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GRIDSS: the Genomic Rearrangement IDentification Software Suite
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PoN: bed & bedpe #647

Closed acarbome7 closed 1 year ago

acarbome7 commented 1 year ago

Hello! I am trying to generate a panel of normals bedpe and files from 35 germline VCFs. However, I end up with bed and bedpe empty files and no error. Below is the log:

[Thu Nov 02 10:19:02 CET 2023] GeneratePonBedpe INPUT=[043-0080-01ND.vcf, 1064-01-5ND.vcf, 1182-01-01ND.vcf, 1227-02-01ND.vcf, 1242-01-01ND.vcf, 1296-01-01ND.vcf, 1310-01-01ND.vcf, 1318-01-01ND.vcf, 1321-01-03ND.vcf, 1336-01-02ND.vcf, 1337-01-02ND.vcf, 1347-01-09ND.vcf, 1359-01-08ND.vcf, 1598-01-05ND.vcf, 1606-01-02ND.vcf, 1607-01-06ND.vcf, 1623-01-2ND.vcf, 1654-01-01ND.vcf, 1664-01-01ND.vcf, 1674-01-05ND.vcf, 1683-01-01ND.vcf, 1714-02-01ND.vcf, 1722-01-01ND.vcf, 1726-01-02ND.vcf, 1796-01-03ND.vcf, 1829-01-04ND.vcf, 1887-01-03ND.vcf, 1888-01-03ND.vcf, 1952-01-05ND.vcf, 1963-01-02ND.vcf, 2565-01-01ND.vcf, 2942-01-03ND.vcf, 3200-01-02ND.vcf, 3565-01-04ND.vcf, 872-01-01ND.vcf] OUTPUT_BEDPE=/PoN/files/gridss_pon_breakpoint.bedpe OUTPUT_BED=/PoN/files/gridss_pon_single_breakend.bed NORMAL_ORDINAL=[1] REFERENCE_SEQUENCE=/PoN/files/Homo_sapiens.GRCh38.dna.primary_assembly.fa    MIN_BREAKPOINT_QUAL=75.0 MIN_BREAKEND_QUAL=428.0 INCLUDE_IMPRECISE_CALLS=false WORKER_THREADS=12 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
[Thu Nov 02 10:19:02 CET 2023] Executing as cli79639@sln35 on Linux 4.4.120-721-94.17-default amd64; Java HotSpot(TM) 64-Bit Server VM 12.0.2+10; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.13.2-gridss
INFO    2023-11-02 10:19:02     GridssConfiguration     maxCoverage=25000
INFO    2023-11-02 10:19:02     GridssConfiguration     minMapq=20
INFO    2023-11-02 10:19:02     GridssConfiguration     fallbackMapq=20
INFO    2023-11-02 10:19:02     GridssConfiguration     fallbackBaseq=20
INFO    2023-11-02 10:19:02     GridssConfiguration     minAnchorShannonEntropy=0.5
INFO    2023-11-02 10:19:02     GridssConfiguration     dovetailMargin=4
INFO    2023-11-02 10:19:02     GridssConfiguration     softclip.minAverageQual=5.0
INFO    2023-11-02 10:19:02     GridssConfiguration     softclip.minLength=5
INFO    2023-11-02 10:19:02     GridssConfiguration     softclip.minAnchorIdentity=0.95
INFO    2023-11-02 10:19:02     GridssConfiguration     softclip.realignSplitReads=false
INFO    2023-11-02 10:19:02     GridssConfiguration     useReadGroupSampleNameCategoryLabel=true
INFO    2023-11-02 10:19:02     GridssConfiguration     chunkSize=10000000
INFO    2023-11-02 10:19:02     GridssConfiguration     chunkSequenceChangePenalty=250000
INFO    2023-11-02 10:19:02     GridssConfiguration     hashEvidenceID=true
INFO    2023-11-02 10:19:02     GridssConfiguration     adapter=AGATCGGAAGAG
INFO    2023-11-02 10:19:02     GridssConfiguration     adapter=ATGGAATTCTCG
INFO    2023-11-02 10:19:02     GridssConfiguration     adapter=CTGTCTCTTATA
INFO    2023-11-02 10:19:02     GridssConfiguration     scoring.readWeightedRegex=^cons_[0-9]+_r_(?<weight>[0-9]+)_$
INFO    2023-11-02 10:19:02     GridssConfiguration     scoring.model=FastEmpiricalReferenceLikelihood
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.k=25
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.minReads=3
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.includePairAnchors=true
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.pairAnchorMismatchIgnoreEndBases=5
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.writeFiltered=false
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.anchorLength=300
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.removeMisassembledPartialContigsDuringAssembly=true
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.maxExpectedBreakendLengthMultiple=1.5
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.errorCorrection.kmerErrorCorrectionMultiple=10.0
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.errorCorrection.k=21
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.errorCorrection.maxCorrectionsInKmer=3
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.errorCorrection.deduplicateReadKmers=true
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.realignContigs=true
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.recoverAfterError=true
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.downsample.acceptDensityPortion=0.1
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.downsample.targetEvidenceDensity=1
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.downsample.minimumDensityWindowSize=1000
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.downsample.densityDownsampleRateClippedReads=0.9
