.command.err - Workdir - MUTECT2_TUMOR_ONLY (LS0924)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/11/37a6e3fe8bcbe2cee226b5824a456c/.command.err
Size: 11.7 KB
Task: MUTECT2_TUMOR_ONLY (LS0924)
Attempt
Content

22:43:49.962 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
22:43:50.071 INFO  Mutect2 - ------------------------------------------------------------
22:43:50.073 INFO  Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:43:50.073 INFO  Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:43:50.073 INFO  Mutect2 - Executing as ?@nf-1137a6e3fe8bcbe2cee226b5824a456c-f937e-dkks9 on Linux v6.12.88 amd64
22:43:50.073 INFO  Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:43:50.073 INFO  Mutect2 - Start Date/Time: June 8, 2026 at 10:43:49 PM GMT
22:43:50.073 INFO  Mutect2 - ------------------------------------------------------------
22:43:50.073 INFO  Mutect2 - ------------------------------------------------------------
22:43:50.074 INFO  Mutect2 - HTSJDK Version: 4.1.0
22:43:50.074 INFO  Mutect2 - Picard Version: 3.1.1
22:43:50.074 INFO  Mutect2 - Built for Spark Version: 3.5.0
22:43:50.074 INFO  Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:43:50.075 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:43:50.075 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:43:50.075 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:43:50.075 INFO  Mutect2 - Deflater: IntelDeflater
22:43:50.075 INFO  Mutect2 - Inflater: IntelInflater
22:43:50.075 INFO  Mutect2 - GCS max retries/reopens: 20
22:43:50.075 INFO  Mutect2 - Requester pays: disabled
22:43:50.075 INFO  Mutect2 - Initializing engine
22:43:50.253 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.PS2gfDhWpQ/af-only-gnomad.hg38.vcf.gz
22:43:50.368 INFO  FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.PS2gfDhWpQ/TST500C_manifest.bed
22:43:50.401 INFO  IntervalArgumentCollection - Processing 1970331 bp from intervals
22:43:50.429 INFO  Mutect2 - Done initializing engine
22:43:50.438 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
22:43:50.439 INFO  NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
22:43:50.440 INFO  IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:43:50.440 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:43:50.451 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
22:43:50.459 INFO  IntelPairHmm - Using CPU-supported AVX-512 instructions
22:43:50.459 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:43:50.459 INFO  IntelPairHmm - Available threads: 384
22:43:50.460 INFO  IntelPairHmm - Requested threads: 4
22:43:50.460 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:43:50.500 INFO  ProgressMeter - Starting traversal
22:43:50.500 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute
22:43:52.311 INFO  Mutect2 - 3 read(s) filtered by: MappingQualityReadFilter 
0 read(s) filtered by: MappingQualityAvailableReadFilter 
0 read(s) filtered by: MappingQualityNotZeroReadFilter 
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 
3 total reads filtered out of 158 reads processed
22:43:52.312 INFO  ProgressMeter -        chrY:19773323              0.0                 11606         384729.3
22:43:52.312 INFO  ProgressMeter - Traversal complete. Processed 11606 total regions in 0.0 minutes.
22:43:52.322 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 1.6289900000000001E-4
22:43:52.323 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0024445260000000003
22:43:52.323 INFO  SmithWatermanAligner - Total compute time in native Smith-Waterman : 0.01 sec
22:43:52.323 INFO  Mutect2 - Shutting down engine
[June 8, 2026 at 10:43:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=788529152
Using GATK jar /gatk/gatk-package-4.5.0.0-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 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar Mutect2 -R hg38.fa -I LS0924_tumor.bam --tumor-sample LS0924 -L TST500C_manifest.bed -O LS0924.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
22:43:53.526 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
22:43:53.642 INFO  FilterMutectCalls - ------------------------------------------------------------
22:43:53.644 INFO  FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:43:53.645 INFO  FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
22:43:53.645 INFO  FilterMutectCalls - Executing as ?@nf-1137a6e3fe8bcbe2cee226b5824a456c-f937e-dkks9 on Linux v6.12.88 amd64
22:43:53.645 INFO  FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:43:53.645 INFO  FilterMutectCalls - Start Date/Time: June 8, 2026 at 10:43:53 PM GMT
22:43:53.645 INFO  FilterMutectCalls - ------------------------------------------------------------
22:43:53.645 INFO  FilterMutectCalls - ------------------------------------------------------------
22:43:53.646 INFO  FilterMutectCalls - HTSJDK Version: 4.1.0
