/project/umw_biocore/bin/RSEM/rsem-extract-reference-transcripts /share/data/umw_biocore/genome_data/chicken/galGal5/rsem_ref 0 /share/data/umw_biocore/genome_data/chicken/galGal5/ucsc.gtf 1 /share/data/umw_biocore/genome_data/chicken/galGal5/ucsc_into_genesymbol.rsem /share/data/umw_biocore/genome_data/chicken/galGal5/galGal5.fa Parsing gtf File is done! /share/data/umw_biocore/genome_data/chicken/galGal5/galGal5.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 /share/data/umw_biocore/genome_data/chicken/galGal5/rsem_ref.transcripts.fa 0 /share/data/umw_biocore/genome_data/chicken/galGal5/rsem_ref -l 125 Refs.makeRefs finished! Refs.saveRefs finished! /share/data/umw_biocore/genome_data/chicken/galGal5/rsem_ref.transcripts.fa is generated! /share/data/umw_biocore/genome_data/chicken/galGal5/rsem_ref.idx.fa is generated! /project/umw_biocore/bin/bowtie-0.12.9/bowtie-build -f /share/data/umw_biocore/genome_data/chicken/galGal5/rsem_ref.idx.fa /share/data/umw_biocore/genome_data/chicken/galGal5/rsem_ref Settings: Output files: "/share/data/umw_biocore/genome_data/chicken/galGal5/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: /share/data/umw_biocore/genome_data/chicken/galGal5/rsem_ref.idx.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: 00:00:02 bmax according to bmaxDivN setting: 4060824 Using parameters --bmax 3045618 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3045618 --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 Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 3, merged 5; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 3; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 0; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.03041e+06 (target: 3045617) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3045618) 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 1286639 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1286640 Getting block 2 of 8 Reserving size (3045618) 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 2981695 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2981696 Getting block 3 of 8 Reserving size (3045618) 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 2174008 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2174009 Getting block 4 of 8 Reserving size (3045618) 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: 00:00:00 Sorting block of length 1647052 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1647053 Getting block 5 of 8 Reserving size (3045618) 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: 00:00:00 Sorting block of length 2679251 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2679252 Getting block 6 of 8 Reserving size (3045618) 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: 00:00:00 Sorting block of length 2069794 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2069795 Getting block 7 of 8 Reserving size (3045618) 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 2103298 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2103299 Getting block 8 of 8 Reserving size (3045618) 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: 00:00:00 Sorting block of length 1301553 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1301554 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5017051 fchr[G]: 8572404 fchr[T]: 12405235 fchr[$]: 16243297 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 9038425 bytes to primary EBWT file: /share/data/umw_biocore/genome_data/chicken/galGal5/rsem_ref.1.ebwt Wrote 2030420 bytes to secondary EBWT file: /share/data/umw_biocore/genome_data/chicken/galGal5/rsem_ref.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16243297 bwtLen: 16243298 sz: 4060825 bwtSz: 4060825 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 507604 offsSz: 2030416 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 36258 numSides: 72516 numLines: 72516 ebwtTotLen: 4641024 ebwtTotSz: 4641024 reverse: 0 Total time for call to driver() for forward index: 00:00:21 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 bmax according to bmaxDivN setting: 4060824 Using parameters --bmax 3045618 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3045618 --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 Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:02 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.03041e+06 (target: 3045617) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3045618) 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: 00:00:00 Sorting block of length 1122163 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1122164 Getting block 2 of 8 Reserving size (3045618) 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: 00:00:00 Sorting block of length 2727569 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2727570 Getting block 3 of 8 Reserving size (3045618) 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 1102519 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1102520 Getting block 4 of 8 Reserving size (3045618) 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 3036731 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3036732 Getting block 5 of 8 Reserving size (3045618) 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 2628549 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2628550 Getting block 6 of 8 Reserving size (3045618) 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 2349262 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2349263 Getting block 7 of 8 Reserving size (3045618) 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: 00:00:00 Sorting block of length 2164760 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2164761 Getting block 8 of 8 Reserving size (3045618) 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: 00:00:00 Sorting block of length 1111737 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1111738 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5017051 fchr[G]: 8572404 fchr[T]: 12405235 fchr[$]: 16243297 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 9038425 bytes to primary EBWT file: /share/data/umw_biocore/genome_data/chicken/galGal5/rsem_ref.rev.1.ebwt Wrote 2030420 bytes to secondary EBWT file: /share/data/umw_biocore/genome_data/chicken/galGal5/rsem_ref.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16243297 bwtLen: 16243298 sz: 4060825 bwtSz: 4060825 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 507604 offsSz: 2030416 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 36258 numSides: 72516 numLines: 72516 ebwtTotLen: 4641024 ebwtTotSz: 4641024 reverse: 0 Total time for backward call to driver() for mirror index: 00:00:17