Settings: Output files: "/scratch/8793030.1.linga/tophat2/tmp/segment_juncs.*.bt2" 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 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: /scratch/8793030.1.linga/tophat2/tmp/segment_juncs.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: 00:00:00 bmax according to bmaxDivN setting: 2521150 Using parameters --bmax 1890863 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1890863 --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: 00:00:01 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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.68077e+06 (target: 1890862) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (1890863) 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 1884738 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1884739 Getting block 2 of 6 Reserving size (1890863) 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 1595451 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1595452 Getting block 3 of 6 Reserving size (1890863) 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 1842929 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1842930 Getting block 4 of 6 Reserving size (1890863) 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 1268518 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1268519 Getting block 5 of 6 Reserving size (1890863) 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 1690455 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1690456 Getting block 6 of 6 Reserving size (1890863) 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 1802504 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1802505 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2504354 fchr[G]: 5036043 fchr[T]: 7568292 fchr[$]: 10084600 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21164005 bytes to primary EBWT file: /scratch/8793030.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2521156 bytes to secondary EBWT file: /scratch/8793030.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10084600 bwtLen: 10084601 sz: 2521150 bwtSz: 2521151 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 630288 offsSz: 2521152 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52524 numLines: 52524 ebwtTotLen: 3361536 ebwtTotSz: 3361536 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:08 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 reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 2521150 Using parameters --bmax 1890863 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1890863 --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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.26057e+06 (target: 1890862) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1890863) 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 1456245 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1456246 Getting block 2 of 8 Reserving size (1890863) 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 1388373 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1388374 Getting block 3 of 8 Reserving size (1890863) 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 1206245 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1206246 Getting block 4 of 8 Reserving size (1890863) 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 1186682 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1186683 Getting block 5 of 8 Reserving size (1890863) 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 1109862 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1109863 Getting block 6 of 8 Reserving size (1890863) 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 1571509 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1571510 Getting block 7 of 8 Reserving size (1890863) 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 1868719 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1868720 Getting block 8 of 8 Reserving size (1890863) 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 296958 (Using difference cover) Sorting block time: 00:00:00 Returning block of 296959 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2504354 fchr[G]: 5036043 fchr[T]: 7568292 fchr[$]: 10084600 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21164005 bytes to primary EBWT file: /scratch/8793030.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2521156 bytes to secondary EBWT file: /scratch/8793030.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10084600 bwtLen: 10084601 sz: 2521150 bwtSz: 2521151 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 630288 offsSz: 2521152 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52524 numLines: 52524 ebwtTotLen: 3361536 ebwtTotSz: 3361536 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:08