-mode true         -R /nobackup/lnsingh/MTRNA/lib/rCRS.fa         -V /nobackup/lnsingh/MTRNA/out/COVSUBJ_0121_1_N_HA_filtered.humanspliced.gvcf.gz         -L MT         -O /nobackup/lnsingh/MTRNA/out/COVSUBJ_0121_1_N_HA_filtered.humanspliced.filtered.gvcf.gz

Using GATK jar /nobackupp16/swbuild/hsp/COVID19/anaconda3/envs/COVIRT_GATK/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-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 -Xmx22G -Djava.io.tmpdir=/nobackup/lnsingh/MTRNA/tmp -jar /nobackupp16/swbuild/hsp/COVID19/anaconda3/envs/COVIRT_GATK/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar FilterMutectCalls --disable-read-filter MappingQualityReadFilter --disable-read-filter MappingQualityNotZeroReadFilter --disable-read-filter MappingQualityAvailableReadFilter --mitochondria-mode true -R /nobackup/lnsingh/MTRNA/lib/rCRS.fa -V /nobackup/lnsingh/MTRNA/out/COVSUBJ_0121_1_N_HA_filtered.humanspliced.gvcf.gz -L MT -O /nobackup/lnsingh/MTRNA/out/COVSUBJ_0121_1_N_HA_filtered.humanspliced.filtered.gvcf.gz

07:33:14.927 WARN  GATKReadFilterPluginDescriptor - Disabled filter (MappingQualityReadFilter) is not enabled by this tool

07:33:14.928 WARN  GATKReadFilterPluginDescriptor - Disabled filter (MappingQualityNotZeroReadFilter) is not enabled by this tool

07:33:14.928 WARN  GATKReadFilterPluginDescriptor - Disabled filter (MappingQualityAvailableReadFilter) is not enabled by this tool

07:33:15.003 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/nobackupp16/swbuild/hsp/COVID19/anaconda3/envs/COVIRT_GATK/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

Sep 20, 2020 7:33:15 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

INFO: Failed to detect whether we are running on Google Compute Engine.

07:33:15.360 INFO  FilterMutectCalls - ------------------------------------------------------------

07:33:15.361 INFO  FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.1.7.0

07:33:15.361 INFO  FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/

07:33:15.361 INFO  FilterMutectCalls - Executing as lnsingh@pfe26 on Linux v4.12.14-122.23.1.20200609-nasa amd64

07:33:15.361 INFO  FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12

07:33:15.361 INFO  FilterMutectCalls - Start Date/Time: September 20, 2020 7:33:14 AM PDT

07:33:15.361 INFO  FilterMutectCalls - ------------------------------------------------------------

07:33:15.361 INFO  FilterMutectCalls - ------------------------------------------------------------

07:33:15.362 INFO  FilterMutectCalls - HTSJDK Version: 2.21.2

07:33:15.362 INFO  FilterMutectCalls - Picard Version: 2.21.9

07:33:15.362 INFO  FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2

07:33:15.362 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

07:33:15.362 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

07:33:15.362 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

07:33:15.362 INFO  FilterMutectCalls - Deflater: IntelDeflater

07:33:15.362 INFO  FilterMutectCalls - Inflater: IntelInflater

07:33:15.363 INFO  FilterMutectCalls - GCS max retries/reopens: 20

07:33:15.363 INFO  FilterMutectCalls - Requester pays: disabled

07:33:15.363 INFO  FilterMutectCalls - Initializing engine

07:33:16.008 INFO  FeatureManager - Using codec VCFCodec to read file file:///nobackup/lnsingh/MTRNA/out/COVSUBJ_0121_1_N_HA_filtered.humanspliced.gvcf.gz

07:33:16.053 INFO  IntervalArgumentCollection - Processing 16569 bp from intervals

07:33:16.059 INFO  FilterMutectCalls - Done initializing engine

07:33:16.157 INFO  ProgressMeter - Starting traversal

07:33:16.157 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute

07:33:16.158 INFO  FilterMutectCalls - Starting pass 0 through the variants

07:33:17.341 INFO  FilterMutectCalls - Finished pass 0 through the variants

07:33:17.404 INFO  FilterMutectCalls - Shutting down engine

[September 20, 2020 7:33:17 AM PDT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.04 minutes.

Runtime.totalMemory()=1256194048

java.lang.IllegalArgumentException: alpha must be greater than 0 but got NaN

at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:727)

at org.broadinstitute.hellbender.utils.param.ParamUtils.isPositive(ParamUtils.java:165)

at org.broadinstitute.hellbender.tools.walkers.readorientation.BetaDistributionShape.<init>(BetaDistributionShape.java:13)

at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BinomialCluster.getFuzzyBinomial(BinomialCluster.java:43)

at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BinomialCluster.<init>(BinomialCluster.java:17)

at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.initializeClusters(SomaticClusteringModel.java:184)

at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.learnAndClearAccumulatedData(SomaticClusteringModel.java:325)

at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.learnParameters(Mutect2FilteringEngine.java:153)

at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls.afterNthPass(FilterMutectCalls.java:165)

at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:44)

at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048)

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)