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Salida para la ejecución de GATK usando el script ./gatk
Colaboradores
La ejecución de GATK con el útil ./gatk
la secuencia de comandos produjo la siguiente salida de ejemplo.
[root@genomics1 gatk-4.2.0.0]# ./gatk --java-options "-Xmx4G" \ HaplotypeCaller \ -I /mnt/genomics/GATK/TEST\ DATA/bam/workshop_1906_2-germline_bams_father.bam \ -R /mnt/genomics/GATK/TEST\ DATA/ref/workshop_1906_2-germline_ref_ref.fasta \ -O /mnt/genomics/GATK/TEST\ DATA/variants.vcf Using GATK jar /mnt/genomics/GATK/gatk-4.2.0.0/gatk-package-4.2.0.0-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 -Xmx4G -jar /mnt/genomics/GATK/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar HaplotypeCaller -I /mnt/genomics/GATK/TEST DATA/bam/workshop_1906_2-germline_bams_father.bam -R /mnt/genomics/GATK/TEST DATA/ref/workshop_1906_2-germline_ref_ref.fasta -O /mnt/genomics/GATK/TEST DATA/variants.vcf 23:29:45.553 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 11:29:45 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 23:29:45.686 INFO HaplotypeCaller - ------------------------------------------------------------ 23:29:45.686 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.0.0 23:29:45.686 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 23:29:45.687 INFO HaplotypeCaller - Executing as root@genomics1.healthylife.fp on Linux v4.18.0-305.3.1.el8_4.x86_64 amd64 23:29:45.687 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.12+7-LTS 23:29:45.687 INFO HaplotypeCaller - Start Date/Time: August 17, 2021 at 11:29:45 PM EDT 23:29:45.687 INFO HaplotypeCaller - ------------------------------------------------------------ 23:29:45.687 INFO HaplotypeCaller - ------------------------------------------------------------ 23:29:45.687 INFO HaplotypeCaller - HTSJDK Version: 2.24.0 23:29:45.687 INFO HaplotypeCaller - Picard Version: 2.25.0 23:29:45.687 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 23:29:45.688 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 23:29:45.688 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 23:29:45.688 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 23:29:45.688 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 23:29:45.688 INFO HaplotypeCaller - Deflater: IntelDeflater 23:29:45.688 INFO HaplotypeCaller - Inflater: IntelInflater 23:29:45.688 INFO HaplotypeCaller - GCS max retries/reopens: 20 23:29:45.688 INFO HaplotypeCaller - Requester pays: disabled 23:29:45.688 INFO HaplotypeCaller - Initializing engine 23:29:45.804 INFO HaplotypeCaller - Done initializing engine 23:29:45.809 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output 23:29:45.818 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 23:29:45.819 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 23:29:45.852 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions 23:29:45.852 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 23:29:45.852 INFO IntelPairHmm - Available threads: 16 23:29:45.852 INFO IntelPairHmm - Requested threads: 4 23:29:45.852 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 23:29:45.868 INFO ProgressMeter - Starting traversal 23:29:45.868 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 23:29:47.772 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position 20:9999900 and possibly subsequent; at least 10 samples must have called genotypes 23:29:55.868 INFO ProgressMeter - 20:18885652 0.2 63390 380340.0 23:30:04.389 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 23:30:04.389 INFO ProgressMeter - 20:63024652 0.3 210522 681999.9 23:30:04.389 INFO ProgressMeter - Traversal complete. Processed 210522 total regions in 0.3 minutes. 23:30:04.395 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012129203000000002 23:30:04.395 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.267345217 23:30:04.395 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 1.23 sec 23:30:04.395 INFO HaplotypeCaller - Shutting down engine [August 17, 2021 at 11:30:04 PM EDT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.31 minutes. Runtime.totalMemory()=2111832064 [root@genomics1 gatk-4.2.0.0]#
Observe que el archivo de salida se encuentra en la ubicación especificada después de la ejecución.