Skip to content

Instantly share code, notes, and snippets.

@cboursnell

cboursnell/gridss error

Created August 7, 2017 14:25
Show Gist options
  • Save cboursnell/7c8276dbc20eaacd360287a56eda0832 to your computer and use it in GitHub Desktop.
Save cboursnell/7c8276dbc20eaacd360287a56eda0832 to your computer and use it in GitHub Desktop.
Download ZIP
Raw
gridss error
java -ea -Xmx31g -Dsamjdk.create_index=true -Dsamjdk.use_async_io_read_samtools=true -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=true -Dsamjdk.compression_level=1 -cp gridss-1.4.1-jar-with-dependencies.jar gridss.CallVariants TMP_DIR=. WORKING_DIR=. REFERENCE_SEQUENCE=genome.fa INPUT=normal.sort.bam INPUT=tumour.sort.bam OUTPUT=test04 ASSEMBLY=assembly_output | tee -a gridss.log
[Mon Aug 07 15:11:00 BST 2017] gridss.CallVariants OUTPUT=test04 ASSEMBLY=assembly_output INPUT=[normal.sort.bam, tumour.sort.bam] WORKING_DIR=. TMP_DIR=[.] REFERENCE_SEQUENCE=genome.fa READ_PAIR_CONCORDANT_PERCENT=0.995 WORKER_THREADS=8 IGNORE_DUPLICATES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=1 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Mon Aug 07 15:11:00 BST 2017] Executing as boursn01@nm16bs014739 on Linux 4.4.0-83-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11; Picard version: 1.4.1
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
INFO 2017-08-07 15:11:00 GridssConfiguration maxCoverage=10000
INFO 2017-08-07 15:11:00 GridssConfiguration minMapq=10
INFO 2017-08-07 15:11:00 GridssConfiguration fallbackMapq=20
INFO 2017-08-07 15:11:00 GridssConfiguration multimapping=false
INFO 2017-08-07 15:11:00 GridssConfiguration minAnchorShannonEntropy=0.5
INFO 2017-08-07 15:11:00 GridssConfiguration dovetailMargin=4
INFO 2017-08-07 15:11:00 GridssConfiguration softclip.minAverageQual=5.0
INFO 2017-08-07 15:11:00 GridssConfiguration softclip.minLength=4
INFO 2017-08-07 15:11:00 GridssConfiguration softclip.minAnchorIdentity=0.95
INFO 2017-08-07 15:11:00 GridssConfiguration multimappingUniqueAssemblyAllocation=true
INFO 2017-08-07 15:11:00 GridssConfiguration multimappingUniqueVariantAllocation=true
INFO 2017-08-07 15:11:00 GridssConfiguration useReadGroupSampleNameCategoryLabel=true
INFO 2017-08-07 15:11:00 GridssConfiguration chunkSize=10000000
INFO 2017-08-07 15:11:00 GridssConfiguration chunkSequenceChangePenalty=250000
INFO 2017-08-07 15:11:00 GridssConfiguration hashEvidenceID=true
INFO 2017-08-07 15:11:00 GridssConfiguration adapter=AGATCGGAAGAG
INFO 2017-08-07 15:11:00 GridssConfiguration adapter=ATGGAATTCTCG
INFO 2017-08-07 15:11:00 GridssConfiguration adapter=CTGTCTCTTATA
INFO 2017-08-07 15:11:00 GridssConfiguration scoring.model=FastEmpiricalReferenceLikelihood
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.k=25
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.minReads=3
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.includePairAnchors=true
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.pairAnchorMismatchIgnoreEndBases=5
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.excludeNonSupportingEvidence=false
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.writeFiltered=true
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.anchorLength=100
