Building a SMALL index INFO 2020-09-09 09:21:02 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I ../output/sampl1/tophat/accepted_hits.bam -O ../output/sampl1/tophat/accepted_hits.addsort.bam -SO coordinate -ID sampl1 -LB sampl1 -PL Illumina -PU run -SM sampl1 ********** 09:21:02.844 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Sep 09 09:21:02 CST 2020] AddOrReplaceReadGroups INPUT=../output/sampl1/tophat/accepted_hits.bam OUTPUT=../output/sampl1/tophat/accepted_hits.addsort.bam SORT_ORDER=coordinate RGID=sampl1 RGLB=sampl1 RGPL=Illumina RGPU=run RGSM=sampl1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Sep 09 09:21:02 CST 2020] Executing as GDYJY01@localhost.localdomain on Linux 3.10.0-957.21.3.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_222-b10; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.23.3 INFO 2020-09-09 09:21:02 AddOrReplaceReadGroups Created read-group ID=sampl1 PL=Illumina LB=sampl1 SM=sampl1 INFO 2020-09-09 09:21:15 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 12s. Last read position: Chr4:9,075,626 [Wed Sep 09 09:21:24 CST 2020] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.37 minutes. Runtime.totalMemory()=1920466944 INFO 2020-09-09 09:21:25 MarkDuplicates ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** MarkDuplicates -SORTING_COLLECTION_SIZE_RATIO 0.5 -MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 80000 -I ../output/sampl1/tophat/accepted_hits.addsort.bam -O ../output/sampl1/tophat/accepted_hits.mkdup.addsort.bam -CREATE_INDEX true -VALIDATION_STRINGENCY SILENT -M ../output/sampl1/output4.metrics ********** 09:21:26.326 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Sep 09 09:21:26 CST 2020] MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=80000 SORTING_COLLECTION_SIZE_RATIO=0.5 INPUT=[../output/sampl1/tophat/accepted_hits.addsort.bam] OUTPUT=../output/sampl1/tophat/accepted_hits.mkdup.addsort.bam METRICS_FILE=../output/sampl1/output4.metrics VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Sep 09 09:21:26 CST 2020] Executing as GDYJY01@localhost.localdomain on Linux 3.10.0-957.21.3.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_222-b10; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.23.3 INFO 2020-09-09 09:21:26 MarkDuplicates Start of doWork freeMemory: 2037369248; totalMemory: 2058354688; maxMemory: 28631367680 INFO 2020-09-09 09:21:26 MarkDuplicates Reading input file and constructing read end information. INFO 2020-09-09 09:21:26 MarkDuplicates Will retain up to 207473678 data points before spilling to disk. INFO 2020-09-09 09:21:43 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 15s. Last read position: Chr4:9,075,626 INFO 2020-09-09 09:21:43 MarkDuplicates Tracking 1571 as yet unmatched pairs. 442 records in RAM. INFO 2020-09-09 09:21:47 MarkDuplicates Read 1775427 records. 0 pairs never matched. INFO 2020-09-09 09:21:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 2607120216; totalMemory: 4500488192; maxMemory: 28631367680 INFO 2020-09-09 09:21:51 MarkDuplicates Will retain up to 894730240 duplicate indices before spilling to disk. INFO 2020-09-09 09:21:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2020-09-09 09:21:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2020-09-09 09:21:59 MarkDuplicates Sorting list of duplicate records. INFO 2020-09-09 09:22:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 4534196872; totalMemory: 11740381184; maxMemory: 28631367680 INFO 2020-09-09 09:22:00 MarkDuplicates Marking 397117 records as duplicates. INFO 2020-09-09 09:22:00 MarkDuplicates Found 39082 optical duplicate clusters. INFO 2020-09-09 09:22:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2020-09-09 09:22:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2020-09-09 09:22:26 MarkDuplicates Duplicate Index cleanup. INFO 2020-09-09 09:22:26 MarkDuplicates Getting Memory Stats. INFO 2020-09-09 09:22:26 MarkDuplicates Before output close freeMemory: 13794127288; totalMemory: 13884719104; maxMemory: 28631367680 INFO 2020-09-09 09:22:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2020-09-09 09:22:26 MarkDuplicates After output close freeMemory: 13625830840; totalMemory: 13716422656; maxMemory: 28631367680 [Wed Sep 09 09:22:26 CST 2020] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1.01 minutes. Runtime.totalMemory()=13716422656 Using GATK jar /home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-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 -jar /home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar HaplotypeCaller --native-pair-hmm-threads 50 -R ../input/ref.fa -I ../output/sampl1/tophat/accepted_hits.mkdup.addsort.bam -ERC GVCF -O ../output/sampl1/tophat/accepted_hits.g.vcf --genotyping-mode DISCOVERY --pcr-indel-model CONSERVATIVE --sample-ploidy 2 --min-base-quality-score 10 --kmer-size 10 --kmer-size 25 09:22:32.016 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Sep 09, 2020 9:22:33 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:22:33.795 INFO HaplotypeCaller - ------------------------------------------------------------ 09:22:33.796 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.2.0 09:22:33.796 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:22:33.797 INFO HaplotypeCaller - Executing as GDYJY01@localhost.localdomain on Linux v3.10.0-957.21.3.el7.x86_64 amd64 09:22:33.797 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_222-b10 09:22:33.797 INFO HaplotypeCaller - Start Date/Time: 2020年9月9日上午09时22分31秒 09:22:33.798 INFO HaplotypeCaller - ------------------------------------------------------------ 09:22:33.798 INFO HaplotypeCaller - ------------------------------------------------------------ 09:22:33.799 INFO HaplotypeCaller - HTSJDK Version: 2.19.0 09:22:33.799 INFO HaplotypeCaller - Picard Version: 2.19.0 09:22:33.799 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:22:33.799 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:22:33.799 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:22:33.799 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:22:33.800 INFO HaplotypeCaller - Deflater: IntelDeflater 09:22:33.800 INFO HaplotypeCaller - Inflater: IntelInflater 09:22:33.800 INFO HaplotypeCaller - GCS max retries/reopens: 20 09:22:33.800 INFO HaplotypeCaller - Requester pays: disabled 09:22:33.800 INFO HaplotypeCaller - Initializing engine 09:22:34.434 INFO HaplotypeCaller - Done initializing engine 09:22:34.437 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 09:22:34.445 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output 09:22:34.445 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 09:22:34.463 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 09:22:34.530 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 09:22:34.601 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 09:22:34.602 INFO IntelPairHmm - Available threads: 50 09:22:34.602 INFO IntelPairHmm - Requested threads: 50 09:22:34.602 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 09:22:34.658 INFO ProgressMeter - Starting traversal 09:22:34.659 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 09:22:42.648 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:22:42.648 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:22:42.911 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:22:44.663 INFO ProgressMeter - Chr1:2075155 0.2 7190 43127.1 09:22:54.664 INFO ProgressMeter - Chr1:4798715 0.3 16660 49967.5 09:23:04.696 INFO ProgressMeter - Chr1:7439957 0.5 25690 51318.4 09:23:14.699 INFO ProgressMeter - Chr1:10653147 0.7 36710 55010.0 09:23:24.700 INFO ProgressMeter - Chr1:15128459 0.8 51880 62205.0 09:23:34.705 INFO ProgressMeter - Chr1:21167067 1.0 72340 72284.6 09:23:42.777 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:23:44.708 INFO ProgressMeter - Chr1:25862216 1.2 88390 75709.9 09:23:54.708 INFO ProgressMeter - Chr1:30310331 1.3 103670 77704.9 09:24:04.708 INFO ProgressMeter - Chr1:34469354 1.5 117930 78577.2 09:24:14.708 INFO ProgressMeter - Chr1:39601907 1.7 135560 81296.2 09:24:24.709 INFO ProgressMeter - Chr10:519419 1.8 149990 81775.6 09:24:34.730 INFO ProgressMeter - Chr10:7436962 2.0 173390 86643.7 09:24:41.025 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:24:44.748 INFO ProgressMeter - Chr10:13389301 2.2 193520 89255.8 09:24:54.749 INFO ProgressMeter - Chr10:19477015 2.3 214270 91771.0 09:25:04.758 INFO ProgressMeter - Chr11:2845062 2.5 236890 94693.5 09:25:14.758 INFO ProgressMeter - Chr11:7918834 2.7 254210 95269.8 09:25:24.758 INFO ProgressMeter - Chr11:17260202 2.8 285630 100751.9 09:25:34.784 INFO ProgressMeter - Chr11:24836781 3.0 311390 103724.6 09:25:37.440 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:25:44.798 INFO ProgressMeter - Chr12:1389328 3.2 330440 104273.2 09:25:54.804 INFO ProgressMeter - Chr12:6556149 3.3 348000 104324.4 09:26:05.275 INFO ProgressMeter - Chr12:11322730 3.5 364220 103758.5 09:26:15.284 INFO ProgressMeter - Chr12:20064597 3.7 393630 107051.5 09:26:25.283 INFO ProgressMeter - Chr12:26455030 3.8 415350 108059.0 09:26:35.283 INFO ProgressMeter - Chr2:3515819 4.0 431280 107540.4 09:26:45.285 INFO ProgressMeter - Chr2:8772253 4.2 449200 107538.7 09:26:55.289 INFO ProgressMeter - Chr2:16857478 4.3 476580 109714.2 09:27:05.291 INFO ProgressMeter - Chr2:22417922 4.5 495500 109854.0 09:27:15.291 INFO ProgressMeter - Chr2:28457034 4.7 516170 110358.8 09:27:25.294 INFO