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_PhiX --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_PhiX --exportSet=1 --read1Export=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Aligned/Project_Demo/Sample_PhiX/PhiX_TTAGGC_L001_R1_001_export.txt.gz --read2Export=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Aligned/Project_Demo/Sample_PhiX/PhiX_TTAGGC_L001_R2_001_export.txt.gz --target=split 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_PhiX --target=commit SYNCH_EXPORT5 0 synch export5 finished N/A TASKS () phix/0000 0 task sortRmDupSplit 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_PhiX --chrom='phix' --binId=0000 --target=split SYNCH_SORT 0 synch sortRmDupSplit waiting N/A TASKS (phix/0000[0],) SYNC_RM_SPLIT_TEMP 0 synch syncRmSplitTemp waiting N/A TASKS (SYNCH_SORT[0],) SYNCH_SORT2 0 task sortRemoveTemps waiting SYNC_RM_SPLIT_TEMP /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_PhiX' --target=removeTemps SYNCH_DUPL2 0 task sortDupStats waiting SYNCH_SORT /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/generateStats.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --target=duplicates REPORT 0 task sortDupReport waiting SYNCH_DUPL2 /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/generateReports.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --target=duplicates buildphix/0000 0 task sortMerge to BAM for phix waiting SYNCH_SORT /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_PhiX --chrom='phix' --binId=0000 --target=merge SYNCH_MERGE_BAM_phix_DONE 0 synch sortMerge to BAM for phix waiting N/A TASKS (buildphix/0000[0],) SORTED2BAM_phix 0 task Merging BAMs for phix waiting SYNCH_MERGE_BAM_phix_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_PhiX --chrom=phix SYNCH_MERGE_phix_DONE 0 synch sortMerge for phix waiting N/A TASKS (SORTED2BAM_phix[0],) SYNCH_MERGE_BAM_DONE 0 synch sortMerge to BAM waiting N/A TASKS (SYNCH_MERGE_BAM_phix_DONE[0],) SYNCH_SORT2 1 task sortRemoveTemps waiting SYNCH_MERGE_BAM_DONE /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_PhiX' --target=removeTemps SYNCH_MERGE_DONE 0 synch sortMerge waiting N/A TASKS (SYNCH_MERGE_phix_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_PhiX/cachedRefSeq /illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/PhiX/NCBI/1993-04-28/Sequence/Chromosomes/phix.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_PhiX/cachedRefSeq --maskRefSeqFiles='*' --outDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --targets continue refSeq_DONE 0 synch Split reference into single-entry fastas. waiting N/A TASKS (SPLIT_REF_SEQ[0],) PREREQ_INDEL_FINDER_phix/0000 0 synch Indel finder prereq for phix/0000 waiting N/A TASKS (refSeq_DONE[0],SYNCH_MERGE_phix_DONE[0],) INDEL_FINDER_phix/0000 0 task GROUPER phix 0000 waiting PREREQ_INDEL_FINDER_phix/0000 /illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/runGrouperBin.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --chrom=phix --binId=0000 INDEL_FINDER_phix 0 synch Indel finder bin-level processing waiting N/A TASKS (INDEL_FINDER_phix/0000[0],) INDEL_FINDER 0 synch Indel finder chrom-level processing waiting N/A TASKS (INDEL_FINDER_phix[0],) PREREQ_VARIANTS_phix/0000 0 synch Variants prereq for phix/0000 waiting N/A TASKS (refSeq_DONE[0],SYNCH_MERGE_phix_DONE[0],INDEL_FINDER_phix/0000[0],) VARIANTS_phix/0000 0 task Computing small variants for phix 0000 waiting PREREQ_VARIANTS_phix/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_PhiX --chrom='phix' --binId=0000 VARIANTS_phix 0 synch Small variant caller bin-level processing for chrom phix waiting N/A TASKS (VARIANTS_phix/0000[0],) VARIANTS_FILTER_phix 0 task Aggregating small variant calls for phix waiting VARIANTS_phix /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_PhiX --chrom='phix' VARIANTS 0 synch Small variant caller sequence-level processing waiting N/A TASKS (VARIANTS_FILTER_phix[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_PhiX REPORT 1 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_PhiX refSeqClean_PREREQ 0 synch Cleanup reference cache prerequisites. waiting N/A TASKS (SYNCH_EXPORT5[0],SYNCH_SORT2[1],INDEL_FINDER[0],REPORT[1],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_PhiX --targets continue --chromNameSource=contigName --refSequences=/illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/PhiX/NCBI/1993-04-28/Sequence/Chromosomes --maskRefSeqFiles=phix.fa && rm -rf /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX/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_PhiX && 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_PhiX/Build.finished