# This section contains CASAVA parameters for PROJECT_CONFIGURATION [PROJECT_CONFIGURATION] QVCutoff 90 QVCutoffSingle 10 alignabilityBatchSize 15000000 alignabilityForceRegenerate 0 alignabilityReadLength 30 alignabilitySuppressWarnings 0 appVersion CASAVA-1.8.2 applicationType DNA bamWholeGenome 0 barcodes binSizeBuild 50000000 binSizeProject 50000000 buildId e30fc4287d3cb96e876d7e614a057e13 chromNameSource contigName chromNameValidation off chromosomes phi CTA_150bp CTA_250bp CTA_350bp CTA_450bp CTA_550bp CTA_650bp CTA_750bp CTA_850bp CTL_150bp CTL_250bp CTL_350bp CTL_450bp CTL_550bp CTL_650bp CTL_750bp CTL_850bp CTE2_150bp CTE2_250bp CTE2_350bp CTE2_450bp CTE2_550bp CTE2_650bp CTE2_750bp CTE2_850bp CTE1_123bp CTE1_223bp CTE1_323bp CTE1_423bp CTE1_523bp CTE1_623bp CTE1_723bp CTE1_823bp TAGSET1 CONTROL_INDEX SAMPLE_INDEX_ACAGTG SAMPLE_INDEX_ATCACG SAMPLE_INDEX_CGATGT SAMPLE_INDEX_GCCAAT SAMPLE_INDEX_TGACCA SAMPLE_INDEX_TTAGGC SAMPLE_INDEX_ACTTGA SAMPLE_INDEX_CAGATC SAMPLE_INDEX_CTTGTA SAMPLE_INDEX_GATCAG SAMPLE_INDEX_GGCTAC SAMPLE_INDEX_TAGCTT cmdGunzip gunzip cmdGzip gzip cmdSamtools /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/samtools configured 1 consensusIncludeIndels 0 currentRunId 22_44_14_18_10_11 dataSetSuffix dirBuild /illumina/development/casava/Version_1_8_branch/bin/100723_EAS346_0188_FC626BWAAXX.generation/Build/Project_FC626BWAAXX/Sample_lane8 dirBuildExport /illumina/development/casava/Version_1_8_branch/bin/100723_EAS346_0188_FC626BWAAXX.generation/Build/Project_FC626BWAAXX/Sample_lane8/export dirBuildParsed /illumina/development/casava/Version_1_8_branch/bin/100723_EAS346_0188_FC626BWAAXX.generation/Build/Project_FC626BWAAXX/Sample_lane8/Parsed dirBuildTemp /illumina/development/casava/Version_1_8_branch/bin/100723_EAS346_0188_FC626BWAAXX.generation/Build/Project_FC626BWAAXX/Sample_lane8/tmp dirRefSeq /illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/Validation/100723_EAS346_0188_FC626BWAAXX/Data/Intensities/BaseCalls extraBltArgs featureFileName genesListPath ignoreMissingMetadata 0 indelsAlignScoreThresh 100 indelsCovCutoff 3 indelsErrorRate indelsMinContext 6 indelsMinCoverage 1 indelsMinGroupSize 3 indelsPrasThreshold 6 indelsSaveTempFiles 1 indelsSdFlankWeight 5 indelsSpReadThresholdClusters 5 indelsSpReadThresholdIndels 25.0 indelsSrasThreshold 10 isWorkflow 1 isWorkflowAuto 0 isWorkflowMake 1 isWorkflowSGE 0 jobsLimit knownBases_CONTROL_INDEX 7 knownBases_CTA_150bp 150 knownBases_CTA_250bp 250 knownBases_CTA_350bp 350 knownBases_CTA_450bp 450 knownBases_CTA_550bp 550 knownBases_CTA_650bp 650 knownBases_CTA_750bp 750 knownBases_CTA_850bp 850 knownBases_CTE1_123bp 127 knownBases_CTE1_223bp 227 knownBases_CTE1_323bp 