Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.3cc61cc1 21:33:39.936 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so 21:33:40.320 INFO GetSampleName - ------------------------------------------------------------ 21:33:40.325 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.8.1 21:33:40.326 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 21:33:40.326 INFO GetSampleName - Executing as root@69c8f44b9f19 on Linux v4.9.0-0.bpo.6-amd64 amd64 21:33:40.327 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 21:33:40.327 INFO GetSampleName - Start Date/Time: September 12, 2018 9:33:39 PM UTC 21:33:40.328 INFO GetSampleName - ------------------------------------------------------------ 21:33:40.328 INFO GetSampleName - ------------------------------------------------------------ 21:33:40.329 INFO GetSampleName - HTSJDK Version: 2.16.0 21:33:40.329 INFO GetSampleName - Picard Version: 2.18.7 21:33:40.329 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 21:33:40.329 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 21:33:40.329 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 21:33:40.330 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 21:33:40.330 INFO GetSampleName - Deflater: IntelDeflater 21:33:40.330 INFO GetSampleName - Inflater: IntelInflater 21:33:40.330 INFO GetSampleName - GCS max retries/reopens: 20 21:33:40.330 INFO GetSampleName - Using google-cloud-java fork https://github.com/broadinstitute/google-cloud-java/releases/tag/0.20.5-alpha-GCS-RETRY-FIX 21:33:40.331 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 21:33:40.331 INFO GetSampleName - Initializing engine 21:33:48.436 INFO GetSampleName - Done initializing engine 21:33:48.459 INFO ProgressMeter - Starting traversal 21:33:48.460 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 21:33:48.462 INFO ProgressMeter - unmapped 0.0 0 NaN 21:33:48.462 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 21:33:48.463 INFO GetSampleName - Shutting down engine [September 12, 2018 9:33:49 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.15 minutes. Runtime.totalMemory()=225554432 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 gs://broad-references/hg19/v0/Homo_sapiens_assembly19.fasta -I gs://fc-b2843f3a-c485-46fa-b360-fcf511c2c297/Beroukhim_Bando_Craniopharyngiomas_WGS/RP-1390/WGS/10-417-5407_S16_T/v2/10-417-5407_S16_T.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.3cc61cc1 21:33:53.289 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so 21:33:53.553 INFO GetSampleName - ------------------------------------------------------------ 21:33:53.555 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.0.8.1 21:33:53.555 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 21:33:53.555 INFO GetSampleName - Executing as root@69c8f44b9f19 on Linux v4.9.0-0.bpo.6-amd64 amd64 21:33:53.556 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11 21:33:53.556 INFO GetSampleName - Start Date/Time: September 12, 2018 9:33:53 PM UTC 21:33:53.556 INFO GetSampleName - ------------------------------------------------------------ 21:33:53.557 INFO GetSampleName - ------------------------------------------------------------ 21:33:53.557 INFO GetSampleName - HTSJDK Version: 2.16.0 21:33:53.557 INFO GetSampleName - Picard Version: 2.18.7 21:33:53.558 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 21:33:53.558 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 21:33:53.558 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 21:33:53.558 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 21:33:53.558 INFO GetSampleName - Deflater: IntelDeflater 21:33:53.559 INFO GetSampleName - Inflater: IntelInflater 21:33:53.559 INFO GetSampleName - GCS max retries/reopens: 20 21:33:53.559 INFO GetSampleName - Using google-cloud-java fork https://github.com/broadinstitute/google-cloud-java/releases/tag/0.20.5-alpha-GCS-RETRY-FIX 21:33:53.559 WARN GetSampleName -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 21:33:53.560 INFO GetSampleName - Initializing engine 21:34:01.273 INFO GetSampleName - Done initializing engine 21:34:01.280 INFO ProgressMeter - Starting traversal 21:34:01.282 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 21:34:01.283 INFO ProgressMeter - unmapped 0.0 0 0.0 21:34:01.285 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 21:34:01.285 INFO GetSampleName - Shutting down engine [September 12, 2018 9:34:01 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.15 minutes. Runtime.totalMemory()=225538048 