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Salida para la ejecución de GATK utilizando el archivo JAR
Colaboradores
La ejecución de GATK usando el archivo JAR produjo la siguiente salida de muestra.
[root@genomics1 execution]# 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 \ -jar /mnt/genomics/GATK/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar \ HaplotypeCaller \ --input /mnt/genomics/GATK/TEST\ DATA/bam/workshop_1906_2-germline_bams_father.bam \ --output workshop_1906_2-germline_bams_father.validation.vcf \ --reference /mnt/genomics/GATK/TEST\ DATA/ref/workshop_1906_2-germline_ref_ref.fasta \ 22:52:58.430 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/genomics/GATK/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Aug 17, 2021 10:52:58 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 22:52:58.541 INFO HaplotypeCaller - ------------------------------------------------------------ 22:52:58.542 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.0.0 22:52:58.542 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 22:52:58.542 INFO HaplotypeCaller - Executing as root@genomics1.healthylife.fp on Linux v4.18.0-305.3.1.el8_4.x86_64 amd64 22:52:58.542 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_302-b08 22:52:58.542 INFO HaplotypeCaller - Start Date/Time: August 17, 2021 10:52:58 PM EDT 22:52:58.542 INFO HaplotypeCaller - ------------------------------------------------------------ 22:52:58.542 INFO HaplotypeCaller - ------------------------------------------------------------ 22:52:58.542 INFO HaplotypeCaller - HTSJDK Version: 2.24.0 22:52:58.542 INFO HaplotypeCaller - Picard Version: 2.25.0 22:52:58.542 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 22:52:58.542 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 22:52:58.543 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 22:52:58.543 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 22:52:58.543 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 22:52:58.543 INFO HaplotypeCaller - Deflater: IntelDeflater 22:52:58.543 INFO HaplotypeCaller - Inflater: IntelInflater 22:52:58.543 INFO HaplotypeCaller - GCS max retries/reopens: 20 22:52:58.543 INFO HaplotypeCaller - Requester pays: disabled 22:52:58.543 INFO HaplotypeCaller - Initializing engine 22:52:58.804 INFO HaplotypeCaller - Done initializing engine 22:52:58.809 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output 22:52:58.820 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/mnt/genomics/GATK/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 22:52:58.821 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/mnt/genomics/GATK/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 22:52:58.854 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions 22:52:58.854 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 22:52:58.854 INFO IntelPairHmm - Available threads: 16 22:52:58.854 INFO IntelPairHmm - Requested threads: 4 22:52:58.854 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 22:52:58.872 INFO ProgressMeter - Starting traversal 22:52:58.873 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 22:53:00.733 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position 20:9999900 and possibly subsequent; at least 10 samples must have called genotypes 22:53:08.873 INFO ProgressMeter - 20:17538652 0.2 58900 353400.0 22:53:17.681 INFO HaplotypeCaller - 405 read(s) filtered by: MappingQualityReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 0 read(s) filtered by: NotSecondaryAlignmentReadFilter 6628 read(s) filtered by: NotDuplicateReadFilter 0 read(s) filtered by: PassesVendorQualityCheckReadFilter 0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter 0 read(s) filtered by: GoodCigarReadFilter 0 read(s) filtered by: WellformedReadFilter 7033 total reads filtered 22:53:17.681 INFO ProgressMeter - 20:63024652 0.3 210522 671592.9 22:53:17.681 INFO ProgressMeter - Traversal complete. Processed 210522 total regions in 0.3 minutes. 22:53:17.687 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010347438 22:53:17.687 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.259172573 22:53:17.687 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 1.27 sec 22:53:17.687 INFO HaplotypeCaller - Shutting down engine [August 17, 2021 10:53:17 PM EDT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.32 minutes. Runtime.totalMemory()=5561122816 [root@genomics1 execution]#
Observe que el archivo de salida se encuentra en la ubicación especificada después de la ejecución.