ProgressMeter - Chr2:34987797 4.8 538590 111188.9 09:27:35.295 INFO ProgressMeter - Chr3:5120121 5.0 559540 111671.3 09:27:45.318 INFO ProgressMeter - Chr3:11841708 5.2 582670 112535.6 09:27:53.727 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:27:55.318 INFO ProgressMeter - Chr3:18298200 5.3 604710 113150.1 09:28:05.318 INFO ProgressMeter - Chr3:26008810 5.5 630790 114460.5 09:28:15.339 INFO ProgressMeter - Chr3:31459385 5.7 649470 114383.6 09:28:25.365 INFO ProgressMeter - Chr3:36133565 5.8 665620 113876.6 09:28:35.366 INFO ProgressMeter - Chr4:7963925 6.0 693470 115351.8 09:28:45.366 INFO ProgressMeter - Chr4:15563111 6.2 719150 116396.5 09:28:55.369 INFO ProgressMeter - Chr4:21204726 6.3 738270 116351.6 09:29:05.372 INFO ProgressMeter - Chr4:25709978 6.5 753820 115760.7 09:29:15.380 INFO ProgressMeter - Chr4:31344229 6.7 773050 115748.9 09:29:25.382 INFO ProgressMeter - Chr5:1260162 6.8 791660 115648.7 09:29:29.285 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:29:35.384 INFO ProgressMeter - Chr5:8365321 7.0 815790 116340.6 09:29:45.386 INFO ProgressMeter - Chr5:16809024 7.2 844210 117597.9 09:29:55.388 INFO ProgressMeter - Chr5:23648704 7.3 867490 118098.4 09:30:05.390 INFO ProgressMeter - Chr5:28929300 7.5 885590 117887.2 09:30:15.394 INFO ProgressMeter - Chr6:3602341 7.7 901510 117400.7 09:30:25.396 INFO ProgressMeter - Chr6:9233132 7.8 920730 117356.2 09:30:35.396 INFO ProgressMeter - Chr6:13724239 8.0 936300 116858.1 09:30:45.413 INFO ProgressMeter - Chr6:18747780 8.2 953710 116601.4 09:30:55.463 INFO ProgressMeter - Chr6:24760560 8.3 974290 116727.3 09:31:05.462 INFO ProgressMeter - Chr6:30826176 8.5 995010 116876.0 09:31:15.463 INFO ProgressMeter - Chr7:4832949 8.7 1013040 116708.8 09:31:25.472 INFO ProgressMeter - Chr7:12545436 8.8 1039100 117453.8 09:31:25.597 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:31:36.712 INFO ProgressMeter - Chr7:20727058 9.0 1066940 118099.9 09:31:46.719 INFO ProgressMeter - Chr7:24810209 9.2 1081050 117492.7 09:31:56.724 INFO ProgressMeter - Chr8:1245726 9.4 1102130 117651.5 09:32:06.724 INFO ProgressMeter - Chr8:9710546 9.5 1130880 118610.3 09:32:16.724 INFO ProgressMeter - Chr8:19472124 9.7 1163810 119967.0 09:32:26.725 INFO ProgressMeter - Chr8:26121874 9.9 1186440 120233.9 09:32:35.485 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:32:36.734 INFO ProgressMeter - Chr9:5109007 10.0 1211670 120749.4 09:32:46.738 INFO ProgressMeter - Chr9:11059685 10.2 1231760 120745.2 09:32:56.744 INFO ProgressMeter - Chr9:19016877 10.4 1258820 121413.0 09:33:04.630 INFO HaplotypeCaller - 880342 read(s) filtered by: ((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter) AND WellformedReadFilter) 397117 read(s) filtered by: (((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter) 397117 read(s) filtered by: ((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) 397117 read(s) filtered by: (((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) 397117 read(s) filtered by: ((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) 397117 read(s) filtered by: NotDuplicateReadFilter 483225 read(s) filtered by: WellformedReadFilter 09:33:04.630 INFO ProgressMeter - ChrUn:630958 10.5 1276668 121593.0 09:33:04.630 INFO ProgressMeter - Traversal complete. Processed 1276668 total regions in 10.5 minutes. 09:33:04.669 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.079782163 09:33:04.669 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 16.148689676 09:33:04.669 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 9.42 sec 09:33:04.669 INFO HaplotypeCaller - Shutting down engine [2020年9月9日上午09时33分04秒] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 10.54 minutes. Runtime.totalMemory()=1841823744 Using GATK jar /home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-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 -jar /home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar GenotypeGVCFs -R ../input/ref.fa -O ../output/sampl1/tophat/accepted_hits.raw.vcf -V ../output/sampl1/tophat/accepted_hits.g.vcf --sample-ploidy 2 09:33:08.815 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Sep 09, 2020 9:33:10 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:33:10.594 INFO GenotypeGVCFs - ------------------------------------------------------------ 09:33:10.595 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.1.2.0 09:33:10.595 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:33:10.595 INFO GenotypeGVCFs - Executing as GDYJY01@localhost.localdomain on Linux v3.10.0-957.21.3.el7.x86_64 amd64 09:33:10.596 INFO GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_222-b10 09:33:10.596 INFO GenotypeGVCFs - Start Date/Time: 2020年9月9日上午09时33分08秒 