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 gs://broad-references/hg19/v0/Homo_sapiens_assembly19.fasta -I gs://fc-b2843f3a-c485-46fa-b360-fcf511c2c297/Beroukhim_Bando_Craniopharyngiomas_WGS/RP-1390/WGS/10-417-5407_N/v2/10-417-5407_N.bam -O normal_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.3cc61cc1 USAGE: Mutect2 [arguments] Call somatic SNVs and indels via local assembly of haplotypes Version:4.0.8.1 Required Arguments: --input,-I:String BAM/SAM/CRAM file containing reads This argument must be specified at least once. Required. --output,-O:File File to which variants should be written Required. --reference,-R:String Reference sequence file Required. --tumor-sample,-tumor:String BAM sample name of tumor. May be URL-encoded as output by GetSampleName with -encode argument. Required. Optional Arguments: --activity-profile-out:String Output the raw activity profile results in IGV format Default value: null. --add-output-sam-program-record,-add-output-sam-program-record:Boolean If true, adds a PG tag to created SAM/BAM/CRAM files. Default value: true. Possible values: {true, false} --add-output-vcf-command-line,-add-output-vcf-command-line:Boolean If true, adds a command line header line to created VCF files. Default value: true. Possible values: {true, false} --af-of-alleles-not-in-resource,-default-af:Double Population allele fraction assigned to alleles not found in germline resource. Please see docs/mutect/mutect2.pdf fora derivation of the default value. Default value: -1.0. --alleles:FeatureInput The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES Default value: null. --annotate-with-num-discovered-alleles:Boolean If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site Default value: false. Possible values: {true, false} --annotation,-A:String One or more specific annotations to add to variant calls This argument may be specified 0 or more times. Default value: null. Possible Values: {AS_BaseQualityRankSumTest, AS_FisherStrand, AS_InbreedingCoeff, AS_MappingQualityRankSumTest, AS_QualByDepth, AS_ReadPosRankSumTest, AS_RMSMappingQuality, AS_StrandOddsRatio, BaseQuality, BaseQualityRankSumTest, ChromosomeCounts, ClippingRankSumTest, Coverage, DepthPerAlleleBySample, DepthPerSampleHC, ExcessHet, FisherStrand, FragmentLength, GenotypeSummaries, InbreedingCoeff, LikelihoodRankSumTest, MappingQuality, MappingQualityRankSumTest, MappingQualityZero, OxoGReadCounts, PossibleDeNovo, QualByDepth, ReadOrientationArtifact, ReadPosition, ReadPosRankSumTest, ReferenceBases, RMSMappingQuality, SampleList, StrandArtifact, StrandBiasBySample, StrandOddsRatio, TandemRepeat, UniqueAltReadCount} --annotation-group,-G:String One or more groups of annotations to apply to variant calls This argument may be specified 0 or more times. Default value: null. Possible Values: {AS_StandardAnnotation, NonStandardMutectAnnotation, ReducibleAnnotation, StandardAnnotation, StandardHCAnnotation, StandardMutectAnnotation} --annotations-to-exclude,-AX:String One or more specific annotations to exclude from variant calls This argument may be specified 0 or more times. Default value: null. Possible Values: {BaseQuality, Coverage, DepthPerAlleleBySample, FragmentLength, MappingQuality, OxoGReadCounts, ReadPosition, ReferenceBases, StrandArtifact, TandemRepeat} --arguments_file:File read one or more arguments files and add them to the command line This argument may be specified 0 or more times. Default value: null. --assembly-region-out:String Output the assembly region to this IGV formatted file Default value: null. --base-quality-score-threshold:Byte Base qualities below this threshold will be reduced to the minimum (6) Default value: 18. --cloud-index-prefetch-buffer,-CIPB:Integer Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset. Default value: -1. --cloud-prefetch-buffer,-CPB:Integer Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40. --contamination-fraction-to-filter,-contamination:Double Fraction of contamination in sequencing data (for all samples) to aggressively remove Default value: 0.0. --create-output-bam-index,-OBI:Boolean If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. Default value: true. Possible values: {true, false} --create-output-bam-md5,-OBM:Boolean If true, create a MD5 digest for any BAM/SAM/CRAM file created Default value: false. Possible values: {true, false} --create-output-variant-index,-OVI:Boolean If true, create a VCF index when writing a coordinate-sorted VCF file. Default