/project/umw_biocore/bin/RSEM/rsem-extract-reference-transcripts rsem_ref 0 ucsc.gtf 1 ucsc_into_genesymbol.rsem rn6ucsc.fa Parsed 200000 lines Parsed 400000 lines Parsed 600000 lines Parsing gtf File is done! rn6ucsc.fa is processed! Extracting sequences is done! Group File is generated! Transcript Information File is generated! Chromosome List File is generated! Extracted Sequences File is generated! /project/umw_biocore/bin/RSEM/rsem-preref rsem_ref.transcripts.fa 0 rsem_ref -l 125 Refs.makeRefs finished! Refs.saveRefs finished! rsem_ref.transcripts.fa is generated! rsem_ref.idx.fa is generated! /project/umw_biocore/bin/bowtie-0.12.9/bowtie-build -f rsem_ref.idx.fa rsem_ref Settings: Output files: "rsem_ref.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 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: rsem_ref.idx.fa Reading reference sizes Time reading reference sizes: 00:00:02 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 bmax according to bmaxDivN setting: 18662787 Using parameters --bmax 13997091 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 13997091 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:02 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: 00:00:01 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 Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:05 Splitting and merging Splitting and merging time: 00:00:00 Split 3, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:05 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.06644e+07 (target: 13997090) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 10784721 (Using difference cover) Sorting block time: 00:00:09 Returning block of 10784722 Getting block 2 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 9186750 (Using difference cover) Sorting block time: 00:00:09 Returning block of 9186751 Getting block 3 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:02 Sorting block of length 11553892 (Using difference cover) Sorting block time: 00:00:11 Returning block of 11553893 Getting block 4 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:02 Sorting block of length 10423755 (Using difference cover) Sorting block time: 00:00:10 Returning block of 10423756 Getting block 5 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:02 Sorting block of length 10957622 (Using difference cover) Sorting block time: 00:00:11 Returning block of 10957623 Getting block 6 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:02 Sorting block of length 10524644 (Using difference cover) Sorting block time: 00:00:10 Returning block of 10524645 Getting block 7 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 11219761 (Using difference cover) Sorting block time: 00:00:11 Returning block of 11219762 Exited Ebwt loop fchr[A]: 0 fchr[C]: 22989465 fchr[G]: 40407090 fchr[T]: 58012243 fchr[$]: 74651151 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 26891133 bytes to primary EBWT file: rsem_ref.1.ebwt Wrote 9331400 bytes to secondary EBWT file: rsem_ref.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 74651151 bwtLen: 74651152 sz: 18662788 bwtSz: 18662788 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2332849 offsSz: 9331396 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 166633 numSides: 333266 numLines: 333266 ebwtTotLen: 21329024 ebwtTotSz: 21329024 reverse: 0 Total time for call to driver() for forward index: 00:01:47 Reading reference sizes Time reading reference sizes: 00:00:01 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 bmax according to bmaxDivN setting: 18662787 Using parameters --bmax 13997091 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 13997091 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:02 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:01 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 Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:05 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:04 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:04 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.06644e+07 (target: 13997090) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 12404541 (Using difference cover) Sorting block time: 00:00:11 Returning block of 12404542 Getting block 2 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 7619023 (Using difference cover) Sorting block time: 00:00:08 Returning block of 7619024 Getting block 3 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 13091747 (Using difference cover) Sorting block time: 00:00:13 Returning block of 13091748 Getting block 4 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 13060270 (Using difference cover) Sorting block time: 00:00:14 Returning block of 13060271 Getting block 5 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 8756110 (Using difference cover) Sorting block time: 00:00:09 Returning block of 8756111 Getting block 6 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:02 Sorting block of length 13126344 (Using difference cover) Sorting block time: 00:00:13 Returning block of 13126345 Getting block 7 of 7 Reserving size (13997091) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 6593110 (Using difference cover) Sorting block time: 00:00:06 Returning block of 6593111 Exited Ebwt loop fchr[A]: 0 fchr[C]: 22989465 fchr[G]: 40407090 fchr[T]: 58012243 fchr[$]: 74651151 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 26891133 bytes to primary EBWT file: rsem_ref.rev.1.ebwt Wrote 9331400 bytes to secondary EBWT file: rsem_ref.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 74651151 bwtLen: 74651152 sz: 18662788 bwtSz: 18662788 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2332849 offsSz: 9331396 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 166633 numSides: 333266 numLines: 333266 ebwtTotLen: 21329024 ebwtTotSz: 21329024 reverse: 0 Total time for backward call to driver() for mirror index: 00:01:50