Settings: Output files: "refs/ERCC92.fa.*.ht2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Local offset rate: 3 (one in 8) Local fTable chars: 6 Local sequence length: 57344 Local sequence overlap between two consecutive indexes: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: refs/ERCC92.fa Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 Time to read SNPs and splice sites: 00:00:00 Using parameters --bmax 15516 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 15516 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 11821.3 (target: 15515) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering GFM loop Getting block 1 of 7 Reserving size (15516) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% bucket 1: 50% bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 8454 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 8455 for bucket 1 Getting block 2 of 7 Reserving size (15516) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 15081 for bucket 2 (Using difference cover) Sorting block time: 00:00:00 Returning block of 15082 for bucket 2 Getting block 3 of 7 Reserving size (15516) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 10928 for bucket 3 (Using difference cover) Sorting block time: 00:00:00 Returning block of 10929 for bucket 3 Getting block 4 of 7 Reserving size (15516) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 11972 for bucket 4 (Using difference cover) Sorting block time: 00:00:00 Returning block of 11973 for bucket 4 Getting block 5 of 7 Reserving size (15516) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 10% bucket 5: 20% bucket 5: 30% bucket 5: 40% bucket 5: 50% bucket 5: 60% bucket 5: 70% bucket 5: 80% bucket 5: 90% bucket 5: 100% Sorting block of length 9615 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 9616 for bucket 5 Getting block 6 of 7 Reserving size (15516) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 14632 for bucket 6 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14633 for bucket 6 Getting block 7 of 7 Reserving size (15516) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 12067 for bucket 7 (Using difference cover) Sorting block time: 00:00:00 Returning block of 12068 for bucket 7 Exited GFM loop fchr[A]: 0 fchr[C]: 24248 fchr[G]: 42274 fchr[T]: 60911 fchr[$]: 82755 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 4224613 bytes to primary GFM file: refs/ERCC92.fa.1.ht2 Wrote 20696 bytes to secondary GFM file: refs/ERCC92.fa.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Returning from initFromVector Wrote 787267 bytes to primary GFM file: refs/ERCC92.fa.5.ht2 Wrote 20800 bytes to secondary GFM file: refs/ERCC92.fa.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HierEbwt constructor Headers: len: 82755 gbwtLen: 82756 nodes: 82756 sz: 20689 gbwtSz: 20690 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5173 offsSz: 20692 lineSz: 64 sideSz: 64 sideGbwtSz: 48 sideGbwtLen: 192 numSides: 432 numLines: 432 gbwtTotLen: 27648 gbwtTotSz: 27648 reverse: 0 linearFM: Yes Total time for call to driver() for forward index: 00:00:01 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.2 //========================== featureCounts setting ===========================\\ || || || Input files : 6 BAM files || || P HBR_1.bam || || P HBR_2.bam || || P HBR_3.bam || || P UHR_1.bam || || P UHR_2.bam || || P UHR_3.bam || || || || Output file : counts.txt || || Summary : counts.txt.summary || || Annotation : ERCC92.gtf (GTF) || || Dir for temp files : ./ || || || || Threads : 1 || || Level : meta-feature level || || Paired-end : no || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file ERCC92.gtf ... || || Features : 92 || || Meta-features : 92 || || Chromosomes/contigs : 92 || || || || Process BAM file HBR_1.bam... || || Paired-end reads are included. || || Assign reads to features... || || Total reads : 237142 || || Successfully assigned reads : 111944 (47.2%) || || Running time : 0.01 minutes || || || || Process BAM file HBR_2.bam... || || Paired-end reads are included. || || Assign reads to features... || || Total reads : 289652 || || Successfully assigned reads : 137434 (47.4%) || || Running time : 0.01 minutes || || || || Process BAM file HBR_3.bam... || || Paired-end reads are included. || || Assign reads to features... || || Total reads : 259572 || || Successfully assigned reads : 122702 (47.3%) || || Running time : 0.01 minutes || || || || Process BAM file UHR_1.bam... || || Paired-end reads are included. || || Assign reads to features... || || Total reads : 454784 || || Successfully assigned reads : 236660 (52.0%) || || Running time : 0.01 minutes || || || || Process BAM file UHR_2.bam... || || Paired-end reads are included. || || Assign reads to features... || || Total reads : 324746 || || Successfully assigned reads : 158100 (48.7%) || || Running time : 0.01 minutes || || || || Process BAM file UHR_3.bam... || || Paired-end reads are included. || || Assign reads to features... || || Total reads : 370884 || || Successfully assigned reads : 196596 (53.0%) || || Running time : 0.01 minutes || || || || Read assignment finished. || || || || Summary of counting results can be found in file "counts.txt.summary" || || || \\===================== http://subread.sourceforge.net/ ======================// Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colnames, colSums, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: locfit locfit 1.5-9.1 2013-03-22 Loading required package: lattice Welcome to 'DESeq'. For improved performance, usability and functionality, please consider migrating to 'DESeq2'. Warning messages: 1: In log(ifelse(y == 0, 1, y/mu)) : NaNs produced 2: step size truncated due to divergence Attaching package: ‘gplots’ The following object is masked from ‘package:stats’: lowess