value: true. Possible values: {true, false} --create-output-variant-md5,-OVM:Boolean If true, create a a MD5 digest any VCF file created. Default value: false. Possible values: {true, false} --disable-bam-index-caching,-DBIC:Boolean If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified. Default value: false. Possible values: {true, false} --disable-read-filter,-DF:String Read filters to be disabled before analysis This argument may be specified 0 or more times. Default value: null. Possible Values: {GoodCigarReadFilter, MappedReadFilter, MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter, MappingQualityReadFilter, NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter, NotSecondaryAlignmentReadFilter, PassesVendorQualityCheckReadFilter, ReadLengthReadFilter, WellformedReadFilter} --disable-sequence-dictionary-validation,-disable-sequence-dictionary-validation:Boolean If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk! Default value: false. Possible values: {true, false} --downsampling-stride,-stride:Integer Downsample a pool of reads starting within a range of one or more bases. Default value: 1. --exclude-intervals,-XL:StringOne or more genomic intervals to exclude from processing This argument may be specified 0 or more times. Default value: null. --founder-id,-founder-id:String Samples representing the population "founders" This argument may be specified 0 or more times. Default value: null. --gatk-config-file:String A configuration file to use with the GATK. Default value: null. --gcs-max-retries,-gcs-retries:Integer If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection Default value: 20. --genotype-germline-sites:Boolean (EXPERIMENTAL) Call all apparent germline site even though they will ultimately be filtered. Default value: false. Possible values: {true, false} --genotype-pon-sites:Boolean Call sites in the PoN even though they will ultimately be filtered. Default value: false. Possible values: {true, false} --genotyping-mode:GenotypingOutputMode Specifies how to determine the alternate alleles to use for genotyping Default value: DISCOVERY. Possible values: {DISCOVERY, GENOTYPE_GIVEN_ALLELES} --germline-resource:FeatureInput Population vcf of germline sequencing containing allele fractions. Default value: null. --graph-output,-graph:String Write debug assembly graph information to this file Default value: null. --help,-h:Boolean display the help message Default value: false. Possible values: {true, false} --heterozygosity:Double Heterozygosity value used to compute prior likelihoods for any locus. See the GATKDocs for full details on the meaning of this population genetics concept Default value: 0.001. --heterozygosity-stdev:Double Standard deviation of heterozygosity for SNP and indel calling. Default value: 0.01. --ignore-itr-artifacts:BooleanTurn off read transformer that clips artifacts associated with end repair insertions near inverted tandem repeats. Default value: false. Possible values: {true, false} --indel-heterozygosity:Double Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept Default value: 1.25E-4. --initial-pcr-qual:Integer PCR error rate for overlapping fragments in isActive() Default value: 40. --initial-tumor-lod,-init-lod:Double LOD threshold to consider pileup active. Default value: 2.0. --interval-exclusion-padding,-ixp:Integer Amount of padding (in bp) to add to each interval you are excluding. Default value: 0. --interval-merging-rule,-imr:IntervalMergingRule Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL, OVERLAPPING_ONLY} --interval-padding,-ip:IntegerAmount of padding (in bp) to add to each interval you are including. Default value: 0. --interval-set-rule,-isr:IntervalSetRule Set merging approach to use for combining interval inputs Default value: UNION. Possible values: {UNION, INTERSECTION} --intervals,-L:String One or more genomic intervals over which to operate This argument may be specified 0 or more times. Default value: null. --lenient,-LE:Boolean Lenient processing of VCF files Default value: false. Possible values: {true, false} --max-population-af,-max-af:Double Maximum population allele frequency in tumor-only mode. Default value: 0.01. --max-reads-per-alignment-start:Integer Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable. Default value: 50. --min-base-quality-score,-mbq:Byte Minimum base quality required to consider a base for calling Default value: 10. --native-pair-hmm-threads:Integer How many threads should a native pairHMM