09:33:10.596 INFO GenotypeGVCFs - ------------------------------------------------------------ 09:33:10.596 INFO GenotypeGVCFs - ------------------------------------------------------------ 09:33:10.597 INFO GenotypeGVCFs - HTSJDK Version: 2.19.0 09:33:10.597 INFO GenotypeGVCFs - Picard Version: 2.19.0 09:33:10.597 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:33:10.598 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:33:10.598 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:33:10.598 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:33:10.598 INFO GenotypeGVCFs - Deflater: IntelDeflater 09:33:10.598 INFO GenotypeGVCFs - Inflater: IntelInflater 09:33:10.598 INFO GenotypeGVCFs - GCS max retries/reopens: 20 09:33:10.598 INFO GenotypeGVCFs - Requester pays: disabled 09:33:10.599 INFO GenotypeGVCFs - Initializing engine 09:33:11.283 INFO FeatureManager - Using codec VCFCodec to read file file:///home/GDYJY01/pipelineRNV/RNV_detection/scripts/../output/sampl1/tophat/accepted_hits.g.vcf 09:33:11.361 INFO GenotypeGVCFs - Done initializing engine 09:33:11.429 INFO ProgressMeter - Starting traversal 09:33:11.429 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 09:33:11.542 WARN ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location Chr1:18072 the annotation MLEAC=[1, 0] was not a numerical value and was ignored 09:33:21.430 INFO ProgressMeter - Chr3:10373106 0.2 563000 3378000.0 09:33:30.871 INFO ProgressMeter - ChrSy:554185 0.3 1194435 3686527.8 09:33:30.871 INFO ProgressMeter - Traversal complete. Processed 1194435 total variants in 0.3 minutes. 09:33:30.927 INFO GenotypeGVCFs - Shutting down engine [2020年9月9日上午09时33分30秒] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.37 minutes. Runtime.totalMemory()=3313500160 Using GATK jar /home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-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 -jar /home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar VariantFiltration -R ../input/ref.fa -O ../output/sampl1/tophat/accepted_hits.filter.vcf -V ../output/sampl1/tophat/accepted_hits.raw.vcf -window 35 -cluster 3 --filter-name FilterFS --filter-expression FS > 30.0 --filter-name FilterQD --filter-expression QD < 2.0 09:33:35.094 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Sep 09, 2020 9:33:36 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:33:36.919 INFO VariantFiltration - ------------------------------------------------------------ 09:33:36.920 INFO VariantFiltration - The Genome Analysis Toolkit (GATK) v4.1.2.0 09:33:36.920 INFO VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:33:36.921 INFO VariantFiltration - Executing as GDYJY01@localhost.localdomain on Linux v3.10.0-957.21.3.el7.x86_64 amd64 09:33:36.921 INFO VariantFiltration - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_222-b10 09:33:36.921 INFO VariantFiltration - Start Date/Time: 2020年9月9日上午09时33分35秒 09:33:36.922 INFO VariantFiltration - ------------------------------------------------------------ 09:33:36.922 INFO VariantFiltration - ------------------------------------------------------------ 09:33:36.923 INFO VariantFiltration - HTSJDK Version: 2.19.0 09:33:36.923 INFO VariantFiltration - Picard Version: 2.19.0 09:33:36.923 INFO VariantFiltration - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:33:36.923 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:33:36.923 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:33:36.923 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:33:36.924 INFO VariantFiltration - Deflater: IntelDeflater 09:33:36.924 INFO VariantFiltration - Inflater: IntelInflater 09:33:36.924 INFO VariantFiltration - GCS max retries/reopens: 20 09:33:36.924 INFO VariantFiltration - Requester pays: disabled 09:33:36.924 INFO VariantFiltration - Initializing engine 09:33:37.565 INFO FeatureManager - Using codec VCFCodec to read file file:///home/GDYJY01/pipelineRNV/RNV_detection/scripts/../output/sampl1/tophat/accepted_hits.raw.vcf 09:33:37.613 INFO VariantFiltration - Done initializing engine 09:33:37.754 INFO ProgressMeter - Starting traversal 09:33:37.754 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute log4j:WARN No appenders could be found for logger (org.apache.commons.jexl2.JexlEngine). log4j:WARN Please initialize the log4j system properly. log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info. 09:33:38.963 INFO ProgressMeter - Chr8:1113198 0.0 5467 271315.1 09:33:38.963 INFO ProgressMeter - Traversal complete. Processed 5467 total variants in 0.0 minutes. 