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biomarble / onekeyReseq

GNU General Public License v3.0
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need help #1

Closed zxljiqixuexi closed 2 years ago

zxljiqixuexi commented 2 years ago

开始运行：parallel -j 11 <commands/2.SNP/s1.HC.sh

下列命令运行错误，详情见日志(log)文件夹： parallel -j 11 <commands/2.SNP/s1.HC.sh

[COMMAND] parallel -j 11 <commands/2.SNP/s1.HC.sh Picked up _JAVA_OPTIONS: -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp 13:23:11.912 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jul 20, 2022 1:23:12 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 13:23:12.480 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:12.481 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.5.0 13:23:12.481 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 13:23:12.482 INFO HaplotypeCaller - Executing as linux@ZXL-PC on Linux v4.4.0-22000-Microsoft amd64 13:23:12.482 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.15-internal+0-adhoc..src 13:23:12.482 INFO HaplotypeCaller - Start Date/Time: July 20, 2022 at 1:23:11 PM CST 13:23:12.482 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:12.482 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:12.483 INFO HaplotypeCaller - HTSJDK Version: 2.24.1 13:23:12.483 INFO HaplotypeCaller - Picard Version: 2.25.4 13:23:12.483 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 13:23:12.483 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 13:23:12.483 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 13:23:12.484 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 13:23:12.484 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 13:23:12.484 INFO HaplotypeCaller - Deflater: IntelDeflater 13:23:12.484 INFO HaplotypeCaller - Inflater: IntelInflater 13:23:12.484 INFO HaplotypeCaller - GCS max retries/reopens: 20 13:23:12.484 INFO HaplotypeCaller - Requester pays: disabled 13:23:12.484 INFO HaplotypeCaller - Initializing engine 13:23:12.800 INFO IntervalArgumentCollection - Processing 366924 bp from intervals 13:23:12.806 INFO HaplotypeCaller - Done initializing engine 13:23:12.809 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled 13:23:12.826 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output 13:23:12.826 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 13:23:12.844 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 13:23:12.846 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 13:23:12.869 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 13:23:12.870 INFO IntelPairHmm - Available threads: 12 13:23:12.870 INFO IntelPairHmm - Requested threads: 4 13:23:12.870 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 13:23:13.012 INFO ProgressMeter - Starting traversal 13:23:13.012 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 13:23:16.226 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position Mt:7042 and possibly subsequent; at least 10 samples must have called genotypes 13:23:23.098 INFO ProgressMeter - Mt:44261 0.2 230 1368.2 13:23:33.338 INFO ProgressMeter - Mt:350594 0.3 1380 4073.6 13:23:34.933 INFO HaplotypeCaller - 669 read(s) filtered by: MappingQualityReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 0 read(s) filtered by: NotSecondaryAlignmentReadFilter 60 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 729 total reads filtered 13:23:34.933 INFO ProgressMeter - Mt:366183 0.4 1463 4004.4 13:23:34.974 INFO ProgressMeter - Traversal complete. Processed 1463 total regions in 0.4 minutes. 13:23:34.979 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0021442 13:23:34.979 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 4.8666199 13:23:34.979 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 1.18 sec 13:23:34.980 INFO HaplotypeCaller - Shutting down engine [July 20, 2022 at 1:23:34 PM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.39 minutes. Runtime.totalMemory()=6488588288 Using GATK jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-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 -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp -jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar HaplotypeCaller -R /mnt/f/3.ReSeq/genome/sequences.fa -I /mnt/f/3.ReSeq/1.mapping/MarkDup/sample1.MarkDup.bam -O /mnt/f/3.ReSeq/2.SNP/1.GVCF/sample1.Mt.gvcf.gz --emit-ref-confidence GVCF --do-not-run-physical-phasing -L Mt -stand-call-conf 30 Picked up _JAVA_OPTIONS: -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp 13:23:11.765 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jul 20, 2022 1:23:12 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 13:23:12.408 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:12.409 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.5.0 13:23:12.409 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 13:23:12.409 INFO HaplotypeCaller - Executing as linux@ZXL-PC on Linux v4.4.0-22000-Microsoft amd64 13:23:12.410 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.15-internal+0-adhoc..src 13:23:12.410 INFO HaplotypeCaller - Start Date/Time: July 20, 2022 at 1:23:11 PM CST 13:23:12.410 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:12.410 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:12.411 INFO HaplotypeCaller - HTSJDK Version: 2.24.1 13:23:12.411 INFO HaplotypeCaller - Picard Version: 2.25.4 13:23:12.411 