Settings: Output files: "/scratch/8793310.1.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/8793310.1.linga/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: 2666712 Using parameters --bmax 2000034 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2000034 --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 Avg bucket size: 1.52383e+06 (target: 2000033) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2000034) 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 1629607 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1629608 Getting block 2 of 7 Reserving size (2000034) 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 1688370 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1688371 Getting block 3 of 7 Reserving size (2000034) 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 1529600 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1529601 Getting block 4 of 7 Reserving size (2000034) 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 1284581 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1284582 Getting block 5 of 7 Reserving size (2000034) 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 1988197 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1988198 Getting block 6 of 7 Reserving size (2000034) 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 936519 (Using difference cover) Sorting block time: 00:00:01 Returning block of 936520 Getting block 7 of 7 Reserving size (2000034) 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 1609970 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1609971 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2651263 fchr[G]: 5325183 fchr[T]: 7990595 fchr[$]: 10666850 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22139252 bytes to primary EBWT file: /scratch/8793310.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2666720 bytes to secondary EBWT file: /scratch/8793310.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10666850 bwtLen: 10666851 sz: 2666713 bwtSz: 2666713 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 666679 offsSz: 2666716 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 55557 numLines: 55557 ebwtTotLen: 3555648 ebwtTotSz: 3555648 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: 2666712 Using parameters --bmax 2000034 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2000034 --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: 1.52383e+06 (target: 2000033) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2000034) 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 1096341 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1096342 Getting block 2 of 7 Reserving size (2000034) 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 1592622 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1592623 Getting block 3 of 7 Reserving size (2000034) 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 863676 (Using difference cover) Sorting block time: 00:00:00 Returning block of 863677 Getting block 4 of 7 Reserving size (2000034) 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 1852321 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1852322 Getting block 5 of 7 Reserving size (2000034) 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 1522340 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1522341 Getting block 6 of 7 Reserving size (2000034) 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 1988624 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1988625 Getting block 7 of 7 Reserving size (2000034) 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 1750920 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1750921 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2651263 fchr[G]: 5325183 fchr[T]: 7990595 fchr[$]: 10666850 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22139252 bytes to primary EBWT file: /scratch/8793310.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2666720 bytes to secondary EBWT file: /scratch/8793310.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10666850 bwtLen: 10666851 sz: 2666713 bwtSz: 2666713 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 666679 offsSz: 2666716 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 55557 numLines: 55557 ebwtTotLen: 3555648 ebwtTotSz: 3555648 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:08