Output for execution of GATK using the ./gatk script

Contributors

The execution of GATK using the ./gatk script produced the following sample output.

[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]#

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