SYNCH_EXPORT1 0 task export1 waiting N/A /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/sortExport.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008 --target=check EXP_LANE_SPLIT_1 0 task Split export set 1 waiting SYNCH_EXPORT1 /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/sortExport.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008 --exportSet=1 --read1Export=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Aligned/Project_Demo/Sample_AR008/AR008_ACTTGA_L001_R1_001_export.txt.gz --read2Export=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Aligned/Project_Demo/Sample_AR008/AR008_ACTTGA_L001_R2_001_export.txt.gz --target=splitSingle SYNCH_EXPORT2 0 synch export2 waiting N/A TASKS (EXP_LANE_SPLIT_1[0],) SYNCH_EXPORT3 0 task export3 waiting SYNCH_EXPORT2 /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/sortExport.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008 --target=commit buildchr22/0000 0 task sortMerge to BAM for chr22 waiting SYNCH_EXPORT3 /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/splitUnSorted.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008 --chrom='chr22' --binId=0000 --target=mergeSingle SYNCH_MERGE_BAM_chr22_DONE 0 synch sortMerge to BAM for chr22 waiting N/A TASKS (buildchr22/0000[0],) SORTED2BAM_chr22 0 task Merging BAMs for chr22 waiting SYNCH_MERGE_BAM_chr22_DONE /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/concatChromBam.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008 --chrom=chr22 SYNCH_MERGE_chr22_DONE 0 synch sortMerge for chr22 waiting N/A TASKS (SORTED2BAM_chr22[0],) SYNCH_MERGE_BAM_DONE 0 synch sortMerge to BAM waiting N/A TASKS (SYNCH_MERGE_BAM_chr22_DONE[0],) SYNCH_SORT2 0 task sortRemoveTemps waiting SYNCH_MERGE_BAM_DONE /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/sortExport.pl --projectDir='/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008' --target=removeTemps SYNCH_MERGE_DONE 0 synch sortMerge waiting N/A TASKS (SYNCH_MERGE_chr22_DONE[0],) PREREQ_refSeq_DONE 0 synch RefSeq prerequisites waiting N/A TASKS (SYNCH_EXPORT1[0],) SPLIT_REF_SEQ 0 task Split reference waiting PREREQ_refSeq_DONE /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/transformFasta.pl --chromNameSource=contigName --targetPath=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/cachedRefSeq /illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Sequence/Chromosomes/chr22.fa && /illumina/development/casava/Version_1_8_branch/bin/configureBuild.pl --chromNameSource=fileName --refSequences=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/cachedRefSeq --maskRefSeqFiles='*' --outDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008 --targets continue refSeq_DONE 0 synch Split reference into single-entry fastas. waiting N/A TASKS (SPLIT_REF_SEQ[0],) PREREQ_VARIANTS_chr22/0000 0 synch Variants prereq for chr22/0000 waiting N/A TASKS (refSeq_DONE[0],SYNCH_MERGE_chr22_DONE[0],) VARIANTS_chr22/0000 0 task Computing small variants for chr22 0000 waiting PREREQ_VARIANTS_chr22/0000 /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/callSmallVariants.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008 --chrom='chr22' --binId=0000 VARIANTS_chr22 0 synch Small variant caller bin-level processing for chrom chr22 waiting N/A TASKS (VARIANTS_chr22/0000[0],) VARIANTS_FILTER_chr22 0 task Aggregating small variant calls for chr22 waiting VARIANTS_chr22 /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/filterSmallVariants.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008 --chrom='chr22' VARIANTS 0 synch Small variant caller sequence-level processing waiting N/A TASKS (VARIANTS_FILTER_chr22[0],) VARIANTS_STATS 0 task Small variants stats waiting VARIANTS /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/generateVariantsStats.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008 REPORT 0 task Small variants report waiting VARIANTS_STATS /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/generateVariantsReports.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008 EXON_COORDS 0 task making exon_coords.txt waiting N/A gunzip -c '/illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Annotation/Genes/refFlat.txt.gz' | /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/nonoverlappingExonCoords.pl --chromNameSource=contigName --verbose=1 > '/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/features/exon_coords.txt' SYNCH_RNA_COUNT 0 synch rnaCount waiting N/A TASKS (EXON_COORDS[0],SYNCH_EXPORT3[0],) PREREQ_RNA_COUNT_chr22 0 synch Prereq for rna-counting on chrom chr22 waiting N/A TASKS (SYNCH_RNA_COUNT[0],VARIANTS_chr22[0],) rnaExonCountschr22 0 task Calculate exon and gene counts RPKM for chr22 waiting PREREQ_RNA_COUNT_chr22 /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/DataAnalysis/rnaExonCounts.pl --chrom='chr22' --featureFile='/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/features/exon_coords.txt' --geneCountsFile='/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/Parsed/chr22/chr22_genes_count.txt' --totalBases=$(( `grep -vE '^#' '/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/stats/Reads.idx' |cut -f6 |paste -sd+` )) /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/Parsed/chr22/0000/sites.txt.gz > '/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/Parsed/chr22/chr22_exon_count.txt' rnaSpliceCountschr22 0 task Calculate splice RPKM for chr22 waiting SYNCH_RNA_COUNT /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/DataAnalysis/rnaSpliceCounts.pl --chrom='chr22' --totalReads=$(( `grep -vE '^#' '/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/stats/Reads.idx' |cut -f5 |paste -sd+` )) <'/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/Parsed/chr22/tmpSpliceJunctionCounts.txt' > '/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/Parsed/chr22/chr22_splice_count.txt' && rm '/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/Parsed/chr22/tmpSpliceJunctionCounts.txt' refSeqClean_PREREQ 0 synch Cleanup reference cache prerequisites. waiting N/A TASKS (SYNCH_SORT2[0],rnaSpliceCountschr22[0],rnaExonCountschr22[0],REPORT[0],SYNCH_MERGE_DONE[0],) SPLIT_REF_SEQ_CLEANUP 0 task Split reference cleanup waiting refSeqClean_PREREQ /illumina/development/casava/Version_1_8_branch/bin/configureBuild.pl --outDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008 --targets continue --chromNameSource=contigName --refSequences=/illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Sequence/Chromosomes --maskRefSeqFiles=chr22.fa && rm -rf /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/cachedRefSeq ALL_DONE 0 synch The checkpoint that gets executed after everything is done waiting N/A TASKS (SPLIT_REF_SEQ_CLEANUP[0],) postRunCmd 0 task --postRunCmd script waiting ALL_DONE cd /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008 && CASAVA_FULL_ETCDIR="/illumina/development/casava/Version_1_8_branch/etc/CASAVA-1.8.2" CASAVA_FULL_DATADIR="/illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2" CASAVA_FULL_BINDIR="/illumina/development/casava/Version_1_8_branch/bin" CASAVA_FULL_LIBDIR="/illumina/development/casava/Version_1_8_branch/lib/CASAVA-1.8.2" CASAVA_FULL_LIBEXECDIR="/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2" CASAVA_FULL_PERL_LIBDIR="/illumina/development/casava/Version_1_8_branch/lib/CASAVA-1.8.2/perl" touch /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_AR008/Build.finished