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.removeMisassembledPartialContigsDuringAssembly=true
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.maxExpectedBreakendLengthMultiple=1.5
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.errorCorrection.collapseBubblesOnly=true
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.errorCorrection.maxBaseMismatchForCollapse=2
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.errorCorrection.maxPathCollapseLengthMultiple=2.0
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.downsample.acceptDensityPortion=0.5
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.downsample.targetEvidenceDensity=5.0
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.downsample.minimumDensityWindowSize=1000
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.positional.maxPathLengthMultiple=1.1
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.positional.retainWidthMultiple=5.0
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.positional.flushWidthMultiple=10.0
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.positional.maximumNodeDensity=5.0
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.positional.trimSelfIntersectingReads=true
INFO 2017-08-07 15:11:00 GridssConfiguration assembly.positional.forceFullMemoizationRecalculationAt=0.8
INFO 2017-08-07 15:11:00 GridssConfiguration variantcalling.minReads=2
INFO 2017-08-07 15:11:00 GridssConfiguration variantcalling.minScore=50.0
INFO 2017-08-07 15:11:00 GridssConfiguration variantcalling.minSize=32
INFO 2017-08-07 15:11:00 GridssConfiguration variantcalling.lowQuality=500.0
INFO 2017-08-07 15:11:00 GridssConfiguration variantcalling.callOnlyAssemblies=false
INFO 2017-08-07 15:11:00 GridssConfiguration variantcalling.breakendMargin=10
INFO 2017-08-07 15:11:00 GridssConfiguration variantcalling.writeFiltered=false
INFO 2017-08-07 15:11:00 GridssConfiguration variantcalling.simplecalls=false
INFO 2017-08-07 15:11:00 GridssConfiguration variantcalling.maxBreakendHomologyLength=300
INFO 2017-08-07 15:11:00 GridssConfiguration variantcalling.breakendHomologyAlignmentMargin=10
INFO 2017-08-07 15:11:00 GridssConfiguration terminateOnFirstError=true
INFO 2017-08-07 15:11:00 GridssConfiguration visualisation.directory=visualisation
INFO 2017-08-07 15:11:00 GridssConfiguration visualisation.buffers=false
INFO 2017-08-07 15:11:00 GridssConfiguration visualisation.bufferTrackingItervalInSeconds=60
INFO 2017-08-07 15:11:00 GridssConfiguration visualisation.timeouts=false
INFO 2017-08-07 15:11:00 GridssConfiguration visualisation.evidenceAllocation=false
INFO 2017-08-07 15:11:00 GridssConfiguration visualisation.assemblyProgress=false
INFO 2017-08-07 15:11:00 GridssConfiguration visualisation.assemblyGraph=false
INFO 2017-08-07 15:11:00 GridssConfiguration visualisation.assemblyGraphFullSize=false
INFO 2017-08-07 15:11:00 GridssConfiguration visualisation.assemblyContigMemoization=false
INFO 2017-08-07 15:11:00 GridssConfiguration visualisation.assemblyTelemetry=false
INFO 2017-08-07 15:11:00 MultipleSamFileCommandLineProgram Loading aligner
INFO 2017-08-07 15:11:00 AlignerFactory sswjni library loading successful.
INFO 2017-08-07 15:11:00 MultipleSamFileCommandLineProgram Using 8 worker threads
INFO 2017-08-07 15:11:00 CallVariants Extracting evidence.
