Settings: Output files: "/scratch/9351451.1.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/9351451.1.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: 00:00:01 bmax according to bmaxDivN setting: 7672610 Using parameters --bmax 5754458 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 5754458 --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: 00:00:01 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: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 7; 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 0; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.8363e+06 (target: 5754457) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (5754458) 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 3292856 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3292857 Getting block 2 of 8 Reserving size (5754458) 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 5397597 (Using difference cover) Sorting block time: 00:00:05 Returning block of 5397598 Getting block 3 of 8 Reserving size (5754458) 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 1157913 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1157914 Getting block 4 of 8 Reserving size (5754458) 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 5117824 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5117825 Getting block 5 of 8 Reserving size (5754458) 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 4820082 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4820083 Getting block 6 of 8 Reserving size (5754458) 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 3186052 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3186053 Getting block 7 of 8 Reserving size (5754458) 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 4801118 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4801119 Getting block 8 of 8 Reserving size (5754458) 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 2916994 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2916995 Exited Ebwt loop fchr[A]: 0 fchr[C]: 7597675 fchr[G]: 15358323 fchr[T]: 22977148 fchr[$]: 30690443 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 54044139 bytes to primary EBWT file: /scratch/9351451.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 7672616 bytes to secondary EBWT file: /scratch/9351451.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 30690443 bwtLen: 30690444 sz: 7672611 bwtSz: 7672611 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1918153 offsSz: 7672612 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 159847 numLines: 159847 ebwtTotLen: 10230208 ebwtTotSz: 10230208 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:46 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: 7672610 Using parameters --bmax 5754458 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 5754458 --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: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 4.38435e+06 (target: 5754457) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (5754458) 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 3109893 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3109894 Getting block 2 of 7 Reserving size (5754458) 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 5682736 (Using difference cover) Sorting block time: 00:00:05 Returning block of 5682737 Getting block 3 of 7 Reserving size (5754458) 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 4655368 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4655369 Getting block 4 of 7 Reserving size (5754458) 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 3952701 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3952702 Getting block 5 of 7 Reserving size (5754458) 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 4537751 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4537752 Getting block 6 of 7 Reserving size (5754458) 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 5078625 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5078626 Getting block 7 of 7 Reserving size (5754458) 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 3673363 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3673364 Exited Ebwt loop fchr[A]: 0 fchr[C]: 7597675 fchr[G]: 15358323 fchr[T]: 22977148 fchr[$]: 30690443 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 54044139 bytes to primary EBWT file: /scratch/9351451.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 7672616 bytes to secondary EBWT file: /scratch/9351451.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 30690443 bwtLen: 30690444 sz: 7672611 bwtSz: 7672611 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1918153 offsSz: 7672612 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 159847 numLines: 159847 ebwtTotLen: 10230208 ebwtTotSz: 10230208 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:42