Settings: Output files: "CB_Spleen_tp172/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: CB_Spleen_tp172/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: 5053684 Using parameters --bmax 3790263 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3790263 --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: 00:00:01 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: 00:00:01 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: 2.88782e+06 (target: 3790262) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3790263) 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 3654371 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3654372 Getting block 2 of 7 Reserving size (3790263) 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 1369035 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1369036 Getting block 3 of 7 Reserving size (3790263) 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 3037533 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3037534 Getting block 4 of 7 Reserving size (3790263) 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 3254252 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3254253 Getting block 5 of 7 Reserving size (3790263) 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 3449564 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3449565 Getting block 6 of 7 Reserving size (3790263) 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 3253381 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3253382 Getting block 7 of 7 Reserving size (3790263) 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 2196594 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2196595 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4844917 fchr[G]: 10232473 fchr[T]: 15175586 fchr[$]: 20214736 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37285565 bytes to primary EBWT file: CB_Spleen_tp172/tmp/segment_juncs.1.bt2 Wrote 5053692 bytes to secondary EBWT file: CB_Spleen_tp172/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20214736 bwtLen: 20214737 sz: 5053684 bwtSz: 5053685 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1263422 offsSz: 5053688 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 105286 numLines: 105286 ebwtTotLen: 6738304 ebwtTotSz: 6738304 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:17 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: 5053684 Using parameters --bmax 3790263 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3790263 --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: 00:00:01 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.88782e+06 (target: 3790262) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3790263) 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 3213419 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3213420 Getting block 2 of 7 Reserving size (3790263) 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 3130057 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3130058 Getting block 3 of 7 Reserving size (3790263) 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 1485054 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1485055 Getting block 4 of 7 Reserving size (3790263) 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 3356345 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3356346 Getting block 5 of 7 Reserving size (3790263) 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 3738999 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3739000 Getting block 6 of 7 Reserving size (3790263) 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 2135567 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2135568 Getting block 7 of 7 Reserving size (3790263) 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 3155289 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3155290 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4844917 fchr[G]: 10232473 fchr[T]: 15175586 fchr[$]: 20214736 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37285565 bytes to primary EBWT file: CB_Spleen_tp172/tmp/segment_juncs.rev.1.bt2 Wrote 5053692 bytes to secondary EBWT file: CB_Spleen_tp172/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20214736 bwtLen: 20214737 sz: 5053684 bwtSz: 5053685 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1263422 offsSz: 5053688 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 105286 numLines: 105286 ebwtTotLen: 6738304 ebwtTotSz: 6738304 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:18