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onekeyreseq's Introduction

Feature

  • OneKey analysis from clean reads to variant VCF
  • support multiple sample analysis
  • parallel computing by default
  • all analysis commands saved in files
  • Servers with large memory recommended
  • No QC procedure, using Clean reads as input

input file directory prepare

graph TB

analysisDir ---->fq
analysisDir-->sample.list.txt
fq-->*.R1.fq.gz
fq-->*.R2.fq.gz

analysisDir ---->genome
genome-->sequences.fa
genome-->genes.gtf
Loading

Dependencies

install dependencies using conda:

mamba create -n WGS perl=5.26.2 gatk4=4.2.5  bwa=0.7.17  samtools=1.15  vcftools=0.1.16 snpeff=5.1 python=3.7 parallel=20211222 bcftools=1.15 multiqc=1.12

Usage

#activate environment 
conda activate WGS

#change working directory to analysisDir
cd /mnt/d/workshop/3.ReSeq

#run
bash onekeyReseq

Results

directory meaning
1.mapping mapping results
mapStat.html is the analysis report
2.SNP SNP/InDel Results
snp.indel.anno.addid.vcf is the final variant file
commands .sh is the detail commands
.sh.ok means the step is done normally
log log files
stdout.log is the log of standard output，stderr.log is the log of standard error

onekeyreseq's People

Contributors

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Stargazers

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Watchers

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onekeyreseq's Issues

need help

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

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