327 knownBases_CTE1_423bp 427 knownBases_CTE1_523bp 527 knownBases_CTE1_623bp 627 knownBases_CTE1_723bp 727 knownBases_CTE1_823bp 827 knownBases_CTE2_150bp 150 knownBases_CTE2_250bp 250 knownBases_CTE2_350bp 350 knownBases_CTE2_450bp 450 knownBases_CTE2_550bp 550 knownBases_CTE2_650bp 650 knownBases_CTE2_750bp 750 knownBases_CTE2_850bp 850 knownBases_CTL_150bp 150 knownBases_CTL_250bp 250 knownBases_CTL_350bp 350 knownBases_CTL_450bp 450 knownBases_CTL_550bp 550 knownBases_CTL_650bp 650 knownBases_CTL_750bp 750 knownBases_CTL_850bp 850 knownBases_SAMPLE_INDEX_ACAGTG 6 knownBases_SAMPLE_INDEX_ACTTGA 6 knownBases_SAMPLE_INDEX_ATCACG 6 knownBases_SAMPLE_INDEX_CAGATC 6 knownBases_SAMPLE_INDEX_CGATGT 6 knownBases_SAMPLE_INDEX_CTTGTA 6 knownBases_SAMPLE_INDEX_GATCAG 6 knownBases_SAMPLE_INDEX_GCCAAT 6 knownBases_SAMPLE_INDEX_GGCTAC 6 knownBases_SAMPLE_INDEX_TAGCTT 6 knownBases_SAMPLE_INDEX_TGACCA 6 knownBases_SAMPLE_INDEX_TTAGGC 6 knownBases_TAGSET1 13 knownBases_phi 5386 lanes makeFlags maskRefSeqFiles controls.fasta nonoverlappingExonCoordsParams --verbose=1 poissonAlnCutoff 24 postRunCmd touch /illumina/development/casava/Version_1_8_branch/bin/100723_EAS346_0188_FC626BWAAXX.generation/Build/Project_FC626BWAAXX/Sample_lane8/Build.finished previousRunId 22_44_14_18_10_11 projectId 22_44_14_18_10_11 qualityType Phred64 read readMode single readSampleRateEnd 1.0 readSampleRateInput 1.0 readSampleRateStart 1.0 readSampleRateStep 0.1 refFlatFile refSeqCacheDirName cachedRefSeq refSeqLocked yes regExpMitochondria ^cM.fa$|^chrM.fa$|^cMT.fa$|^chrMT.fa$|^M$|^MT$ removeTemps ON rmDup YES rnaCountMethod readBases samtoolsRefFile /illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/Validation/100723_EAS346_0188_FC626BWAAXX/Data/Intensities/BaseCalls/controls.fasta seqGeneMd2RefFlatParams sgeQmakeFlags -cwd -v PATH singleScoreForPE NO skipVariableMetadata 1 snpMaxRatio 3 snpThreshold 10 snpThreshold2 6 sortBufferSize 1984 sortMaxBatchSize 128 spliceJunction splice_sites-auto.fa svRank_DepthWindow 1000 svRank_alnCutoff 24 svRank_covCutoff 10 svRank_maxFragmentSize 10000000 svRank_maxSD 100 svRank_minObservations 5 svRank_minSingleScore 10 svRank_numLongSD 3 svRank_numShortSD 5 task2MakeParams --finishedPrefix tmp/make/tasks_2011-10-18_22-42-40.txt/ timeStamp_CONTROL_INDEX 1298938027 timeStamp_CTA_150bp 1298938027 timeStamp_CTA_250bp 1298938027 timeStamp_CTA_350bp 1298938027 timeStamp_CTA_450bp 1298938027 timeStamp_CTA_550bp 1298938027 timeStamp_CTA_650bp 1298938027 timeStamp_CTA_750bp 1298938027 timeStamp_CTA_850bp 1298938027 timeStamp_CTE1_123bp 1298938027 timeStamp_CTE1_223bp 1298938027 timeStamp_CTE1_323bp 1298938027 timeStamp_CTE1_423bp 1298938027 