Settings: Output files: "/scratch/8793238.1.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/8793238.1.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: 2847400 Using parameters --bmax 2135550 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2135550 --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 Split 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.4237e+06 (target: 2135549) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2135550) 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 1883357 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1883358 Getting block 2 of 8 Reserving size (2135550) 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 1751090 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1751091 Getting block 3 of 8 Reserving size (2135550) 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 1689344 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1689345 Getting block 4 of 8 Reserving size (2135550) 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 1212018 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1212019 Getting block 5 of 8 Reserving size (2135550) 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 1819400 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1819401 Getting block 6 of 8 Reserving size (2135550) 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 577481 (Using difference cover) Sorting block time: 00:00:00 Returning block of 577482 Getting block 7 of 8 Reserving size (2135550) 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 2062720 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2062721 Getting block 8 of 8 Reserving size (2135550) 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 394183 (Using difference cover) Sorting block time: 00:00:00 Returning block of 394184 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2839002 fchr[G]: 5682302 fchr[T]: 8523398 fchr[$]: 11389600 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23356470 bytes to primary EBWT file: /scratch/8793238.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2847408 bytes to secondary EBWT file: /scratch/8793238.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11389600 bwtLen: 11389601 sz: 2847400 bwtSz: 2847401 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 711851 offsSz: 2847404 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 59321 numLines: 59321 ebwtTotLen: 3796544 ebwtTotSz: 3796544 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:11 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: 2847400 Using parameters --bmax 2135550 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2135550 --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: 1.4237e+06 (target: 2135549) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2135550) 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 2105355 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2105356 Getting block 2 of 8 Reserving size (2135550) 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 653853 (Using difference cover) Sorting block time: 00:00:01 Returning block of 653854 Getting block 3 of 8 Reserving size (2135550) 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 1765522 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1765523 Getting block 4 of 8 Reserving size (2135550) 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 641834 (Using difference cover) Sorting block time: 00:00:00 Returning block of 641835 Getting block 5 of 8 Reserving size (2135550) 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 1566445 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1566446 Getting block 6 of 8 Reserving size (2135550) 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 897144 (Using difference cover) Sorting block time: 00:00:01 Returning block of 897145 Getting block 7 of 8 Reserving size (2135550) 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 1968663 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1968664 Getting block 8 of 8 Reserving size (2135550) 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 1790777 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1790778 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2839002 fchr[G]: 5682302 fchr[T]: 8523398 fchr[$]: 11389600 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23356470 bytes to primary EBWT file: /scratch/8793238.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2847408 bytes to secondary EBWT file: /scratch/8793238.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11389600 bwtLen: 11389601 sz: 2847400 bwtSz: 2847401 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 711851 offsSz: 2847404 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 59321 numLines: 59321 ebwtTotLen: 3796544 ebwtTotSz: 3796544 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:10