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 13:23:12.411 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 13:23:12.411 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 13:23:12.411 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 13:23:12.411 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 13:23:12.411 INFO HaplotypeCaller - Deflater: IntelDeflater 13:23:12.411 INFO HaplotypeCaller - Inflater: IntelInflater 13:23:12.411 INFO HaplotypeCaller - GCS max retries/reopens: 20 13:23:12.411 INFO HaplotypeCaller - Requester pays: disabled 13:23:12.412 INFO HaplotypeCaller - Initializing engine 13:23:12.682 INFO IntervalArgumentCollection - Processing 154478 bp from intervals 13:23:12.688 INFO HaplotypeCaller - Done initializing engine 13:23:12.690 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled 13:23:12.698 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output 13:23:12.699 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 13:23:12.731 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 13:23:12.733 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 13:23:12.767 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 13:23:12.767 INFO IntelPairHmm - Available threads: 12 13:23:12.768 INFO IntelPairHmm - Requested threads: 4 13:23:12.768 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 13:23:12.878 INFO ProgressMeter - Starting traversal 13:23:12.878 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 13:23:15.912 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position Pt:1503 and possibly subsequent; at least 10 samples must have called genotypes 13:23:23.108 INFO ProgressMeter - Pt:7445 0.2 50 293.3 13:23:33.282 INFO ProgressMeter - Pt:27825 0.3 170 499.9 13:23:43.703 INFO ProgressMeter - Pt:58924 0.5 370 720.2 13:23:53.799 INFO ProgressMeter - Pt:113988 0.7 630 923.8 13:24:04.516 INFO ProgressMeter - Pt:127484 0.9 720 836.6 13:24:06.427 INFO HaplotypeCaller - 9575 read(s) filtered by: MappingQualityReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 11 read(s) filtered by: NotSecondaryAlignmentReadFilter 1258 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 10844 total reads filtered 13:24:06.428 INFO ProgressMeter - Pt:152634 0.9 816 914.3 13:24:06.428 INFO ProgressMeter - Traversal complete. Processed 816 total regions in 0.9 minutes. 13:24:06.644 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.1287826 13:24:06.650 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 8.2351758 13:24:06.651 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 11.88 sec 13:24:06.652 INFO HaplotypeCaller - Shutting down engine [July 20, 2022 at 1:24:06 PM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.92 minutes. Runtime.totalMemory()=6253707264 Using GATK jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-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 -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp -jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar HaplotypeCaller -R /mnt/f/3.ReSeq/genome/sequences.fa -I /mnt/f/3.ReSeq/1.mapping/MarkDup/sample1.MarkDup.bam -O /mnt/f/3.ReSeq/2.SNP/1.GVCF/sample1.Pt.gvcf.gz --emit-ref-confidence GVCF --do-not-run-physical-phasing -L Pt -stand-call-conf 30 Picked up _JAVA_OPTIONS: -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp 13:24:17.306 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jul 20, 2022 1:24:17 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 13:24:17.711 INFO HaplotypeCaller - ------------------------------------------------------------ 13:24:17.712 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.5.0 13:24:17.712 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 13:24:17.713 INFO HaplotypeCaller - Executing as linux@ZXL-PC on Linux v4.4.0-22000-Microsoft amd64 13:24:17.713 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.15-internal+0-adhoc..src 13:24:17.713 INFO HaplotypeCaller - Start Date/Time: July 20, 2022 at 1:24:17 PM CST 13:24:17.713 INFO HaplotypeCaller - ------------------------------------------------------------ 13:24:17.713 INFO HaplotypeCaller - ------------------------------------------------------------ 13:24:17.715 INFO HaplotypeCaller - HTSJDK Version: 2.24.1 13:24:17.715 INFO HaplotypeCaller - Picard Version: 2.25.4 13:24:17.715 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 13:24:17.715 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 13:24:17.715 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 13:24:17.715 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 13:24:17.715 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 13:24:17.715 INFO HaplotypeCaller - Deflater: IntelDeflater 13:24:17.715 INFO HaplotypeCaller - Inflater: IntelInflater 13:24:17.716 INFO HaplotypeCaller - GCS max retries/reopens: 20 13:24:17.716 INFO HaplotypeCaller - Requester pays: disabled 13:24:17.716 INFO HaplotypeCaller - Initializing engine 13:24:18.392 INFO IntervalArgumentCollection - Processing 366924 bp from intervals 13:24:18.396 INFO HaplotypeCaller - Done initializing engine 13:24:18.399 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled 13:24:18.405 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output 13:24:18.405 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 13:24:18.421 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 13:24:18.441 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 13:24:18.488 