implementation use Default value: 4. --native-pair-hmm-use-double-precision:Boolean use double precision in the native pairHmm. This is slower but matches the java implementation better Default value: false. Possible values: {true, false} --normal-lod:Double LOD threshold for calling normal variant non-germline. Default value: 2.2. --normal-sample,-normal:StringBAM sample name of normal. May be URL-encoded as output by GetSampleName with -encode argument. Default value: null. --num-reference-samples-if-no-call:Integer Number of hom-ref genotypes to infer at sites not present in a panel Default value: 0. --orientation-bias-artifact-priors:File table of prior artifact probabilities for the read orientation filter model Default value: null. --output-mode:OutputMode Specifies which type of calls we should output Default value: EMIT_VARIANTS_ONLY. Possible values: {EMIT_VARIANTS_ONLY, EMIT_ALL_CONFIDENT_SITES, EMIT_ALL_SITES} --panel-of-normals,-pon:FeatureInput VCF file of sites observed in normal. Default value: null. --pedigree,-ped:File Pedigree file for determining the population "founders" Default value: null. --population-callset,-population:FeatureInput Callset to use in calculating genotype priors Default value: null. --QUIET:Boolean Whether to suppress job-summary info on System.err. Default value: false. Possible values: {true, false} --read-filter,-RF:String Read filters to be applied before analysis This argument may be specified 0 or more times. Default value: null. Possible Values: {AlignmentAgreesWithHeaderReadFilter, AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator, FirstOfPairReadFilter, FragmentLengthReadFilter, GoodCigarReadFilter, HasReadGroupReadFilter, LibraryReadFilter, MappedReadFilter, MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter, MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter, MateOnSameContigOrNoMappedMateReadFilter, MetricsReadFilter, NonZeroFragmentLengthReadFilter, NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter, NotOpticalDuplicateReadFilter, NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter, OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter, PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter, ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupReadFilter, ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter, ReadNameReadFilter, ReadStrandFilter, SampleReadFilter, SecondOfPairReadFilter, SeqIsStoredReadFilter, ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter, WellformedReadFilter} --read-index,-read-index:String Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically. This argument may be specified 0 or more times. Default value: null. --read-validation-stringency,-VS:ValidationStringency Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default value: SILENT. Possible values: {STRICT, LENIENT, SILENT} --recover-dangling-heads:Boolean This argument is deprecated since version 3.3 Default value: false. Possible values: {true, false} --sample-ploidy,-ploidy:Integer Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy). Default value: 2. --seconds-between-progress-updates,-seconds-between-progress-updates:Double Output traversal statistics every time this many seconds elapse Default value: 10.0. --sequence-dictionary,-sequence-dictionary:String Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file. Default value: null. --sites-only-vcf-output:Boolean If true, don't emit genotype fields when writing vcf file output. Default value: false. Possible values: {true, false} --standard-min-confidence-threshold-for-calling,-stand-call-conf:Double The minimum phred-scaled confidence threshold at which variants should be called Default value: 10.0. --TMP_DIR:File Undocumented option This argument may be specified 0 or more times. Default value: null. --tumor-lod-to-emit,-emit-lod:Double LOD threshold to emit tumor variant to VCF. Default value: 3.0. --use-jdk-deflater,-jdk-deflater:Boolean Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false. Possible values: {true, false} --use-jdk-inflater,-jdk-inflater:Boolean Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false. Possible values: {true, false} --use-new-qual-calculator,-new-qual:Boolean If provided, we will use the new AF model instead of the so-called exact model Default value: false. Possible values: {true, false} --verbosity,-verbosity:LogLevel Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING, INFO, DEBUG} --version:Boolean display the version number