/project/umw_biocore/bin/RSEM/rsem-extract-reference-transcripts /share/data/umw_biocore/genome_data/rat/rn5/rsem_ref 0 /share/data/umw_biocore/genome_data/rat/rn5/ucsc.gtf 1 /share/data/umw_biocore/genome_data/rat/rn5/ucsc_into_genesymbol.rsem /share/data/umw_biocore/genome_data/rat/rn5/rn5.fa Parsed 200000 lines Parsing gtf File is done! /share/data/umw_biocore/genome_data/rat/rn5/rn5.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/rat/rn5/rsem_ref.transcripts.fa 0 /share/data/umw_biocore/genome_data/rat/rn5/rsem_ref -l 125 Refs.makeRefs finished! Refs.saveRefs finished! /share/data/umw_biocore/genome_data/rat/rn5/rsem_ref.transcripts.fa is generated! /share/data/umw_biocore/genome_data/rat/rn5/rsem_ref.idx.fa is generated! /project/umw_biocore/bin/bowtie-0.12.9/bowtie-build -f /share/data/umw_biocore/genome_data/rat/rn5/rsem_ref.idx.fa /share/data/umw_biocore/genome_data/rat/rn5/rsem_ref Settings: Output files: "/share/data/umw_biocore/genome_data/rat/rn5/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/rat/rn5/rsem_ref.idx.fa 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: 10739129 Using parameters --bmax 8054347 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 8054347 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:01 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: 00:00:05 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: 00:00:03 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: 00:00:03 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 6.13664e+06 (target: 8054346) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (8054347) 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 4326119 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4326120 Getting block 2 of 7 Reserving size (8054347) 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 7103633 (Using difference cover) Sorting block time: 00:00:06 Returning block of 7103634 Getting block 3 of 7 Reserving size (8054347) 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 5086221 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5086222 Getting block 4 of 7 Reserving size (8054347) 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 6762009 (Using difference cover) Sorting block time: 00:00:06 Returning block of 6762010 Getting block 5 of 7 Reserving size (8054347) 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 7382606 (Using difference cover) Sorting block time: 00:00:06 Returning block of 7382607 Getting block 6 of 7 Reserving size (8054347) 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 4856930 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4856931 Getting block 7 of 7 Reserving size (8054347) 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 7438993 (Using difference cover) Sorting block time: 00:00:06 Returning block of 7438994 Exited Ebwt loop fchr[A]: 0 fchr[C]: 12569110 fchr[G]: 22831287 fchr[T]: 33169454 fchr[$]: 42956517 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 16970490 bytes to primary EBWT file: /share/data/umw_biocore/genome_data/rat/rn5/rsem_ref.1.ebwt Wrote 5369572 bytes to secondary EBWT file: /share/data/umw_biocore/genome_data/rat/rn5/rsem_ref.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 42956517 bwtLen: 42956518 sz: 10739130 bwtSz: 10739130 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1342392 offsSz: 5369568 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 95886 numSides: 191772 numLines: 191772 ebwtTotLen: 12273408 ebwtTotSz: 12273408 reverse: 0 Total time for call to driver() for forward index: 00:01:04 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 bmax according to bmaxDivN setting: 10739129 Using parameters --bmax 8054347 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 8054347 --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: 00:00:00 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: 00:00:04 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:03 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.36956e+06 (target: 8054346) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (8054347) 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 5926165 (Using difference cover) Sorting block time: 00:00:05 Returning block of 5926166 Getting block 2 of 8 Reserving size (8054347) 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 3573745 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3573746 Getting block 3 of 8 Reserving size (8054347) 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 6393666 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6393667 Getting block 4 of 8 Reserving size (8054347) 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 5918965 (Using difference cover) Sorting block time: 00:00:05 Returning block of 5918966 Getting block 5 of 8 Reserving size (8054347) 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 5059404 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5059405 Getting block 6 of 8 Reserving size (8054347) 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 7641407 (Using difference cover) Sorting block time: 00:00:07 Returning block of 7641408 Getting block 7 of 8 Reserving size (8054347) 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 2726915 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2726916 Getting block 8 of 8 Reserving size (8054347) 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 5716243 (Using difference cover) Sorting block time: 00:00:05 Returning block of 5716244 Exited Ebwt loop fchr[A]: 0 fchr[C]: 12569110 fchr[G]: 22831287 fchr[T]: 33169454 fchr[$]: 42956517 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 16970490 bytes to primary EBWT file: /share/data/umw_biocore/genome_data/rat/rn5/rsem_ref.rev.1.ebwt Wrote 5369572 bytes to secondary EBWT file: /share/data/umw_biocore/genome_data/rat/rn5/rsem_ref.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 42956517 bwtLen: 42956518 sz: 10739130 bwtSz: 10739130 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1342392 offsSz: 5369568 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 95886 numSides: 191772 numLines: 191772 ebwtTotLen: 12273408 ebwtTotSz: 12273408 reverse: 0 Total time for backward call to driver() for mirror index: 00:01:03