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 13:24:18.489 INFO IntelPairHmm - Available threads: 12 13:24:18.489 INFO IntelPairHmm - Requested threads: 4 13:24:18.489 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 13:24:18.656 INFO ProgressMeter - Starting traversal 13:24:18.656 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 13:24:20.758 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position Mt:4950 and possibly subsequent; at least 10 samples must have called genotypes 13:24:23.684 WARN DepthPerSampleHC - Annotation will not be calculated at position Mt:20887 and possibly subsequent; genotype for sample sample2 is not called 13:24:23.684 WARN StrandBiasBySample - Annotation will not be calculated at position Mt:20887 and possibly subsequent; genotype for sample sample2 is not called 13:24:28.862 INFO ProgressMeter - Mt:204159 0.2 880 5173.4 13:24:33.464 INFO HaplotypeCaller - 688 read(s) filtered by: MappingQualityReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 2 read(s) filtered by: NotSecondaryAlignmentReadFilter 62 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 752 total reads filtered 13:24:33.465 INFO ProgressMeter - Mt:366762 0.2 1531 6203.4 13:24:33.465 INFO ProgressMeter - Traversal complete. Processed 1531 total regions in 0.2 minutes. 13:24:33.470 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0018266 13:24:33.470 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 2.2117823000000003 13:24:33.470 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 1.04 sec 13:24:33.471 INFO HaplotypeCaller - Shutting down engine [July 20, 2022 at 1:24:33 PM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.27 minutes. Runtime.totalMemory()=3212836864 Using GATK jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-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 -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp -jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar HaplotypeCaller -R /mnt/f/3.ReSeq/genome/sequences.fa -I /mnt/f/3.ReSeq/1.mapping/MarkDup/sample2.MarkDup.bam -O /mnt/f/3.ReSeq/2.SNP/1.GVCF/sample2.Mt.gvcf.gz --emit-ref-confidence GVCF --do-not-run-physical-phasing -L Mt -stand-call-conf 30 Picked up _JAVA_OPTIONS: -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp Using GATK jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-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 -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp -jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar HaplotypeCaller -R /mnt/f/3.ReSeq/genome/sequences.fa -I /mnt/f/3.ReSeq/1.mapping/MarkDup/sample2.MarkDup.bam -O /mnt/f/3.ReSeq/2.SNP/1.GVCF/sample2.Pt.gvcf.gz --emit-ref-confidence GVCF --do-not-run-physical-phasing -L Pt -stand-call-conf 30 Picked up _JAVA_OPTIONS: -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp 13:23:13.477 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jul 20, 2022 1:23:13 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 13:23:13.866 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:13.867 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.5.0 13:23:13.867 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 13:23:13.868 INFO HaplotypeCaller - Executing as linux@ZXL-PC on Linux v4.4.0-22000-Microsoft amd64 13:23:13.868 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.15-internal+0-adhoc..src 13:23:13.868 INFO HaplotypeCaller - Start Date/Time: July 20, 2022 at 1:23:13 PM CST 13:23:13.868 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:13.868 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:13.869 INFO HaplotypeCaller - HTSJDK Version: 2.24.1 13:23:13.869 INFO HaplotypeCaller - Picard Version: 2.25.4 13:23:13.869 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 13:23:13.869 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 13:23:13.869 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 13:23:13.870 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 13:23:13.870 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 13:23:13.870 INFO HaplotypeCaller - Deflater: IntelDeflater 13:23:13.870 INFO HaplotypeCaller - Inflater: IntelInflater 13:23:13.870 INFO HaplotypeCaller - GCS max retries/reopens: 20 13:23:13.870 INFO HaplotypeCaller - Requester pays: disabled 13:23:13.870 INFO HaplotypeCaller - Initializing engine 13:23:14.145 INFO IntervalArgumentCollection - Processing 18585056 bp from intervals 13:23:14.184 INFO HaplotypeCaller - Done initializing engine 13:23:14.186 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled 13:23:14.192 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output 13:23:14.192 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 13:23:14.207 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 13:23:14.209 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 13:23:14.251 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 13:23:14.251 INFO IntelPairHmm - Available threads: 12 13:23:14.252 INFO IntelPairHmm - Requested threads: 4 13:23:14.252 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 13:23:14.330 INFO ProgressMeter - Starting traversal 13:23:14.331 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 13:23:18.187 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position 4:15489 and possibly subsequent; at least 10 samples must have called genotypes 13:23:24.783 INFO ProgressMeter - 4:186999 0.2 650 