Settings: Output files: "/scratch/8793333.1.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/8793333.1.linga/tophat2/tmp/segment_juncs.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: 00:00:00 bmax according to bmaxDivN setting: 2554175 Using parameters --bmax 1915632 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1915632 --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 1, merged 7; 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 Avg bucket size: 1.45953e+06 (target: 1915631) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1915632) 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 1820239 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1820240 Getting block 2 of 7 Reserving size (1915632) 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 1880901 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1880902 Getting block 3 of 7 Reserving size (1915632) 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 1709936 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1709937 Getting block 4 of 7 Reserving size (1915632) 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 1003805 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1003806 Getting block 5 of 7 Reserving size (1915632) 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 1877120 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1877121 Getting block 6 of 7 Reserving size (1915632) 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 1607254 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1607255 Getting block 7 of 7 Reserving size (1915632) 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 317439 (Using difference cover) Sorting block time: 00:00:00 Returning block of 317440 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2538715 fchr[G]: 5104105 fchr[T]: 7665378 fchr[$]: 10216700 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21384364 bytes to primary EBWT file: /scratch/8793333.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2554180 bytes to secondary EBWT file: /scratch/8793333.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10216700 bwtLen: 10216701 sz: 2554175 bwtSz: 2554176 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 638544 offsSz: 2554176 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 53212 numLines: 53212 ebwtTotLen: 3405568 ebwtTotSz: 3405568 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: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 2554175 Using parameters --bmax 1915632 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1915632 --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 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.27709e+06 (target: 1915631) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1915632) 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 1271152 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1271153 Getting block 2 of 8 Reserving size (1915632) 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 1635331 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1635332 Getting block 3 of 8 Reserving size (1915632) 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 1312643 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1312644 Getting block 4 of 8 Reserving size (1915632) 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 874054 (Using difference cover) Sorting block time: 00:00:00 Returning block of 874055 Getting block 5 of 8 Reserving size (1915632) 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 1582906 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1582907 Getting block 6 of 8 Reserving size (1915632) 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 1497716 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1497717 Getting block 7 of 8 Reserving size (1915632) 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 648201 (Using difference cover) Sorting block time: 00:00:00 Returning block of 648202 Getting block 8 of 8 Reserving size (1915632) 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 1394690 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1394691 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2538715 fchr[G]: 5104105 fchr[T]: 7665378 fchr[$]: 10216700 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21384364 bytes to primary EBWT file: /scratch/8793333.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2554180 bytes to secondary EBWT file: /scratch/8793333.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10216700 bwtLen: 10216701 sz: 2554175 bwtSz: 2554176 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 638544 offsSz: 2554176 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 53212 numLines: 53212 ebwtTotLen: 3405568 ebwtTotSz: 3405568 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:09