Settings: Output files: "/scratch/8793412.1.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/8793412.1.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: 2493375 Using parameters --bmax 1870032 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1870032 --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 Avg bucket size: 1.42478e+06 (target: 1870031) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1870032) 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 1606562 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1606563 Getting block 2 of 7 Reserving size (1870032) 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 966186 (Using difference cover) Sorting block time: 00:00:00 Returning block of 966187 Getting block 3 of 7 Reserving size (1870032) 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 1837011 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1837012 Getting block 4 of 7 Reserving size (1870032) 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 1462303 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1462304 Getting block 5 of 7 Reserving size (1870032) 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 996215 (Using difference cover) Sorting block time: 00:00:00 Returning block of 996216 Getting block 6 of 7 Reserving size (1870032) 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 1498951 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1498952 Getting block 7 of 7 Reserving size (1870032) 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 1606266 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1606267 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2475424 fchr[G]: 4984781 fchr[T]: 7494400 fchr[$]: 9973500 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 20978682 bytes to primary EBWT file: /scratch/8793412.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2493380 bytes to secondary EBWT file: /scratch/8793412.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 9973500 bwtLen: 9973501 sz: 2493375 bwtSz: 2493376 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 623344 offsSz: 2493376 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 51946 numLines: 51946 ebwtTotLen: 3324544 ebwtTotSz: 3324544 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:07 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 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 2493375 Using parameters --bmax 1870032 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1870032 --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 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: 1.24669e+06 (target: 1870031) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1870032) 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 1864844 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1864845 Getting block 2 of 8 Reserving size (1870032) 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 294175 (Using difference cover) Sorting block time: 00:00:00 Returning block of 294176 Getting block 3 of 8 Reserving size (1870032) 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 1857386 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1857387 Getting block 4 of 8 Reserving size (1870032) 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 1656111 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1656112 Getting block 5 of 8 Reserving size (1870032) 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 1574719 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1574720 Getting block 6 of 8 Reserving size (1870032) 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 784679 (Using difference cover) Sorting block time: 00:00:00 Returning block of 784680 Getting block 7 of 8 Reserving size (1870032) 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 1097289 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1097290 Getting block 8 of 8 Reserving size (1870032) 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 844290 (Using difference cover) Sorting block time: 00:00:00 Returning block of 844291 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2475424 fchr[G]: 4984781 fchr[T]: 7494400 fchr[$]: 9973500 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 20978682 bytes to primary EBWT file: /scratch/8793412.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2493380 bytes to secondary EBWT file: /scratch/8793412.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 9973500 bwtLen: 9973501 sz: 2493375 bwtSz: 2493376 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 623344 offsSz: 2493376 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 51946 numLines: 51946 ebwtTotLen: 3324544 ebwtTotSz: 3324544 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:09