INFO 2017-08-07 15:11:00 SAMEvidenceSource Calculating metrics for tumour.sort.bam
INFO 2017-08-07 15:11:00 SAMEvidenceSource Calculating metrics for normal.sort.bam
[Mon Aug 07 15:11:00 BST 2017] gridss.analysis.CollectGridssMetrics GRIDSS_PROGRAM=[CollectCigarMetrics, CollectMapqMetrics, CollectTagMetrics, CollectIdsvMetrics, ReportThresholdCoverage] THRESHOLD_COVERAGE=10000 INPUT=tumour.sort.bam OUTPUT=./tumour.sort.bam.gridss.working/tumour.sort.bam FILE_EXTENSION=null PROGRAM=[CollectAlignmentSummaryMetrics, QualityScoreDistribution, CollectInsertSizeMetrics] TMP_DIR=[.] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=1 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false REFERENCE_SEQUENCE=genome.fa GA4GH_CLIENT_SECRETS=client_secrets.json ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INCLUDE_UNPAIRED=false
[Mon Aug 07 15:11:00 BST 2017] Executing as boursn01@nm16bs014739 on Linux 4.4.0-83-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11; Picard version: 1.4.1
[Mon Aug 07 15:11:00 BST 2017] gridss.analysis.CollectGridssMetrics GRIDSS_PROGRAM=[CollectCigarMetrics, CollectMapqMetrics, CollectTagMetrics, CollectIdsvMetrics, ReportThresholdCoverage] THRESHOLD_COVERAGE=10000 INPUT=normal.sort.bam OUTPUT=./normal.sort.bam.gridss.working/normal.sort.bam FILE_EXTENSION=null PROGRAM=[CollectAlignmentSummaryMetrics, QualityScoreDistribution, CollectInsertSizeMetrics] TMP_DIR=[.] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=1 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false REFERENCE_SEQUENCE=genome.fa GA4GH_CLIENT_SECRETS=client_secrets.json ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INCLUDE_UNPAIRED=false
[Mon Aug 07 15:11:00 BST 2017] Executing as boursn01@nm16bs014739 on Linux 4.4.0-83-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11; Picard version: 1.4.1
INFO 2017-08-07 15:11:15 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 13s. Last read position: chr1:3,960,420
INFO 2017-08-07 15:11:15 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 13s. Last read position: chr1:1,906,560
INFO 2017-08-07 15:12:41 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 85s. Last read position: chrUn_KI270748v1:73,316
INFO 2017-08-07 15:12:41 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 85s. Last read position: JTFH01000922.1:29
INFO 2017-08-07 15:12:41 RExecutor Executing R script via command: Rscript ./script4236729025556424790.R ./tumour.sort.bam.gridss.working/tumour.sort.bam.quality_distribution_metrics ./tumour.sort.bam.gridss.working/tumour.sort.bam.quality_distribution.pdf tumour.sort.bam
INFO 2017-08-07 15:12:41 RExecutor Executing R script via command: Rscript ./script3368070025129654434.R ./normal.sort.bam.gridss.working/normal.sort.bam.quality_distribution_metrics ./normal.sort.bam.gridss.working/normal.sort.bam.quality_distribution.pdf normal.sort.bam
INFO 2017-08-07 15:12:42 ProcessExecutor null device
INFO 2017-08-07 15:12:42 ProcessExecutor 1
INFO 2017-08-07 15:12:42 ProcessExecutor null device
INFO 2017-08-07 15:12:42 ProcessExecutor 1
INFO 2017-08-07 15:13:06 RExecutor Executing R script via command: Rscript ./script5771354580802315869.R ./tumour.sort.bam.gridss.working/tumour.sort.bam.insert_size_metrics ./tumour.sort.bam.gridss.working/tumour.sort.bam.insert_size_histogram.pdf tumour.sort.bam
INFO 2017-08-07 15:13:07 ProcessExecutor null device
INFO 2017-08-07 15:13:07 ProcessExecutor 1
[Mon Aug 07 15:13:07 BST 2017] gridss.analysis.CollectGridssMetrics done. Elapsed time: 2.11 minutes.
Runtime.totalMemory()=5176819712
INFO 2017-08-07 15:13:07 SAMEvidenceSource Extracting SV reads from tumour.sort.bam
[Mon Aug 07 15:13:07 BST 2017] gridss.ExtractSVReads METRICS_OUTPUT=./tumour.sort.bam.gridss.working/tumour.sort.bam.sv_metrics MIN_CLIP_LENGTH=4 READ_PAIR_CONCORDANCE_METHOD=PERCENTAGE FIXED_READ_PAIR_CONCORDANCE_MIN_FRAGMENT_SIZE=0 FIXED_READ_PAIR_CONCORDANCE_MAX_FRAGMENT_SIZE=0 READ_PAIR_CONCORDANT_PERCENT=0.995 INSERT_SIZE_METRICS=./tumour.sort.bam.gridss.working/tumour.sort.bam.insert_size_metrics UNMAPPED_READS=false INPUT=tumour.sort.bam OUTPUT=./tumour.sort.bam.gridss.working/gridss.tmp.extracted.tumour.sort.bam.sv.bam TMP_DIR=[.] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=1 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false REFERENCE_SEQUENCE=genome.fa GA4GH_CLIENT_SECRETS=client_secrets.json MIN_INDEL_SIZE=1 CLIPPED=true INDELS=true SPLIT=true SINGLE_MAPPED_PAIRED=true DISCORDANT_READ_PAIRS=true ASSUME_SORTED=true STOP_AFTER=0 IGNORE_DUPLICATES=true
[Mon Aug 07 15:13:07 BST 2017] Executing as boursn01@nm16bs014739 on Linux 4.4.0-83-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11; Picard version: 1.4.1
WARNING 2017-08-07 15:13:07 ByReadNameSinglePassSamProgram File reports sort order 'coordinate', assuming it's queryname sorted anyway.
