Output for execution of GATK using the jar file

Contributors

Execution of GATK using the jar file produced the following sample output.

[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]#

Notice that the output file is located at the location specified after the execution.