22:43:53.646 INFO  FilterMutectCalls - Picard Version: 3.1.1
22:43:53.646 INFO  FilterMutectCalls - Built for Spark Version: 3.5.0
22:43:53.646 INFO  FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:43:53.647 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:43:53.647 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:43:53.647 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:43:53.647 INFO  FilterMutectCalls - Deflater: IntelDeflater
22:43:53.647 INFO  FilterMutectCalls - Inflater: IntelInflater
22:43:53.647 INFO  FilterMutectCalls - GCS max retries/reopens: 20
22:43:53.647 INFO  FilterMutectCalls - Requester pays: disabled
22:43:53.647 INFO  FilterMutectCalls - Initializing engine
22:43:53.821 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.PS2gfDhWpQ/LS0924.mutect2.raw.vcf.gz
22:43:53.916 INFO  FilterMutectCalls - Done initializing engine
22:43:53.972 INFO  ProgressMeter - Starting traversal
22:43:53.972 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:43:53.973 INFO  FilterMutectCalls - Starting pass 0 through the variants
22:43:54.032 INFO  FilterMutectCalls - Finished pass 0 through the variants
22:43:54.056 INFO  FilterMutectCalls - Starting pass 1 through the variants
22:43:54.069 INFO  FilterMutectCalls - Finished pass 1 through the variants
22:43:54.070 INFO  FilterMutectCalls - Starting pass 2 through the variants
22:43:54.078 INFO  FilterMutectCalls - Finished pass 2 through the variants
22:43:54.078 INFO  FilterMutectCalls - Starting pass 3 through the variants
22:43:54.103 INFO  FilterMutectCalls - Finished pass 3 through the variants
22:43:54.108 INFO  FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
22:43:54.108 INFO  FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter 

22:43:54.109 INFO  ProgressMeter -             unmapped              0.0                    40          17777.8
22:43:54.109 INFO  ProgressMeter - Traversal complete. Processed 40 total variants in 0.0 minutes.
22:43:54.114 INFO  FilterMutectCalls - Shutting down engine
[June 8, 2026 at 10:43:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=486539264
Using GATK jar /gatk/gatk-package-4.5.0.0-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 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar FilterMutectCalls -R hg38.fa -V LS0924.mutect2.raw.vcf.gz --stats LS0924.mutect2.raw.vcf.gz.stats -O LS0924.mutect2.filtered.vcf.gz
22:43:55.263 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
22:43:55.355 INFO  SelectVariants - ------------------------------------------------------------
22:43:55.356 INFO  SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:43:55.357 INFO  SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
22:43:55.357 INFO  SelectVariants - Executing as ?@nf-1137a6e3fe8bcbe2cee226b5824a456c-f937e-dkks9 on Linux v6.12.88 amd64
22:43:55.357 INFO  SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:43:55.357 INFO  SelectVariants - Start Date/Time: June 8, 2026 at 10:43:55 PM GMT
22:43:55.357 INFO  SelectVariants - ------------------------------------------------------------
22:43:55.357 INFO  SelectVariants - ------------------------------------------------------------
22:43:55.358 INFO  SelectVariants - HTSJDK Version: 4.1.0
22:43:55.358 INFO  SelectVariants - Picard Version: 3.1.1
22:43:55.358 INFO  SelectVariants - Built for Spark Version: 3.5.0
22:43:55.358 INFO  SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:43:55.358 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:43:55.358 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:43:55.358 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:43:55.358 INFO  SelectVariants - Deflater: IntelDeflater
22:43:55.358 INFO  SelectVariants - Inflater: IntelInflater
22:43:55.358 INFO  SelectVariants - GCS max retries/reopens: 20
22:43:55.359 INFO  SelectVariants - Requester pays: disabled
22:43:55.359 INFO  SelectVariants - Initializing engine
22:43:55.463 INFO  FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.PS2gfDhWpQ/LS0924.mutect2.filtered.vcf.gz
22:43:55.535 INFO  SelectVariants - Done initializing engine
22:43:55.576 INFO  ProgressMeter - Starting traversal
22:43:55.577 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:43:55.586 INFO  ProgressMeter -             unmapped              0.0                    10          66666.7
22:43:55.586 INFO  ProgressMeter - Traversal complete. Processed 10 total variants in 0.0 minutes.
22:43:55.590 INFO  SelectVariants - Shutting down engine
[June 8, 2026 at 10:43:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=486539264
Using GATK jar /gatk/gatk-package-4.5.0.0-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 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar SelectVariants -R hg38.fa -V LS0924.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0924.mutect2.pass.vcf.gz