INFO 2017-08-07 15:13:07 ExtractSVReads Not considering multiple read alignments as the input file is not queryname sorted.
INFO 2017-08-07 15:13:09 ByReadNameSinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,906,560
INFO 2017-08-07 15:13:10 RExecutor Executing R script via command: Rscript ./script2618179807651180968.R ./normal.sort.bam.gridss.working/normal.sort.bam.insert_size_metrics ./normal.sort.bam.gridss.working/normal.sort.bam.insert_size_histogram.pdf normal.sort.bam
INFO 2017-08-07 15:13:10 ProcessExecutor null device
INFO 2017-08-07 15:13:10 ProcessExecutor 1
[Mon Aug 07 15:13:10 BST 2017] gridss.analysis.CollectGridssMetrics done. Elapsed time: 2.17 minutes.
Runtime.totalMemory()=5335678976
INFO 2017-08-07 15:13:10 SAMEvidenceSource Extracting SV reads from normal.sort.bam
[Mon Aug 07 15:13:10 BST 2017] gridss.ExtractSVReads METRICS_OUTPUT=./normal.sort.bam.gridss.working/normal.sort.bam.sv_metrics MIN_CLIP_LENGTH=4 READ_PAIR_CONCORDANCE_METHOD=PERCENTAGE FIXED_READ_PAIR_CONCORDANCE_MIN_FRAGMENT_SIZE=0 FIXED_READ_PAIR_CONCORDANCE_MAX_FRAGMENT_SIZE=0 READ_PAIR_CONCORDANT_PERCENT=0.995 INSERT_SIZE_METRICS=./normal.sort.bam.gridss.working/normal.sort.bam.insert_size_metrics UNMAPPED_READS=false INPUT=normal.sort.bam OUTPUT=./normal.sort.bam.gridss.working/gridss.tmp.extracted.normal.sort.bam.sv.bam TMP_DIR=[.] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=1 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false REFERENCE_SEQUENCE=genome.fa GA4GH_CLIENT_SECRETS=client_secrets.json MIN_INDEL_SIZE=1 CLIPPED=true INDELS=true SPLIT=true SINGLE_MAPPED_PAIRED=true DISCORDANT_READ_PAIRS=true ASSUME_SORTED=true STOP_AFTER=0 IGNORE_DUPLICATES=true
[Mon Aug 07 15:13:10 BST 2017] Executing as boursn01@nm16bs014739 on Linux 4.4.0-83-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11; Picard version: 1.4.1
WARNING 2017-08-07 15:13:11 ByReadNameSinglePassSamProgram File reports sort order 'coordinate', assuming it's queryname sorted anyway.
INFO 2017-08-07 15:13:11 ExtractSVReads Not considering multiple read alignments as the input file is not queryname sorted.