09:33:39.018 INFO VariantFiltration - Shutting down engine [2020年9月9日上午09时33分39秒] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 0.07 minutes. Runtime.totalMemory()=2380791808 INFO 2020-09-09 09:47:05 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I ../output/sampl2/tophat/accepted_hits.bam -O ../output/sampl2/tophat/accepted_hits.addsort.bam -SO coordinate -ID sampl2 -LB sampl2 -PL Illumina -PU run -SM sampl2 ********** 09:47:05.569 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Sep 09 09:47:05 CST 2020] AddOrReplaceReadGroups INPUT=../output/sampl2/tophat/accepted_hits.bam OUTPUT=../output/sampl2/tophat/accepted_hits.addsort.bam SORT_ORDER=coordinate RGID=sampl2 RGLB=sampl2 RGPL=Illumina RGPU=run RGSM=sampl2 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Sep 09 09:47:05 CST 2020] Executing as GDYJY01@localhost.localdomain on Linux 3.10.0-957.21.3.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_222-b10; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.23.3 INFO 2020-09-09 09:47:05 AddOrReplaceReadGroups Created read-group ID=sampl2 PL=Illumina LB=sampl2 SM=sampl2 INFO 2020-09-09 09:47:19 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 13s. Last read position: Chr4:19,914,809 [Wed Sep 09 09:47:28 CST 2020] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.38 minutes. Runtime.totalMemory()=2511339520 INFO 2020-09-09 09:47:29 MarkDuplicates ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** MarkDuplicates -SORTING_COLLECTION_SIZE_RATIO 0.5 -MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 80000 -I ../output/sampl2/tophat/accepted_hits.addsort.bam -O ../output/sampl2/tophat/accepted_hits.mkdup.addsort.bam -CREATE_INDEX true -VALIDATION_STRINGENCY SILENT -M ../output/sampl2/output4.metrics ********** 09:47:29.961 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Sep 09 09:47:29 CST 2020] MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=80000 SORTING_COLLECTION_SIZE_RATIO=0.5 INPUT=[../output/sampl2/tophat/accepted_hits.addsort.bam] OUTPUT=../output/sampl2/tophat/accepted_hits.mkdup.addsort.bam METRICS_FILE=../output/sampl2/output4.metrics VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Sep 09 09:47:29 CST 2020] Executing as GDYJY01@localhost.localdomain on Linux 3.10.0-957.21.3.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_222-b10; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.23.3 INFO 2020-09-09 09:47:30 MarkDuplicates Start of doWork freeMemory: 2037369392; totalMemory: 2058354688; maxMemory: 28631367680 INFO 2020-09-09 09:47:30 MarkDuplicates Reading input file and constructing read end information. INFO 2020-09-09 09:47:30 MarkDuplicates Will retain up to 207473678 data points before spilling to disk. INFO 2020-09-09 09:47:42 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 11s. Last read position: Chr4:19,914,809 INFO 2020-09-09 09:47:42 MarkDuplicates Tracking 1259 as yet unmatched pairs. 133 records in RAM. INFO 2020-09-09 09:47:50 MarkDuplicates Read 1748464 records. 0 pairs never matched. INFO 2020-09-09 09:47:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 2610633544; totalMemory: 4500488192; maxMemory: 28631367680 INFO 2020-09-09 09:47:55 MarkDuplicates Will retain up to 894730240 duplicate indices before spilling to disk. INFO 2020-09-09 09:47:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2020-09-09 09:48:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2020-09-09 09:48:00 MarkDuplicates Sorting list of duplicate records. INFO 2020-09-09 09:48:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 4532625232; totalMemory: 11738808320; maxMemory: 28631367680 INFO 2020-09-09 09:48:02 MarkDuplicates Marking 386390 records as duplicates. INFO 2020-09-09 09:48:02 MarkDuplicates Found 37769 optical duplicate clusters. INFO 2020-09-09 09:48:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2020-09-09 09:48:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2020-09-09 09:48:34 MarkDuplicates Duplicate Index cleanup. INFO 2020-09-09 09:48:34 MarkDuplicates Getting Memory Stats. INFO 2020-09-09 09:48:34 MarkDuplicates Before output close freeMemory: 13792589608; totalMemory: 13883146240; maxMemory: 28631367680 INFO 2020-09-09 09:48:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2020-09-09 09:48:34 MarkDuplicates After output close freeMemory: 13625866024; totalMemory: 13716422656; maxMemory: 28631367680 [Wed Sep 09 09:48:34 CST 2020] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1.08 minutes. Runtime.totalMemory()=13716422656 Using GATK jar /home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-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 -jar /home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar HaplotypeCaller --native-pair-hmm-threads 50 -R ../input/ref.fa -I ../output/sampl2/tophat/accepted_hits.mkdup.addsort.bam -ERC GVCF -O ../output/sampl2/tophat/accepted_hits.g.vcf --genotyping-mode DISCOVERY --pcr-indel-model CONSERVATIVE --sample-ploidy 2 --min-base-quality-score 10 --kmer-size 10 --kmer-size 25 09:48:40.494 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Sep 09, 2020 9:48:42 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:48:42.314 INFO HaplotypeCaller - ------------------------------------------------------------ 09:48:42.315 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.2.0 09:48:42.315 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:48:42.315 INFO HaplotypeCaller - Executing as GDYJY01@localhost.localdomain on Linux v3.10.0-957.21.3.el7.x86_64 amd64 09:48:42.316 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_222-b10 09:48:42.316 INFO HaplotypeCaller - Start Date/Time: 2020年9月9日上午09时48分40秒 09:48:42.316 INFO HaplotypeCaller - ------------------------------------------------------------ 09:48:42.316 INFO HaplotypeCaller - ------------------------------------------------------------ 09:48:42.317 INFO HaplotypeCaller - HTSJDK Version: 2.19.0 09:48:42.317 INFO HaplotypeCaller - Picard Version: 2.19.0 09:48:42.318 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:48:42.318 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:48:42.318 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:48:42.318 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:48:42.318 INFO HaplotypeCaller - Deflater: IntelDeflater 09:48:42.318 INFO HaplotypeCaller - Inflater: IntelInflater 09:48:42.319 INFO HaplotypeCaller - GCS max retries/reopens: 20 09:48:42.319 INFO HaplotypeCaller - Requester pays: disabled 09:48:42.319 INFO HaplotypeCaller - Initializing engine 09:48:42.968 INFO HaplotypeCaller - Done initializing engine 09:48:42.971 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 09:48:42.980 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output 09:48:42.980 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 09:48:43.000 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 09:48:43.003 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 09:48:43.059 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 09:48:43.059 INFO IntelPairHmm - Available threads: 50 09:48:43.059 INFO IntelPairHmm - Requested threads: 50 09:48:43.060 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 09:48:43.126 INFO ProgressMeter - Starting traversal 09:48:43.126 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 09:48:53.131 INFO ProgressMeter - Chr1:2139071 0.2 7450 44677.7 09:49:03.131 INFO ProgressMeter - Chr1:4872873 0.3 17000 50987.3 09:49:13.135 INFO ProgressMeter - Chr1:8873717 0.5 30750 61481.6 09:49:23.137 INFO ProgressMeter - Chr1:13337540 0.7 45970 68937.8 09:49:33.136 INFO ProgressMeter - Chr1:18098268 0.8 62150 74565.1 09:49:43.137 INFO ProgressMeter - Chr1:23452129 1.0 80400 80385.3 09:49:53.139 INFO ProgressMeter - Chr1:26846128 1.2 92050 78885.3 09:50:03.147 INFO ProgressMeter - Chr1:30428664 1.3 104460 78325.4 09:50:13.147 INFO ProgressMeter - Chr1:34269109 1.5 117700 78448.4 09:50:23.149 INFO ProgressMeter - Chr1:38798306 1.7 133300 79961.6 09:50:33.158 INFO ProgressMeter - Chr1:42756272 1.8 146960 80136.7 09:50:36.727 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:50:36.727 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:50:43.159 INFO ProgressMeter - Chr10:6344947 2.0 170260 85106.6 09:50:53.163 INFO ProgressMeter - Chr10:13261259 2.2 193650 89351.5 09:51:03.163 INFO ProgressMeter - Chr10:19508971 2.3 214950 92097.1 09:51:13.165 INFO ProgressMeter - Chr11:453077 2.5 229300 91696.8 09:51:23.164 INFO ProgressMeter - Chr11:5062202 2.7 245030 91864.4 09:51:33.167 INFO ProgressMeter - Chr11:10486047 2.8 263470 92967.0 09:51:43.168 INFO ProgressMeter - Chr11:19222261 3.0 292910 97614.4 09:51:53.169 INFO ProgressMeter - Chr11:25855318 3.2 315610 99643.8 09:52:02.174 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:52:02.175 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:52:03.170 INFO ProgressMeter - Chr12:1609178 3.3 331990 99575.1 09:52:13.195 INFO ProgressMeter - Chr12:9364632 3.5 358480 102389.2 09:52:23.201 INFO ProgressMeter - Chr12:15286833 3.7 378470 103183.9 09:52:33.202 INFO ProgressMeter - Chr12:22682628 3.8 403450 105213.5 09:52:43.214 INFO ProgressMeter - Chr2:443772 4.0 421660 105379.4 09:52:53.213 INFO ProgressMeter - Chr2:4700785 4.2 436410 104702.0 09:53:03.215 INFO ProgressMeter - Chr2:10707370 4.3 456910 105404.7 09:53:13.215 INFO ProgressMeter - Chr2:18085339 4.5 481950 107064.7 09:53:23.216 INFO ProgressMeter - Chr2:24274473 4.7 503150 107783.2 09:53:33.216 INFO ProgressMeter - Chr2:29767529 4.8 521960 107958.2 09:53:43.216 INFO ProgressMeter - Chr2:35156623 5.0 540530 108073.6 09:53:53.225 