Settings: Output files: "/scratch/5678638.1.p/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/5678638.1.p/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: 2954068 Using parameters --bmax 2215551 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2215551 --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: 1.68804e+06 (target: 2215550) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2215551) 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 2092552 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2092553 Getting block 2 of 7 Reserving size (2215551) 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 1514993 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1514994 Getting block 3 of 7 Reserving size (2215551) 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 1550946 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1550947 Getting block 4 of 7 Reserving size (2215551) 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 2092104 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2092105 Getting block 5 of 7 Reserving size (2215551) 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 1383529 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1383530 Getting block 6 of 7 Reserving size (2215551) 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 1767597 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1767598 Getting block 7 of 7 Reserving size (2215551) 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 1414545 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1414546 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2962682 fchr[G]: 5893658 fchr[T]: 8826729 fchr[$]: 11816272 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23451653 bytes to primary EBWT file: /scratch/5678638.1.p/tophat2/tmp/segment_juncs.1.bt2 Wrote 2954076 bytes to secondary EBWT file: /scratch/5678638.1.p/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11816272 bwtLen: 11816273 sz: 2954068 bwtSz: 2954069 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 738518 offsSz: 2954072 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 61544 numLines: 61544 ebwtTotLen: 3938816 ebwtTotSz: 3938816 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:06 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: 2954068 Using parameters --bmax 2215551 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2215551 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:01 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 Split 1, merged 5; 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 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: 1.47703e+06 (target: 2215550) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2215551) 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 1785479 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1785480 Getting block 2 of 8 Reserving size (2215551) 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 646068 (Using difference cover) Sorting block time: 00:00:00 Returning block of 646069 Getting block 3 of 8 Reserving size (2215551) 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 2002928 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2002929 Getting block 4 of 8 Reserving size (2215551) 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 1662065 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1662066 Getting block 5 of 8 Reserving size (2215551) 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 1830032 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1830033 Getting block 6 of 8 Reserving size (2215551) 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 1395371 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1395372 Getting block 7 of 8 Reserving size (2215551) 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 862093 (Using difference cover) Sorting block time: 00:00:00 Returning block of 862094 Getting block 8 of 8 Reserving size (2215551) 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 1632229 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1632230 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2962682 fchr[G]: 5893658 fchr[T]: 8826729 fchr[$]: 11816272 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23451653 bytes to primary EBWT file: /scratch/5678638.1.p/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2954076 bytes to secondary EBWT file: /scratch/5678638.1.p/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11816272 bwtLen: 11816273 sz: 2954068 bwtSz: 2954069 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 738518 offsSz: 2954072 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 61544 numLines: 61544 ebwtTotLen: 3938816 ebwtTotSz: 3938816 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:06