3731.3 13:23:34.827 INFO ProgressMeter - 4:840115 0.3 2920 8548.4 13:23:44.851 INFO ProgressMeter - 4:1941729 0.5 6750 13270.0 13:23:54.853 INFO ProgressMeter - 4:3186155 0.7 11100 16435.5 13:23:55.537 WARN DepthPerSampleHC - Annotation will not be calculated at position 4:3347090 and possibly subsequent; genotype for sample sample2 is not called 13:23:55.537 WARN StrandBiasBySample - Annotation will not be calculated at position 4:3347090 and possibly subsequent; genotype for sample sample2 is not called 13:24:04.903 INFO ProgressMeter - 4:4883919 0.8 17050 20228.6 13:24:14.904 INFO ProgressMeter - 4:7807056 1.0 27250 26992.2 13:24:24.918 INFO ProgressMeter - 4:9713405 1.2 33900 28815.9 13:24:34.918 INFO ProgressMeter - 4:12047944 1.3 42040 31300.3 Using GATK jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-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 -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp -jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar HaplotypeCaller -R /mnt/f/3.ReSeq/genome/sequences.fa -I /mnt/f/3.ReSeq/1.mapping/MarkDup/sample2.MarkDup.bam -O /mnt/f/3.ReSeq/2.SNP/1.GVCF/sample2.4.gvcf.gz --emit-ref-confidence GVCF --do-not-run-physical-phasing -L 4 -stand-call-conf 30 Picked up _JAVA_OPTIONS: -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp 13:23:12.185 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jul 20, 2022 1:23:13 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 13:23:13.259 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:13.260 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.5.0 13:23:13.260 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 13:23:13.261 INFO HaplotypeCaller - Executing as linux@ZXL-PC on Linux v4.4.0-22000-Microsoft amd64 13:23:13.261 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.15-internal+0-adhoc..src 13:23:13.261 INFO HaplotypeCaller - Start Date/Time: July 20, 2022 at 1:23:12 PM CST 13:23:13.261 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:13.261 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:13.262 INFO HaplotypeCaller - HTSJDK Version: 2.24.1 13:23:13.262 INFO HaplotypeCaller - Picard Version: 2.25.4 13:23:13.262 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 13:23:13.262 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 13:23:13.262 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 13:23:13.262 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 13:23:13.262 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 13:23:13.263 INFO HaplotypeCaller - Deflater: IntelDeflater 13:23:13.263 INFO HaplotypeCaller - Inflater: IntelInflater 13:23:13.263 INFO HaplotypeCaller - GCS max retries/reopens: 20 13:23:13.263 INFO HaplotypeCaller - Requester pays: disabled 13:23:13.263 INFO HaplotypeCaller - Initializing engine 13:23:13.486 INFO IntervalArgumentCollection - Processing 18585056 bp from intervals 13:23:13.491 INFO HaplotypeCaller - Done initializing engine 13:23:13.494 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled 13:23:13.509 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output 13:23:13.510 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 13:23:13.547 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 13:23:13.550 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 13:23:13.571 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 13:23:13.571 INFO IntelPairHmm - Available threads: 12 13:23:13.571 INFO IntelPairHmm - Requested threads: 4 13:23:13.571 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 13:23:13.657 INFO ProgressMeter - Starting traversal 13:23:13.658 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 13:23:17.118 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position 4:10597 and possibly subsequent; at least 10 samples must have called genotypes 13:23:23.951 INFO ProgressMeter - 4:180145 0.2 640 3730.7 13:23:33.997 INFO ProgressMeter - 4:913124 0.3 3190 9410.5 13:23:44.004 INFO ProgressMeter - 4:1937469 0.5 6770 13385.6 13:23:47.077 WARN DepthPerSampleHC - Annotation will not be calculated at position 4:2243190 and possibly subsequent; genotype for sample sample1 is not called 13:23:47.078 WARN StrandBiasBySample - Annotation will not be calculated at position 4:2243190 and possibly subsequent; genotype for sample sample1 is not called 13:23:54.044 INFO ProgressMeter - 4:2954264 0.7 10350 15377.0 13:24:04.114 INFO ProgressMeter - 4:3933826 0.8 13800 16410.7 13:24:14.171 INFO ProgressMeter - 4:4010673 1.0 14110 13990.4 13:24:24.291 INFO ProgressMeter - 4:6643040 1.2 23310 19800.9 13:24:34.393 INFO ProgressMeter - 4:8538008 1.3 29960 22265.4 Using GATK jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-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 -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp -jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar HaplotypeCaller -R /mnt/f/3.ReSeq/genome/sequences.fa -I /mnt/f/3.ReSeq/1.mapping/MarkDup/sample1.MarkDup.bam -O /mnt/f/3.ReSeq/2.SNP/1.GVCF/sample1.4.gvcf.gz --emit-ref-confidence GVCF --do-not-run-physical-phasing -L 4 -stand-call-conf 30 Picked up _JAVA_OPTIONS: -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp 13:23:12.793 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jul 20, 2022 1:23:13 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 13:23:13.238 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:13.239 