INFO ProgressMeter - Chr3:4002263 5.2 557140 107799.5 09:54:03.224 INFO ProgressMeter - Chr3:8698637 5.3 573410 107481.5 09:54:13.225 INFO ProgressMeter - Chr3:13791504 5.5 590960 107415.0 09:54:18.985 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:54:23.242 INFO ProgressMeter - Chr3:20797151 5.7 614780 108453.6 09:54:33.245 INFO ProgressMeter - Chr3:26742865 5.8 634970 108815.0 09:54:43.246 INFO ProgressMeter - Chr3:32534985 6.0 654930 109118.9 09:54:53.246 INFO ProgressMeter - Chr4:2156007 6.2 675750 109545.6 09:55:03.246 INFO ProgressMeter - Chr4:10178390 6.3 702810 110935.0 09:55:10.392 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:55:13.248 INFO ProgressMeter - Chr4:18757888 6.5 731860 112558.6 09:55:23.253 INFO ProgressMeter - Chr4:23895819 6.7 749490 112387.8 09:55:33.264 INFO ProgressMeter - Chr4:29113589 6.8 767410 112266.1 09:55:43.266 INFO ProgressMeter - Chr4:34679914 7.0 786590 112332.8 09:55:53.266 INFO ProgressMeter - Chr5:4710190 7.2 805570 112368.8 09:56:03.266 INFO ProgressMeter - Chr5:14224904 7.3 837660 114190.0 09:56:13.269 INFO ProgressMeter - Chr5:21067666 7.5 860940 114755.8 09:56:23.273 INFO ProgressMeter - Chr5:27292103 7.7 882230 115036.7 09:56:33.281 INFO ProgressMeter - Chr6:2164010 7.8 898900 114715.4 09:56:40.120 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:56:43.281 INFO ProgressMeter - Chr6:8090825 8.0 919310 114876.7 09:56:53.281 INFO ProgressMeter - Chr6:13550524 8.2 938150 114839.2 09:57:02.027 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:57:02.028 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 09:57:03.282 INFO ProgressMeter - Chr6:19959432 8.3 960310 115201.5 09:57:13.282 INFO ProgressMeter - Chr6:25891534 8.5 980550 115323.5 09:57:23.286 INFO ProgressMeter - Chr7:430245 8.7 1000450 115401.3 09:57:33.288 INFO ProgressMeter - Chr7:6901494 8.8 1022630 115734.1 09:57:43.290 INFO ProgressMeter - Chr7:14533117 9.0 1048410 116454.6 09:57:54.533 INFO ProgressMeter - Chr7:20727314 9.2 1069480 116372.8 09:58:04.534 INFO ProgressMeter - Chr7:26345754 9.4 1088930 116378.5 09:58:14.535 INFO ProgressMeter - Chr8:2292733 9.5 1108360 116381.8 09:58:24.537 INFO ProgressMeter - Chr8:9603443 9.7 1133210 116944.1 09:58:34.550 INFO ProgressMeter - Chr8:18093084 9.9 1161870 117872.0 09:58:44.549 INFO ProgressMeter - Chr8:24719314 10.0 1184410 118160.8 09:58:54.552 INFO ProgressMeter - Chr9:3206776 10.2 1208030 118545.5 09:59:04.624 INFO ProgressMeter - Chr9:10847031 10.4 1233870 119119.0 09:59:14.675 INFO ProgressMeter - Chr9:17905214 10.5 1257900 119506.2 09:59:24.677 INFO ProgressMeter - Chr9:22889493 10.7 1275030 119245.3 09:59:25.821 INFO HaplotypeCaller - 886000 read(s) filtered by: ((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter) AND WellformedReadFilter) 386390 read(s) filtered by: (((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter) 386390 read(s) filtered by: ((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) 386390 read(s) filtered by: (((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) 386390 read(s) filtered by: ((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) 386390 read(s) filtered by: NotDuplicateReadFilter 499610 read(s) filtered by: WellformedReadFilter 09:59:25.821 INFO ProgressMeter - ChrUn:630901 10.7 1279568 119456.5 09:59:25.821 INFO ProgressMeter - Traversal complete. Processed 1279568 total regions in 10.7 minutes. 09:59:25.839 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.079911916 09:59:25.839 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 15.559073341000001 09:59:25.839 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 9.27 sec 09:59:25.839 INFO HaplotypeCaller - Shutting down engine [2020年9月9日上午09时59分25秒] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 10.76 minutes. Runtime.totalMemory()=2423783424 Using GATK jar /home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-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 -jar /home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar GenotypeGVCFs -R ../input/ref.fa -O ../output/sampl2/tophat/accepted_hits.raw.vcf -V ../output/sampl2/tophat/accepted_hits.g.vcf --sample-ploidy 2 09:59:29.930 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Sep 09, 2020 9:59:31 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:59:31.725 INFO GenotypeGVCFs - ------------------------------------------------------------ 09:59:31.726 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.1.2.0 09:59:31.726 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:59:31.727 INFO GenotypeGVCFs - Executing as GDYJY01@localhost.localdomain on Linux v3.10.0-957.21.3.el7.x86_64 amd64 09:59:31.727 INFO GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_222-b10 