timeStamp_CTE1_523bp 1298938027 timeStamp_CTE1_623bp 1298938027 timeStamp_CTE1_723bp 1298938027 timeStamp_CTE1_823bp 1298938027 timeStamp_CTE2_150bp 1298938027 timeStamp_CTE2_250bp 1298938027 timeStamp_CTE2_350bp 1298938027 timeStamp_CTE2_450bp 1298938027 timeStamp_CTE2_550bp 1298938027 timeStamp_CTE2_650bp 1298938027 timeStamp_CTE2_750bp 1298938027 timeStamp_CTE2_850bp 1298938027 timeStamp_CTL_150bp 1298938027 timeStamp_CTL_250bp 1298938027 timeStamp_CTL_350bp 1298938027 timeStamp_CTL_450bp 1298938027 timeStamp_CTL_550bp 1298938027 timeStamp_CTL_650bp 1298938027 timeStamp_CTL_750bp 1298938027 timeStamp_CTL_850bp 1298938027 timeStamp_SAMPLE_INDEX_ACAGTG 1298938027 timeStamp_SAMPLE_INDEX_ACTTGA 1298938027 timeStamp_SAMPLE_INDEX_ATCACG 1298938027 timeStamp_SAMPLE_INDEX_CAGATC 1298938027 timeStamp_SAMPLE_INDEX_CGATGT 1298938027 timeStamp_SAMPLE_INDEX_CTTGTA 1298938027 timeStamp_SAMPLE_INDEX_GATCAG 1298938027 timeStamp_SAMPLE_INDEX_GCCAAT 1298938027 timeStamp_SAMPLE_INDEX_GGCTAC 1298938027 timeStamp_SAMPLE_INDEX_TAGCTT 1298938027 timeStamp_SAMPLE_INDEX_TGACCA 1298938027 timeStamp_SAMPLE_INDEX_TTAGGC 1298938027 timeStamp_TAGSET1 1298938027 timeStamp_phi 1298938027 toNMScore -1 totalBases_CONTROL_INDEX 7 totalBases_CTA_150bp 150 totalBases_CTA_250bp 250 totalBases_CTA_350bp 350 totalBases_CTA_450bp 450 totalBases_CTA_550bp 550 totalBases_CTA_650bp 650 totalBases_CTA_750bp 750 totalBases_CTA_850bp 850 totalBases_CTE1_123bp 127 totalBases_CTE1_223bp 227 totalBases_CTE1_323bp 327 totalBases_CTE1_423bp 427 totalBases_CTE1_523bp 527 totalBases_CTE1_623bp 627 totalBases_CTE1_723bp 727 totalBases_CTE1_823bp 827 totalBases_CTE2_150bp 150 totalBases_CTE2_250bp 250 totalBases_CTE2_350bp 350 totalBases_CTE2_450bp 450 totalBases_CTE2_550bp 550 totalBases_CTE2_650bp 650 totalBases_CTE2_750bp 750 totalBases_CTE2_850bp 850 totalBases_CTL_150bp 150 totalBases_CTL_250bp 250 totalBases_CTL_350bp 350 totalBases_CTL_450bp 450 totalBases_CTL_550bp 550 totalBases_CTL_650bp 650 totalBases_CTL_750bp 750 totalBases_CTL_850bp 850 totalBases_SAMPLE_INDEX_ACAGTG 6 totalBases_SAMPLE_INDEX_ACTTGA 6 totalBases_SAMPLE_INDEX_ATCACG 6 totalBases_SAMPLE_INDEX_CAGATC 6 totalBases_SAMPLE_INDEX_CGATGT 6 totalBases_SAMPLE_INDEX_CTTGTA 6 totalBases_SAMPLE_INDEX_GATCAG 6 totalBases_SAMPLE_INDEX_GCCAAT 6 totalBases_SAMPLE_INDEX_GGCTAC 6 totalBases_SAMPLE_INDEX_TAGCTT 6 totalBases_SAMPLE_INDEX_TGACCA 6 totalBases_SAMPLE_INDEX_TTAGGC 6 totalBases_TAGSET1 13 totalBases_phi 5386 variantsIndelCovCutoff 3.0 variantsIndelTheta 0.0001 variantsMDFilterCount 2 variantsMDFilterFlank 20 variantsMaxIndelSizePEDefault 300 variantsMaxIndelSizeSEDefault 50 variantsMinQbasecall 0 variantsMinVexp 0.25 