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.downsample.densityDownsampleRateDiscordantReads=0.75
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.positional.maxPathLengthMultiple=1.1
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.positional.retainWidthMultiple=2.0
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.positional.flushWidthMultiple=1.0
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.positional.maximumNodeDensity=2.0
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.positional.trimSelfIntersectingReads=true
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.positional.forceFullMemoizationRecalculationAt=0.8
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.positional.safetyModePathCountThreshold=50000
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.positional.safetyModeContigsToCall=3
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.contigNamePrefix=asm%d-
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.longReadReadLengthThreshold=1000
INFO    2023-11-02 10:19:02     GridssConfiguration     assembly.maximumReproductionExportPackages=5
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.minReads=2
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.minScore=50.0
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.minSize=10
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.callUnassembledBreakpoints=true
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.callUnassembledBreakends=false
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.callFullyAnchoredAssemblyVariants=false
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.breakendMargin=10
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.writeFiltered=false
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.simplecalls=false
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.maxBreakendHomologyLength=300
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.breakendHomologyAlignmentMargin=10
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.requireAssemblyCategorySupport=true
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.callBreakends=true
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.includeSupportingReadNames=false
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.breakpointLowQuality=500.0
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.breakendLowQuality=1500.0
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.breakendMaxAssemblySupportBias=0.5
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.ignoreMissingAssemblyFile=false
INFO    2023-11-02 10:19:02     GridssConfiguration     variantcalling.minimumImpreciseDeletion=500
INFO    2023-11-02 10:19:02     GridssConfiguration     terminateOnFirstError=true
INFO    2023-11-02 10:19:02     GridssConfiguration     visualisation.directory=visualisation
INFO    2023-11-02 10:19:02     GridssConfiguration     visualisation.buffers=false
INFO    2023-11-02 10:19:02     GridssConfiguration     visualisation.bufferTrackingItervalInSeconds=60
INFO    2023-11-02 10:19:02     GridssConfiguration     visualisation.timeouts=false
INFO    2023-11-02 10:19:02     GridssConfiguration     visualisation.evidenceAllocation=false
INFO    2023-11-02 10:19:02     GridssConfiguration     visualisation.assemblyProgress=false
INFO    2023-11-02 10:19:02     GridssConfiguration     visualisation.assemblyTelemetry=false
INFO    2023-11-02 10:19:02     GridssConfiguration     visualisation.maxCliqueTelemetry=false
INFO    2023-11-02 10:19:02     GridssConfiguration     visualisation.assemblyGraph=false
INFO    2023-11-02 10:19:02     GridssConfiguration     visualisation.assemblyGraphFullSize=false
INFO    2023-11-02 10:19:02     GridssConfiguration     visualisation.assemblyContigMemoization=false
INFO    2023-11-02 10:19:02     GridssConfiguration     visualisation.evidenceTracker=false
INFO    2023-11-02 10:19:02     TwoBitBufferedReferenceSequenceFile     Loading reference genome from cache /PoN/files/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gridsscache
INFO    2023-11-02 10:19:09     TwoBitBufferedReferenceSequenceFile     Loading reference genome complete
[Thu Nov 02 10:32:23 CET 2023] gridss.GeneratePonBedpe done. Elapsed time: 13.35 minutes.
Runtime.totalMemory()=2151677952

I have generated each VCF from bam like this:

bcftools mpileup -Ou -f /path_to_hg38/Homo_sapiens.GRCh38.dna.primary_assembly.fa /path_to_bam/1963-01-02ND.bam | bcftools call -mv -Ov -o /path_to_PoN/1963-01-02ND.vcf

And they look fine. I don't know what else to try. I'd appreciate any help. Thanks!

d-cameron commented 1 year ago

GRIDSS PONs can only be generated from VCFs produced by GRIDSS.