INFO 2017-08-07 15:13:11 ByReadNameSinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: JTFH01000922.1:29
INFO 2017-08-07 15:13:11 ExtractSVReads Extracted 265895 reads from tumour.sort.bam
[Mon Aug 07 15:13:11 BST 2017] gridss.ExtractSVReads done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=5604114432
INFO 2017-08-07 15:13:11 SAMFileUtil Sorting ./tumour.sort.bam.gridss.working/gridss.tmp.extracted.tumour.sort.bam.sv.bam
INFO 2017-08-07 15:13:13 ByReadNameSinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:3,960,420
INFO 2017-08-07 15:13:16 ByReadNameSinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chrUn_KI270748v1:73,316
INFO 2017-08-07 15:13:16 ExtractSVReads Extracted 201352 reads from normal.sort.bam
[Mon Aug 07 15:13:16 BST 2017] gridss.ExtractSVReads done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=6487015424
INFO 2017-08-07 15:13:16 SAMFileUtil Sorting ./normal.sort.bam.gridss.working/gridss.tmp.extracted.normal.sort.bam.sv.bam
INFO 2017-08-07 15:13:16 SAMEvidenceSource Computing SAM tags for ./tumour.sort.bam.gridss.working/tumour.sort.bam.sv.bam
[Mon Aug 07 15:13:16 BST 2017] gridss.ComputeSamTags INPUT=./tumour.sort.bam.gridss.working/gridss.tmp.querysorted.tumour.sort.bam.sv.bam OUTPUT=./tumour.sort.bam.gridss.working/gridss.tmp.tagged.tumour.sort.bam.sv.bam TMP_DIR=[.] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=1 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false REFERENCE_SEQUENCE=genome.fa GA4GH_CLIENT_SECRETS=client_secrets.json ASSUME_SORTED=false SOFTEN_HARD_CLIPS=true FIX_MATE_INFORMATION=true RECALCULATE_SA_SUPPLEMENTARY=true TAGS=[R2, mm, Q2, MQ, MC, SA, NM] IGNORE_DUPLICATES=true
[Mon Aug 07 15:13:16 BST 2017] Executing as boursn01@nm16bs014739 on Linux 4.4.0-83-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11; Picard version: 1.4.1
INFO 2017-08-07 15:13:19 SAMEvidenceSource Computing SAM tags for ./normal.sort.bam.gridss.working/normal.sort.bam.sv.bam
[Mon Aug 07 15:13:19 BST 2017] gridss.ComputeSamTags INPUT=./normal.sort.bam.gridss.working/gridss.tmp.querysorted.normal.sort.bam.sv.bam OUTPUT=./normal.sort.bam.gridss.working/gridss.tmp.tagged.normal.sort.bam.sv.bam TMP_DIR=[.] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=1 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false REFERENCE_SEQUENCE=genome.fa GA4GH_CLIENT_SECRETS=client_secrets.json ASSUME_SORTED=false SOFTEN_HARD_CLIPS=true FIX_MATE_INFORMATION=true RECALCULATE_SA_SUPPLEMENTARY=true TAGS=[R2, mm, Q2, MQ, MC, SA, NM] IGNORE_DUPLICATES=true
[Mon Aug 07 15:13:19 BST 2017] Executing as boursn01@nm16bs014739 on Linux 4.4.0-83-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11; Picard version: 1.4.1
[Mon Aug 07 15:13:21 BST 2017] gridss.ComputeSamTags done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=6487015424
INFO 2017-08-07 15:13:21 SAMEvidenceSource Identifying split reads for tumour.sort.bam
[Mon Aug 07 15:13:21 BST 2017] gridss.SoftClipsToSplitReads INPUT=./tumour.sort.bam.gridss.working/gridss.tmp.tagged.tumour.sort.bam.sv.bam OUTPUT=./tumour.sort.bam.gridss.working/gridss.tmp.splitreads.tumour.sort.bam.sv.bam WORKER_THREADS=8 TMP_DIR=[.] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=1 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false REFERENCE_SEQUENCE=genome.fa GA4GH_CLIENT_SECRETS=client_secrets.json MIN_CLIP_LENGTH=15 MIN_CLIP_QUAL=5.0 PROCESS_SECONDARY_ALIGNMENTS=false ALIGNER_COMMAND_LINE=[bwa, mem, -t, %3$d, %2$s, %1$s] IGNORE_DUPLICATES=true