variantsSiteErrorDepDefault 0.6 variantsSiteErrorDepNoMismatch 0.35 variantsSnpCovCutoff 3.0 variantsSnpTheta 0.001 variantsSummaryMinQindel 20 variantsSummaryMinQsnp 20 verbose 0 workflowFile /illumina/development/casava/Version_1_8_branch/bin/100723_EAS346_0188_FC626BWAAXX.generation/Build/Project_FC626BWAAXX/Sample_lane8/tasks.22_44_59_18_10_11.txt [RUN_22_44_14_18_10_11] _runId 22_44_14_18_10_11 appVersion CASAVA-1.8.2 argv --skipVariableMetadata --samtoolsRefFile /illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/Validation/100723_EAS346_0188_FC626BWAAXX/Data/Intensities/BaseCalls/controls.fasta --chromNameValidation off --indelsSaveTempFiles --inSampleDir Aligned/Project_FC626BWAAXX/Sample_lane8 --outDir Build/Project_FC626BWAAXX/Sample_lane8/ --postRunCmd touch /illumina/development/casava/Version_1_8_branch/bin/100723_EAS346_0188_FC626BWAAXX.generation/Build/Project_FC626BWAAXX/Sample_lane8/Build.finished --make --workflowFile Build/Project_FC626BWAAXX/Sample_lane8/tasks_2011-10-18_22-42-40.txt --task2MakeParams=--finishedPrefix tmp/make/tasks_2011-10-18_22-42-40.txt/ currentStatus finished endTime 22_44_59_18_10_11 force 0 startTime 22_44_14_18_10_11 target all targets continue [PROJECT_BIN_SIZES] CONTROL_INDEX 1 CTA_150bp 1 CTA_250bp 1 CTA_350bp 1 CTA_450bp 1 CTA_550bp 1 CTA_650bp 1 CTA_750bp 1 CTA_850bp 1 CTE1_123bp 1 CTE1_223bp 1 CTE1_323bp 1 CTE1_423bp 1 CTE1_523bp 1 CTE1_623bp 1 CTE1_723bp 1 CTE1_823bp 1 CTE2_150bp 1 CTE2_250bp 1 CTE2_350bp 1 CTE2_450bp 1 CTE2_550bp 1 CTE2_650bp 1 CTE2_750bp 1 CTE2_850bp 1 CTL_150bp 1 CTL_250bp 1 CTL_350bp 1 CTL_450bp 1 CTL_550bp 1 CTL_650bp 1 CTL_750bp 1 CTL_850bp 1 SAMPLE_INDEX_ACAGTG 1 SAMPLE_INDEX_ACTTGA 1 SAMPLE_INDEX_ATCACG 1 SAMPLE_INDEX_CAGATC 1 SAMPLE_INDEX_CGATGT 1 SAMPLE_INDEX_CTTGTA 1 SAMPLE_INDEX_GATCAG 1 SAMPLE_INDEX_GCCAAT 1 SAMPLE_INDEX_GGCTAC 1 SAMPLE_INDEX_TAGCTT 1 SAMPLE_INDEX_TGACCA 1 SAMPLE_INDEX_TTAGGC 1 TAGSET1 1 phi 1 # This section contains CASAVA parameters for BUILD_BIN_SIZES [BUILD_BIN_SIZES] CONTROL_INDEX 1 CTA_150bp 1 CTA_250bp 1 CTA_350bp 1 CTA_450bp 1 CTA_550bp 1 CTA_650bp 1 CTA_750bp 1 CTA_850bp 1 CTE1_123bp 1 CTE1_223bp 1 CTE1_323bp 1 CTE1_423bp 1 CTE1_523bp 1 CTE1_623bp 1 CTE1_723bp 1 CTE1_823bp 1 CTE2_150bp 1 CTE2_250bp 1 CTE2_350bp 1 CTE2_450bp 1 CTE2_550bp 1 CTE2_650bp 1 CTE2_750bp 1 CTE2_850bp 1 CTL_150bp 1 CTL_250bp 1 CTL_350bp 1 CTL_450bp 1 CTL_550bp 1 CTL_650bp 1 CTL_750bp 1 CTL_850bp 1 SAMPLE_INDEX_ACAGTG 1 SAMPLE_INDEX_ACTTGA 1 SAMPLE_INDEX_ATCACG 1 SAMPLE_INDEX_CAGATC 1 SAMPLE_INDEX_CGATGT 1 SAMPLE_INDEX_CTTGTA 1 SAMPLE_INDEX_GATCAG 1 SAMPLE_INDEX_GCCAAT 1 SAMPLE_INDEX_GGCTAC 1 SAMPLE_INDEX_TAGCTT 1 SAMPLE_INDEX_TGACCA 1 SAMPLE_INDEX_TTAGGC 1 TAGSET1 1 phi 1