09:59:31.727 INFO GenotypeGVCFs - Start Date/Time: 2020年9月9日上午09时59分29秒 09:59:31.727 INFO GenotypeGVCFs - ------------------------------------------------------------ 09:59:31.727 INFO GenotypeGVCFs - ------------------------------------------------------------ 09:59:31.728 INFO GenotypeGVCFs - HTSJDK Version: 2.19.0 09:59:31.729 INFO GenotypeGVCFs - Picard Version: 2.19.0 09:59:31.729 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:59:31.729 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:59:31.729 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:59:31.729 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:59:31.729 INFO GenotypeGVCFs - Deflater: IntelDeflater 09:59:31.729 INFO GenotypeGVCFs - Inflater: IntelInflater 09:59:31.730 INFO GenotypeGVCFs - GCS max retries/reopens: 20 09:59:31.730 INFO GenotypeGVCFs - Requester pays: disabled 09:59:31.730 INFO GenotypeGVCFs - Initializing engine 09:59:32.360 INFO FeatureManager - Using codec VCFCodec to read file file:///home/GDYJY01/pipelineRNV/RNV_detection/scripts/../output/sampl2/tophat/accepted_hits.g.vcf 09:59:32.430 INFO GenotypeGVCFs - Done initializing engine 09:59:32.504 INFO ProgressMeter - Starting traversal 09:59:32.504 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 09:59:32.561 WARN ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location Chr1:7359 the annotation MLEAC=[1, 0] was not a numerical value and was ignored 09:59:42.515 INFO ProgressMeter - Chr3:30437173 0.2 680000 4075924.1 09:59:50.058 INFO ProgressMeter - ChrSy:558991 0.3 1288418 4403844.1 09:59:50.059 INFO ProgressMeter - Traversal complete. Processed 1288418 total variants in 0.3 minutes. 09:59:50.138 INFO GenotypeGVCFs - Shutting down engine [2020年9月9日上午09时59分50秒] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.34 minutes. Runtime.totalMemory()=3595042816 Using GATK jar /home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-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 -jar /home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar VariantFiltration -R ../input/ref.fa -O ../output/sampl2/tophat/accepted_hits.filter.vcf -V ../output/sampl2/tophat/accepted_hits.raw.vcf -window 35 -cluster 3 --filter-name FilterFS --filter-expression FS > 30.0 --filter-name FilterQD --filter-expression QD < 2.0 09:59:54.189 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/GDYJY01/pipelineRNV/RNV_detection/programs/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Sep 09, 2020 9:59:55 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:59:56.008 INFO VariantFiltration - ------------------------------------------------------------ 09:59:56.009 INFO VariantFiltration - The Genome Analysis Toolkit (GATK) v4.1.2.0 09:59:56.009 INFO VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:59:56.010 INFO VariantFiltration - Executing as GDYJY01@localhost.localdomain on Linux v3.10.0-957.21.3.el7.x86_64 amd64 09:59:56.010 INFO VariantFiltration - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_222-b10 09:59:56.010 INFO VariantFiltration - Start Date/Time: 2020年9月9日上午09时59分54秒 09:59:56.010 INFO VariantFiltration - ------------------------------------------------------------ 09:59:56.010 INFO VariantFiltration - ------------------------------------------------------------ 09:59:56.011 INFO VariantFiltration - HTSJDK Version: 2.19.0 09:59:56.012 INFO VariantFiltration - Picard Version: 2.19.0 09:59:56.012 INFO VariantFiltration - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:59:56.012 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:59:56.012 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:59:56.012 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:59:56.012 INFO VariantFiltration - Deflater: IntelDeflater 09:59:56.013 INFO VariantFiltration - Inflater: IntelInflater 09:59:56.013 INFO VariantFiltration - GCS max retries/reopens: 20 09:59:56.013 INFO VariantFiltration - Requester pays: disabled 09:59:56.013 INFO VariantFiltration - Initializing engine 09:59:56.712 INFO FeatureManager - Using codec VCFCodec to read file file:///home/GDYJY01/pipelineRNV/RNV_detection/scripts/../output/sampl2/tophat/accepted_hits.raw.vcf 09:59:56.769 INFO VariantFiltration - Done initializing engine 09:59:56.888 INFO ProgressMeter - Starting traversal 09:59:56.888 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 09:59:58.651 INFO ProgressMeter - Chr9:20006204 0.0 6039 205524.7 09:59:58.651 INFO ProgressMeter - Traversal complete. Processed 6039 total variants in 0.0 minutes. 09:59:58.714 INFO VariantFiltration - Shutting down engine [2020年9月9日上午09时59分58秒] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 0.08 minutes. Runtime.totalMemory()=2051014656