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.5.0 13:23:13.239 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 13:23:13.240 INFO HaplotypeCaller - Executing as linux@ZXL-PC on Linux v4.4.0-22000-Microsoft amd64 13:23:13.240 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.15-internal+0-adhoc..src 13:23:13.240 INFO HaplotypeCaller - Start Date/Time: July 20, 2022 at 1:23:12 PM CST 13:23:13.240 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:13.241 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:13.241 INFO HaplotypeCaller - HTSJDK Version: 2.24.1 13:23:13.241 INFO HaplotypeCaller - Picard Version: 2.25.4 13:23:13.242 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 13:23:13.242 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 13:23:13.242 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 13:23:13.242 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 13:23:13.242 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 13:23:13.242 INFO HaplotypeCaller - Deflater: IntelDeflater 13:23:13.242 INFO HaplotypeCaller - Inflater: IntelInflater 13:23:13.248 INFO HaplotypeCaller - GCS max retries/reopens: 20 13:23:13.248 INFO HaplotypeCaller - Requester pays: disabled 13:23:13.248 INFO HaplotypeCaller - Initializing engine 13:23:13.795 INFO IntervalArgumentCollection - Processing 19698289 bp from intervals 13:23:13.811 INFO HaplotypeCaller - Done initializing engine 13:23:13.813 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled 13:23:13.819 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output 13:23:13.819 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 13:23:13.846 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 13:23:13.849 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 13:23:13.874 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 13:23:13.875 INFO IntelPairHmm - Available threads: 12 13:23:13.875 INFO IntelPairHmm - Requested threads: 4 13:23:13.875 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 13:23:14.054 INFO ProgressMeter - Starting traversal 13:23:14.054 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 13:23:16.208 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position 2:1357 and possibly subsequent; at least 10 samples must have called genotypes 13:23:24.330 INFO ProgressMeter - 2:57500 0.2 220 1284.5 13:23:34.362 INFO ProgressMeter - 2:808488 0.3 2830 8361.2 13:23:44.414 INFO ProgressMeter - 2:1985375 0.5 6940 13715.4 13:23:54.480 INFO ProgressMeter - 2:3176947 0.7 11080 16444.9 13:24:01.448 WARN DepthPerSampleHC - Annotation will not be calculated at position 2:3501816 and possibly subsequent; genotype for sample sample2 is not called 13:24:01.449 WARN StrandBiasBySample - Annotation will not be calculated at position 2:3501816 and possibly subsequent; genotype for sample sample2 is not called 13:24:04.487 INFO ProgressMeter - 2:3646248 0.8 12790 15216.2 13:24:14.631 INFO ProgressMeter - 2:5015654 1.0 17580 17412.8 13:24:24.670 INFO ProgressMeter - 2:6078985 1.2 21280 18080.9 13:24:34.680 INFO ProgressMeter - 2:8042345 1.3 28140 20941.1 Using GATK jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-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 -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp -jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar HaplotypeCaller -R /mnt/f/3.ReSeq/genome/sequences.fa -I /mnt/f/3.ReSeq/1.mapping/MarkDup/sample2.MarkDup.bam -O /mnt/f/3.ReSeq/2.SNP/1.GVCF/sample2.2.gvcf.gz --emit-ref-confidence GVCF --do-not-run-physical-phasing -L 2 -stand-call-conf 30 Picked up _JAVA_OPTIONS: -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp 13:23:13.409 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jul 20, 2022 1:23:13 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 13:23:13.812 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:13.813 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.5.0 13:23:13.813 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 13:23:13.814 INFO HaplotypeCaller - Executing as linux@ZXL-PC on Linux v4.4.0-22000-Microsoft amd64 13:23:13.814 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.15-internal+0-adhoc..src 13:23:13.814 INFO HaplotypeCaller - Start Date/Time: July 20, 2022 at 1:23:13 PM CST 13:23:13.815 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:13.815 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:13.815 INFO HaplotypeCaller - HTSJDK Version: 2.24.1 13:23:13.816 INFO HaplotypeCaller - Picard Version: 2.25.4 13:23:13.816 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 13:23:13.816 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 13:23:13.816 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 13:23:13.816 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 13:23:13.816 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 13:23:13.816 INFO HaplotypeCaller - Deflater: IntelDeflater 13:23:13.816 INFO HaplotypeCaller - Inflater: IntelInflater 13:23:13.816 INFO HaplotypeCaller - GCS max retries/reopens: 20 13:23:13.816 INFO HaplotypeCaller - Requester pays: disabled 13:23:13.816 INFO HaplotypeCaller - Initializing engine 13:23:14.374 INFO IntervalArgumentCollection - Processing 23459830 bp from intervals 13:23:14.388 INFO HaplotypeCaller - Done initializing engine 13:23:14.390 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled 13:23:14.468 