[Mon Aug 07 15:13:21 BST 2017] Executing as boursn01@nm16bs014739 on Linux 4.4.0-83-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11; Picard version: 1.4.1
INFO 2017-08-07 15:13:22 ExternalProcessFastqAligner Invoking external aligner
INFO 2017-08-07 15:13:22 ExternalProcessFastqAligner bwa mem -t 8 genome.fa ./tumour.sort.bam.gridss.working/tumour.sort.bam.realign.0.fq
[Mon Aug 07 15:13:23 BST 2017] gridss.ComputeSamTags done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=6502219776
INFO 2017-08-07 15:13:23 SAMEvidenceSource Identifying split reads for normal.sort.bam
[Mon Aug 07 15:13:23 BST 2017] gridss.SoftClipsToSplitReads INPUT=./normal.sort.bam.gridss.working/gridss.tmp.tagged.normal.sort.bam.sv.bam OUTPUT=./normal.sort.bam.gridss.working/gridss.tmp.splitreads.normal.sort.bam.sv.bam WORKER_THREADS=8 TMP_DIR=[.] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=1 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false REFERENCE_SEQUENCE=genome.fa GA4GH_CLIENT_SECRETS=client_secrets.json MIN_CLIP_LENGTH=15 MIN_CLIP_QUAL=5.0 PROCESS_SECONDARY_ALIGNMENTS=false ALIGNER_COMMAND_LINE=[bwa, mem, -t, %3$d, %2$s, %1$s] IGNORE_DUPLICATES=true
[Mon Aug 07 15:13:23 BST 2017] Executing as boursn01@nm16bs014739 on Linux 4.4.0-83-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11; Picard version: 1.4.1
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 139830 sequences (7493418 bp)...
INFO 2017-08-07 15:15:15 ExternalProcessFastqAligner Invoking external aligner
INFO 2017-08-07 15:15:15 ExternalProcessFastqAligner bwa mem -t 8 genome.fa ./normal.sort.bam.gridss.working/normal.sort.bam.realign.0.fq
[Mon Aug 07 15:15:15 BST 2017] gridss.SoftClipsToSplitReads done. Elapsed time: 1.91 minutes.
Runtime.totalMemory()=6502219776
ERROR 2017-08-07 15:15:15 CallVariants Fatal exception thrown by worker thread.
htsjdk.samtools.SAMFormatException: Error parsing SAM header. @SQ line missing LN tag. Line:
@SQ SN:JTF; ; Line number 2489
at htsjdk.samtools.SAMTextHeaderCodec.reportErrorParsingLine(SAMTextHeaderCodec.java:246)
at htsjdk.samtools.SAMTextHeaderCodec.access$200(SAMTextHeaderCodec.java:43)
at htsjdk.samtools.SAMTextHeaderCodec$ParsedHeaderLine.requireTag(SAMTextHeaderCodec.java:327)
at htsjdk.samtools.SAMTextHeaderCodec.parseSQLine(SAMTextHeaderCodec.java:215)
at htsjdk.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:111)
at htsjdk.samtools.SAMTextReader.readHeader(SAMTextReader.java:200)
at htsjdk.samtools.SAMTextReader.<init>(SAMTextReader.java:63)
at htsjdk.samtools.SAMTextReader.<init>(SAMTextReader.java:73)
at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:404)
at au.edu.wehi.idsv.alignment.ExternalProcessFastqAligner.align(ExternalProcessFastqAligner.java:48)
at au.edu.wehi.idsv.alignment.SequentialExecutionFastqAligner.align(SequentialExecutionFastqAligner.java:19)
at au.edu.wehi.idsv.SplitReadRealigner.createSupplementaryAlignments(SplitReadRealigner.java:107)
at gridss.SoftClipsToSplitReads.doWork(SoftClipsToSplitReads.java:75)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
at au.edu.wehi.idsv.SAMEvidenceSource.execute(SAMEvidenceSource.java:156)
at au.edu.wehi.idsv.SAMEvidenceSource.ensureExtracted(SAMEvidenceSource.java:226)
at gridss.CallVariants$1$1.call(CallVariants.java:60)
at gridss.CallVariants$1$1.call(CallVariants.java:49)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment