Settings: Output files: "/scratch/8792904.1.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/8792904.1.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: 00:00:01 bmax according to bmaxDivN setting: 2523425 Using parameters --bmax 1892569 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1892569 --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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.26171e+06 (target: 1892568) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1892569) 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 1775445 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1775446 Getting block 2 of 8 Reserving size (1892569) 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 1106176 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1106177 Getting block 3 of 8 Reserving size (1892569) 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 1243251 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1243252 Getting block 4 of 8 Reserving size (1892569) 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 1604980 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1604981 Getting block 5 of 8 Reserving size (1892569) 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 556822 (Using difference cover) Sorting block time: 00:00:00 Returning block of 556823 Getting block 6 of 8 Reserving size (1892569) 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 1408084 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1408085 Getting block 7 of 8 Reserving size (1892569) 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 997391 (Using difference cover) Sorting block time: 00:00:00 Returning block of 997392 Getting block 8 of 8 Reserving size (1892569) 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 1401544 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1401545 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2499214 fchr[G]: 5045373 fchr[T]: 7588156 fchr[$]: 10093700 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21184521 bytes to primary EBWT file: /scratch/8792904.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2523432 bytes to secondary EBWT file: /scratch/8792904.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10093700 bwtLen: 10093701 sz: 2523425 bwtSz: 2523426 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 630857 offsSz: 2523428 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52572 numLines: 52572 ebwtTotLen: 3364608 ebwtTotSz: 3364608 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: 2523425 Using parameters --bmax 1892569 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1892569 --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 2, merged 5; 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: 1.26171e+06 (target: 1892568) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1892569) 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 1559338 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1559339 Getting block 2 of 8 Reserving size (1892569) 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 1697057 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1697058 Getting block 3 of 8 Reserving size (1892569) 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 807077 (Using difference cover) Sorting block time: 00:00:00 Returning block of 807078 Getting block 4 of 8 Reserving size (1892569) 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 1621170 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1621171 Getting block 5 of 8 Reserving size (1892569) 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 711786 (Using difference cover) Sorting block time: 00:00:01 Returning block of 711787 Getting block 6 of 8 Reserving size (1892569) 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 1422729 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1422730 Getting block 7 of 8 Reserving size (1892569) 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 1649937 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1649938 Getting block 8 of 8 Reserving size (1892569) 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 624599 (Using difference cover) Sorting block time: 00:00:00 Returning block of 624600 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2499214 fchr[G]: 5045373 fchr[T]: 7588156 fchr[$]: 10093700 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21184521 bytes to primary EBWT file: /scratch/8792904.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2523432 bytes to secondary EBWT file: /scratch/8792904.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10093700 bwtLen: 10093701 sz: 2523425 bwtSz: 2523426 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 630857 offsSz: 2523428 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52572 numLines: 52572 ebwtTotLen: 3364608 ebwtTotSz: 3364608 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:08