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output 13:23:14.468 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 13:23:14.483 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 13:23:14.485 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 13:23:14.527 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 13:23:14.528 INFO IntelPairHmm - Available threads: 12 13:23:14.528 INFO IntelPairHmm - Requested threads: 4 13:23:14.528 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 13:23:14.683 INFO ProgressMeter - Starting traversal 13:23:14.683 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 13:23:16.735 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position 3:338 and possibly subsequent; at least 10 samples must have called genotypes 13:23:24.750 INFO ProgressMeter - 3:171133 0.2 610 3636.4 13:23:30.324 WARN DepthPerSampleHC - Annotation will not be calculated at position 3:416205 and possibly subsequent; genotype for sample sample2 is not called 13:23:30.325 WARN StrandBiasBySample - Annotation will not be calculated at position 3:416205 and possibly subsequent; genotype for sample sample2 is not called 13:23:35.003 INFO ProgressMeter - 3:812188 0.3 2840 8386.2 13:23:45.005 INFO ProgressMeter - 3:1915236 0.5 6700 13258.1 13:23:55.086 INFO ProgressMeter - 3:2793650 0.7 9780 14524.0 13:24:05.151 INFO ProgressMeter - 3:3001162 0.8 10500 12483.4 13:24:15.168 INFO ProgressMeter - 3:3797775 1.0 13290 13183.7 13:24:25.171 INFO ProgressMeter - 3:4747517 1.2 16640 14164.5 13:24:35.175 INFO ProgressMeter - 3:6030417 1.3 21120 15743.4 Using GATK jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-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 -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp -jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar HaplotypeCaller -R /mnt/f/3.ReSeq/genome/sequences.fa -I /mnt/f/3.ReSeq/1.mapping/MarkDup/sample2.MarkDup.bam -O /mnt/f/3.ReSeq/2.SNP/1.GVCF/sample2.3.gvcf.gz --emit-ref-confidence GVCF --do-not-run-physical-phasing -L 3 -stand-call-conf 30 Picked up _JAVA_OPTIONS: -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp 13:23:11.880 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jul 20, 2022 1:23:12 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 13:23:12.486 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:12.488 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.5.0 13:23:12.488 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 13:23:12.488 INFO HaplotypeCaller - Executing as linux@ZXL-PC on Linux v4.4.0-22000-Microsoft amd64 13:23:12.488 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.15-internal+0-adhoc..src 13:23:12.489 INFO HaplotypeCaller - Start Date/Time: July 20, 2022 at 1:23:11 PM CST 13:23:12.489 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:12.489 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:12.490 INFO HaplotypeCaller - HTSJDK Version: 2.24.1 13:23:12.490 INFO HaplotypeCaller - Picard Version: 2.25.4 13:23:12.490 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 13:23:12.490 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 13:23:12.490 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 13:23:12.490 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 13:23:12.490 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 13:23:12.490 INFO HaplotypeCaller - Deflater: IntelDeflater 13:23:12.490 INFO HaplotypeCaller - Inflater: IntelInflater 13:23:12.490 INFO HaplotypeCaller - GCS max retries/reopens: 20 13:23:12.490 INFO HaplotypeCaller - Requester pays: disabled 13:23:12.491 INFO HaplotypeCaller - Initializing engine 13:23:12.837 INFO IntervalArgumentCollection - Processing 23459830 bp from intervals 13:23:12.868 INFO HaplotypeCaller - Done initializing engine 13:23:12.871 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled 13:23:12.877 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output 13:23:12.878 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 13:23:12.925 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 13:23:12.940 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 13:23:12.957 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 13:23:12.980 INFO IntelPairHmm - Available threads: 12 13:23:12.980 INFO IntelPairHmm - Requested threads: 4 13:23:12.981 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 13:23:13.208 INFO ProgressMeter - Starting traversal 13:23:13.209 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 13:23:18.505 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position 3:154905 and possibly subsequent; at least 10 samples must have called genotypes 13:23:23.234 INFO ProgressMeter - 3:286218 0.2 990 5925.2 13:23:33.259 INFO ProgressMeter - 3:975587 0.3 3400 10174.6 13:23:43.320 INFO ProgressMeter - 3:2164102 0.5 7540 15024.4 13:23:53.353 INFO ProgressMeter - 3:3190639 0.7 11140 16650.1 13:24:03.423 INFO ProgressMeter - 3:3449998 0.8 12030 14374.5 13:24:13.453 INFO ProgressMeter - 3:4498309 1.0 15710 15653.9 13:24:15.680 WARN DepthPerSampleHC - Annotation will not be calculated at position 3:4760343 and possibly subsequent; genotype for sample sample1 is not called 13:24:15.683 WARN StrandBiasBySample - Annotation will not be calculated at position 3:4760343 and possibly subsequent; genotype for sample sample1 is not called 13:24:25.103 INFO ProgressMeter - 3:5541575 1.2 19370 16243.6 13:24:34.802 INFO ProgressMeter - 3:6206314 1.4 21710 15964.6 Using GATK jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-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 -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp -jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar HaplotypeCaller -R /mnt/f/3.ReSeq/genome/sequences.fa -I /mnt/f/3.ReSeq/1.mapping/MarkDup/sample1.MarkDup.bam -O /mnt/f/3.ReSeq/2.SNP/1.GVCF/sample1.3.gvcf.gz --emit-ref-confidence GVCF --do-not-run-physical-phasing -L 3 -stand-call-conf 30 Picked up _JAVA_OPTIONS: -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp 13:23:11.465 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jul 20, 2022 1:23:11 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 13:23:11.981 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:11.982 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.5.0 13:23:11.982 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 13:23:11.982 INFO HaplotypeCaller - Executing as linux@ZXL-PC on Linux v4.4.0-22000-Microsoft amd64 13:23:11.983 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.15-internal+0-adhoc..src 13:23:11.983 INFO HaplotypeCaller - Start Date/Time: July 20, 2022 at 1:23:11 PM CST 13:23:11.983 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:11.983 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:11.984 INFO HaplotypeCaller - HTSJDK Version: 2.24.1 13:23:11.984 INFO HaplotypeCaller - Picard Version: 2.25.4 13:23:11.984 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 13:23:11.984 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 13:23:11.984 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 13:23:11.984 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 13:23:11.984 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 13:23:11.985 INFO HaplotypeCaller - Deflater: IntelDeflater 13:23:11.985 INFO HaplotypeCaller - Inflater: IntelInflater 13:23:11.985 INFO HaplotypeCaller - GCS max retries/reopens: 20 13:23:11.985 INFO HaplotypeCaller - Requester pays: disabled 13:23:11.985 INFO HaplotypeCaller - Initializing engine 13:23:12.342 INFO IntervalArgumentCollection - Processing 19698289 bp from intervals 13:23:12.348 INFO HaplotypeCaller - Done initializing engine 13:23:12.350 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled 13:23:12.357 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output 13:23:12.357 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 13:23:12.385 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 13:23:12.405 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 13:23:12.422 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 13:23:12.422 INFO IntelPairHmm - Available threads: 12 13:23:12.422 INFO IntelPairHmm - Requested threads: 4 13:23:12.423 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 13:23:12.689 INFO ProgressMeter - Starting traversal 13:23:12.689 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 13:23:14.952 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position 2:1891 and possibly subsequent; at least 10 samples must have called genotypes 13:23:22.856 INFO ProgressMeter - 2:153329 0.2 550 3246.1 13:23:33.221 INFO ProgressMeter - 2:925355 0.3 3250 9497.4 13:23:43.285 INFO ProgressMeter - 2:2050142 0.5 7200 14119.5 13:23:53.381 INFO ProgressMeter - 2:3063245 0.7 10760 15865.9 13:24:03.406 INFO ProgressMeter - 2:3380759 0.8 11880 14054.5 13:24:06.024 WARN DepthPerSampleHC - Annotation will not be calculated at position 2:3438343 and possibly subsequent; genotype for sample sample1 is not called 13:24:06.115 WARN StrandBiasBySample - Annotation will not be calculated at position 2:3438343 and possibly subsequent; genotype for sample sample1 is not called 13:24:14.258 INFO ProgressMeter - 2:3621376 1.0 12730 12405.6 13:24:25.550 INFO ProgressMeter - 2:3627095 1.2 12760 10523.9 13:24:35.441 INFO ProgressMeter - 2:4681867 1.4 16440 11920.1 13:24:45.440 INFO ProgressMeter - 2:10671263 1.5 37320 24142.1 13:24:55.442 INFO ProgressMeter - 2:16985792 1.7 59420 34696.8 13:24:59.117 INFO HaplotypeCaller - 2721 read(s) filtered by: MappingQualityReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 2 read(s) filtered by: NotSecondaryAlignmentReadFilter 736 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 3459 total reads filtered 13:24:59.118 INFO ProgressMeter - 2:19696328 1.8 68956 38874.7 13:24:59.118 INFO ProgressMeter - Traversal complete. Processed 68956 total regions in 1.8 minutes. 13:24:59.161 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009107800000000001 13:24:59.161 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 12.3172306 13:24:59.162 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 2.72 sec 13:24:59.162 INFO HaplotypeCaller - Shutting down engine [July 20, 2022 at 1:24:59 PM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 1.80 minutes. Runtime.totalMemory()=13920894976 Using GATK jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-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 -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp -jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar HaplotypeCaller -R /mnt/f/3.ReSeq/genome/sequences.fa -I /mnt/f/3.ReSeq/1.mapping/MarkDup/sample1.MarkDup.bam -O /mnt/f/3.ReSeq/2.SNP/1.GVCF/sample1.2.gvcf.gz --emit-ref-confidence GVCF --do-not-run-physical-phasing -L 2 -stand-call-conf 30 Picked up _JAVA_OPTIONS: -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp 13:23:11.665 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Jul 20, 2022 1:23:12 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 13:23:12.987 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:12.988 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.5.0 13:23:12.988 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 13:23:12.989 INFO HaplotypeCaller - Executing as linux@ZXL-PC on Linux v4.4.0-22000-Microsoft amd64 13:23:12.989 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.15-internal+0-adhoc..src 13:23:12.989 INFO HaplotypeCaller - Start Date/Time: July 20, 2022 at 1:23:11 PM CST 13:23:12.990 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:12.990 INFO HaplotypeCaller - ------------------------------------------------------------ 13:23:12.990 INFO HaplotypeCaller - HTSJDK Version: 2.24.1 13:23:12.991 INFO HaplotypeCaller - Picard Version: 2.25.4 13:23:12.991 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 13:23:12.991 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 13:23:12.991 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 13:23:12.991 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 13:23:12.991 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 13:23:12.991 INFO HaplotypeCaller - Deflater: IntelDeflater 13:23:12.991 INFO HaplotypeCaller - Inflater: IntelInflater 13:23:12.991 INFO HaplotypeCaller - GCS max retries/reopens: 20 13:23:12.991 INFO HaplotypeCaller - Requester pays: disabled 13:23:13.022 INFO HaplotypeCaller - Initializing engine 13:23:13.263 INFO IntervalArgumentCollection - Processing 26975502 bp from intervals 13:23:13.268 INFO HaplotypeCaller - Done initializing engine 13:23:13.277 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled 13:23:13.283 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output 13:23:13.283 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 13:23:13.297 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 13:23:13.300 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 13:23:13.339 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 13:23:13.340 INFO IntelPairHmm - Available threads: 12 13:23:13.340 INFO IntelPairHmm - Requested threads: 4 13:23:13.340 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 13:23:13.437 INFO ProgressMeter - Starting traversal 13:23:13.437 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 13:23:17.918 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position 5:43987 and possibly subsequent; at least 10 samples must have called genotypes 13:23:23.493 INFO ProgressMeter - 5:167871 0.2 600 3580.7 13:23:34.143 INFO ProgressMeter - 5:894329 0.3 3120 9041.3 13:23:40.930 WARN DepthPerSampleHC - Annotation will not be calculated at position 5:1476801 and possibly subsequent; genotype for sample sample1 is not called 13:23:40.930 WARN StrandBiasBySample - Annotation will not be calculated at position 5:1476801 and possibly subsequent; genotype for sample sample1 is not called 13:23:44.156 INFO ProgressMeter - 5:1908663 0.5 6700 13086.8 13:23:54.172 INFO ProgressMeter - 5:3501050 0.7 12260 18059.1 13:24:04.181 INFO ProgressMeter - 5:3732597 0.8 13080 15466.2 13:24:14.431 INFO ProgressMeter - 5:4255358 1.0 14910 14667.5 13:24:24.493 INFO ProgressMeter - 5:4760066 1.2 16660 14068.0 13:24:34.501 INFO ProgressMeter - 5:5608935 1.4 19640 14537.0 13:24:44.501 INFO ProgressMeter - 5:9663439 1.5 33800 22270.3 13:24:54.507 INFO ProgressMeter - 5:13239915 1.7 46310 27492.1 13:25:04.507 INFO ProgressMeter - 5:20660320 1.9 72210 39008.2 13:25:10.371 INFO HaplotypeCaller - 1174 read(s) filtered by: MappingQualityReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 11 read(s) filtered by: NotSecondaryAlignmentReadFilter 935 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 2120 total reads filtered 13:25:10.371 INFO ProgressMeter - 5:26974759 1.9 94303 48388.2 13:25:10.371 INFO ProgressMeter - Traversal complete. Processed 94303 total regions in 1.9 minutes. 13:25:10.413 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0066058 13:25:10.414 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 8.538310000000001 13:25:10.414 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 2.73 sec 13:25:10.414 INFO HaplotypeCaller - Shutting down engine [July 20, 2022 at 1:25:10 PM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 1.98 minutes. Runtime.totalMemory()=14617149440 Using GATK jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-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 -Xmx28683M -Djava.io.tmpdir=/mnt/f/3.ReSeq/tmp -jar /home/linux/miniconda3/envs/Call_SNP/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar HaplotypeCaller -R /mnt/f/3.ReSeq/genome/sequences.fa -I /mnt/f/3.ReSeq/1.mapping/MarkDup/sample1.MarkDup.bam -O /mnt/f/3.ReSeq/2.SNP/1.GVCF/sample1.5.gvcf.gz --emit-ref-confidence GVCF --do-not-run-physical-phasing -L 5 -stand-call-conf 30

biomarble commented 2 years ago

这些信息都是正常输出的信息，没有错误信息，可以把stderr.log和stdout.log两个完整文件发出来我看下

zxljiqixuexi commented 2 years ago

之前试了就其他的电脑可以跑，但是用我这个就跑不了。按教程一步一步的来也能跑通，一步法就不行了。非常感谢，报错信息如下。 1658474874087 stderr.log stdout.log

zxljiqixuexi commented 2 years ago

好吧 谢谢了 可是用的是实例数据，配置比可运行的电脑也高很多

biomarble commented 2 years ago

估计是并行进程数过多，计算机资源不足造成java崩溃。 建议在服务器运行。 或者把程序的第一行

CPU=`getconf _NPROCESSORS_ONLN|xargs -I% echo "% - 1"|bc`

修改为指定并行数（可用文本编辑器修改）

CPU=5