for this tool Default value: false. Possible values: {true, false} Advanced Arguments: --active-probability-threshold:Double Minimum probability for a locus to be considered active. Default value: 0.002. --all-site-pls:Boolean Annotate all sites with PLs Default value: false. Possible values: {true, false} --allow-non-unique-kmers-in-ref:Boolean Allow graphs that have non-unique kmers in the reference Default value: false. Possible values: {true, false} --assembly-region-padding:Integer Number of additional bases of context to include around each assembly region Default value: 100. --bam-output,-bamout:String File to which assembled haplotypes should be written Default value: null. --bam-writer-type:WriterType Which haplotypes should be written to the BAM Default value: CALLED_HAPLOTYPES. Possible values: {ALL_POSSIBLE_HAPLOTYPES, CALLED_HAPLOTYPES} --consensus:Boolean 1000G consensus mode Default value: false. Possible values: {true, false} --contamination-fraction-per-sample-file,-contamination-file:File Tab-separated File containing fraction of contamination in sequencing data (per sample) to aggressively remove. Format should be "" (Contamination is double) per line; No header. Default value: null. --debug,-debug:Boolean Print out very verbose debug information about each triggering active region Default value: false. Possible values: {true, false} --disable-tool-default-annotations,-disable-tool-default-annotations:Boolean Disable all tool default annotations Default value: false. Possible values: {true, false} --disable-tool-default-read-filters,-disable-tool-default-read-filters:Boolean Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on) Default value: false. Possible values: {true, false} --do-not-run-physical-phasing:Boolean Disable physical phasing Default value: false. Possible values: {true, false} --dont-increase-kmer-sizes-for-cycles:Boolean Disable iterating over kmer sizes when graph cycles are detected Default value: false. Possible values: {true, false} --dont-trim-active-regions:Boolean If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping Default value: false. Possible values: {true, false} --dont-use-soft-clipped-bases:Boolean Do not analyze soft clipped bases in the reads Default value: false. Possible values: {true, false} --enable-all-annotations:Boolean Use all possible annotations (not for the faint of heart) Default value: false. Possible values: {true, false} --genotype-filtered-alleles:Boolean Whether to genotype all given alleles, even filtered ones, --genotyping_mode is GENOTYPE_GIVEN_ALLELES Default value: false. Possible values: {true, false} --input-prior:Double Input prior for calls This argument may be specified 0 or more times. Default value: null. --kmer-size:Integer Kmer size to use in the read threading assembler This argument may be specified 0 or more times. Default value: [10, 25]. --max-alternate-alleles:Integer Maximum number of alternate alleles to genotype Default value: 6. --max-assembly-region-size:Integer Maximum size of an assembly region Default value: 300. --max-genotype-count:Integer Maximum number of genotypes to consider at any site Default value: 1024. --max-mnp-distance,-mnp-dist:Integer Two or more phased substitutions separated by this distance or less are merged into MNPs. Default value: 1. --max-num-haplotypes-in-population:Integer Maximum number of haplotypes to consider for your population Default value: 128. --max-prob-propagation-distance:Integer Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions Default value: 50. --max-suspicious-reads-per-alignment-start:Integer Maximum number of suspicious reads (mediocre mapping quality or too many substitutions) allowed in a downsampling stride. Set to 0 to disable. Default value: 0. --min-assembly-region-size:Integer Minimum size of an assembly region Default value: 50. --min-dangling-branch-length:Integer Minimum length of a dangling branch to attempt recovery Default value: 4. --min-pruning:Integer Minimum support to not prune paths in the graph Default value: 2. --num-pruning-samples:Integer Number of samples that must pass the minPruning threshold Default value: 1. --pair-hmm-gap-continuation-penalty:Integer Flat gap continuation penalty for use in the Pair HMM Default value: 10. --pair-hmm-implementation,-pairHMM:Implementation The PairHMM implementation to use for genotype likelihood calculations Default value: FASTEST_AVAILABLE. Possible values: {EXACT, ORIGINAL, LOGLESS_CACHING, AVX_LOGLESS_CACHING, AVX_LOGLESS_CACHING_OMP, EXPERIMENTAL_FPGA_LOGLESS_CACHING, FASTEST_AVAILABLE} --pcr-indel-model:PCRErrorModel The PCR indel model to use Default value: CONSERVATIVE. Possible values: {NONE, HOSTILE, AGGRESSIVE, CONSERVATIVE} --phred-scaled-global-read-mismapping-rate:Integer The global assumed mismapping rate for reads Default value: 45. --showHidden,-showHidden:Boolean display hidden arguments Default value: false. Possible values: {true, false} --smith-waterman:Implementation Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice Default value: JAVA. Possible values: {FASTEST_AVAILABLE, AVX_ENABLED, JAVA} --use-filtered-reads-for-annotations:Boolean Use the contamination-filtered read maps for the purposes of annotating variants Default value: false. Possible values: {true, false} Conditional Arguments for read-filter: Valid only if "AmbiguousBaseReadFilter" is specified: --ambig-filter-bases:Integer Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise, overrides threshold fraction. Default value: null. Cannot be used in conjuction with argument(s) maxAmbiguousBaseFraction --ambig-filter-frac:Double Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjuction with argument(s) maxAmbiguousBases Valid only if "FragmentLengthReadFilter" is specified: --max-fragment-length:Integer Maximum length of fragment (insert size) Default value: 1000000. Valid only if "LibraryReadFilter" is specified: --library,-library:String Name of the library to keep This argument must be specified at least once. Required. Valid only if "MappingQualityReadFilter" is specified: --maximum-mapping-quality:Integer Maximum mapping quality to keep (inclusive) Default value: null. --minimum-mapping-quality:Integer Minimum mapping quality to keep (inclusive) Default value: 20. Valid only if "OverclippedReadFilter" is specified: --dont-require-soft-clips-both-ends:Boolean Allow a read to be filtered out based on having only 1 soft-clipped block. By default, both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped block Default value: false. Possible values: {true, false} --filter-too-short:Integer Minimum number of aligned bases Default value: 30. Valid only if "PlatformReadFilter" is specified: --platform-filter-name:String Platform attribute (PL) to match This argument must be specified at least once. Required. Valid only if "PlatformUnitReadFilter" is specified: --black-listed-lanes:String Platform unit (PU) to filter out This argument must be specified at least once. Required. Valid only if "ReadGroupBlackListReadFilter" is specified: --read-group-black-list:StringThe name of the read group to filter out This argument must be specified at least once. Required. Valid only if "ReadGroupReadFilter" is specified: --keep-read-group:String The name of the read group to keep Required. Valid only if "ReadLengthReadFilter" is specified: --max-read-length:Integer Keep only reads with length at most equal to the specified value Default value: 2147483647. --min-read-length:Integer Keep only reads with length at least equal to the specified value Default value: 30. Valid only if "ReadNameReadFilter" is specified: --read-name:String Keep only reads with this read name Required. Valid only if "ReadStrandFilter" is specified: --keep-reverse-strand-only:Boolean Keep only reads on the reverse strand Required. Possible values: {true, false} Valid only if "SampleReadFilter" is specified: --sample,-sample:String The name of the sample(s) to keep, filtering out all others This argument must be specified at least once. Required. *********************************************************************** A USER ERROR has occurred: X is not a recognized option *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. 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 gs://broad-references/hg19/v0/Homo_sapiens_assembly19.fasta -I gs://fc-b2843f3a-c485-46fa-b360-fcf511c2c297/Beroukhim_Bando_Craniopharyngiomas_WGS/RP-1390/WGS/10-417-5407_S16_T/v2/10-417-5407_S16_T.bam -tumor 10-417-5407_S16_T -I gs://fc-b2843f3a-c485-46fa-b360-fcf511c2c297/Beroukhim_Bando_Craniopharyngiomas_WGS/RP-1390/WGS/10-417-5407_N/v2/10-417-5407_N.bam -normal 10-417-5407_N --germline-resource gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf -L gs://fc-5b570a82-801b-4b0b-9f2d-125fe622ddd5/5c8b3df7-5a19-4e06-b781-2402f7c9e97d/Mutect2/504e7fa0-ff6b-48f0-820a-87525838c74e/call-SplitIntervals/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0000-scattered.intervals -O output.vcf -XA ReferenceBases