Settings: Output files: "refs/22.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/22.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: 00:00:01 Time to read SNPs and splice sites: 00:00:00 Using parameters --bmax 7342458 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 7342458 --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 Avg bucket size: 4.89497e+06 (target: 7342457) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering GFM loop Getting block 1 of 8 Reserving size (7342458) 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 6109124 for bucket 1 (Using difference cover) Sorting block time: 00:00:01 Returning block of 6109125 for bucket 1 Getting block 2 of 8 Reserving size (7342458) 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 4162165 for bucket 2 (Using difference cover) Sorting block time: 00:00:01 Returning block of 4162166 for bucket 2 Getting block 3 of 8 Reserving size (7342458) 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 3242487 for bucket 3 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3242488 for bucket 3 Getting block 4 of 8 Reserving size (7342458) 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 5059508 for bucket 4 (Using difference cover) Sorting block time: 00:00:01 Returning block of 5059509 for bucket 4 Getting block 5 of 8 Reserving size (7342458) 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 2717729 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2717730 for bucket 5 Getting block 6 of 8 Reserving size (7342458) 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 6052533 for bucket 6 (Using difference cover) Sorting block time: 00:00:01 Returning block of 6052534 for bucket 6 Getting block 7 of 8 Reserving size (7342458) 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 6696876 for bucket 7 (Using difference cover) Sorting block time: 00:00:01 Returning block of 6696877 for bucket 7 Getting block 8 of 8 Reserving size (7342458) for bucket 8 Calculating Z arrays for bucket 8 Entering block accumulator loop for bucket 8: bucket 8: 10% bucket 8: 20% bucket 8: 30% bucket 8: 40% bucket 8: 50% bucket 8: 60% bucket 8: 70% bucket 8: 80% bucket 8: 90% bucket 8: 100% Sorting block of length 5119348 for bucket 8 (Using difference cover) Sorting block time: 00:00:01 Returning block of 5119349 for bucket 8 Exited GFM loop fchr[A]: 0 fchr[C]: 10382214 fchr[G]: 19542866 fchr[T]: 28789052 fchr[$]: 39159777 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 17248367 bytes to primary GFM file: refs/22.fa.1.ht2 Wrote 9789952 bytes to secondary GFM file: refs/22.fa.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Returning from initFromVector Wrote 17349465 bytes to primary GFM file: refs/22.fa.5.ht2 Wrote 9969772 bytes to secondary GFM file: refs/22.fa.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HierEbwt constructor Headers: len: 39159777 gbwtLen: 39159778 nodes: 39159778 sz: 9789945 gbwtSz: 9789945 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2447487 offsSz: 9789948 lineSz: 64 sideSz: 64 sideGbwtSz: 48 sideGbwtLen: 192 numSides: 203958 numLines: 203958 gbwtTotLen: 13053312 gbwtTotSz: 13053312 reverse: 0 linearFM: Yes Total time for call to driver() for forward index: 00:00:21 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 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 : 22.gtf (GTF) || || Dir for temp files : ./ || || || || Threads : 1 || || Level : meta-feature level || || Paired-end : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || || Chimeric reads : counted || || Both ends mapped : not required || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file 22.gtf ... || || Features : 26087 || || Meta-features : 1335 || || Chromosomes/contigs : 1 || || || || Process BAM file HBR_1.bam... || || Paired-end reads are included. || || Assign fragments (read pairs) to features... || || || || WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). || || || || Pairing up the read pairs. || || || || Total fragments : 119458 || || Successfully assigned fragments : 39424 (33.0%) || || Running time : 0.01 minutes || || || || Process BAM file HBR_2.bam... || || Paired-end reads are included. || || Assign fragments (read pairs) to features... || || || || WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). || || || || Pairing up the read pairs. || || || || Total fragments : 145995 || || Successfully assigned fragments : 48414 (33.2%) || || Running time : 0.01 minutes || || || || Process BAM file HBR_3.bam... || || Paired-end reads are included. || || Assign fragments (read pairs) to features... || || || || WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). || || || || Pairing up the read pairs. || || || || Total fragments : 130787 || || Successfully assigned fragments : 42833 (32.8%) || || Running time : 0.01 minutes || || || || Process BAM file UHR_1.bam... || || Paired-end reads are included. || || Assign fragments (read pairs) to features... || || || || WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). || || || || Pairing up the read pairs. || || || || Total fragments : 230997 || || Successfully assigned fragments : 67733 (29.3%) || || Running time : 0.01 minutes || || || || Process BAM file UHR_2.bam... || || Paired-end reads are included. || || Assign fragments (read pairs) to features... || || || || WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). || || || || Pairing up the read pairs. || || || || Total fragments : 165053 || || Successfully assigned fragments : 44917 (27.2%) || || Running time : 0.01 minutes || || || || Process BAM file UHR_3.bam... || || Paired-end reads are included. || || Assign fragments (read pairs) to features... || || || || WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). || || || || Pairing up the read pairs. || || || || Total fragments : 188464 || || Successfully assigned fragments : 53883 (28.6%) || || 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'. Attaching package: ‘gplots’ The following object is masked from ‘package:stats’: lowess