Settings: Output files: "CB_Heart_tp1/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_Heart_tp1/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: 3865159 Using parameters --bmax 2898870 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2898870 --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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.20866e+06 (target: 2898869) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2898870) 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 2044861 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2044862 Getting block 2 of 7 Reserving size (2898870) 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 2431704 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2431705 Getting block 3 of 7 Reserving size (2898870) 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 2569357 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2569358 Getting block 4 of 7 Reserving size (2898870) 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 2424523 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2424524 Getting block 5 of 7 Reserving size (2898870) 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 730277 (Using difference cover) Sorting block time: 00:00:00 Returning block of 730278 Getting block 6 of 7 Reserving size (2898870) 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 2498615 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2498616 Getting block 7 of 7 Reserving size (2898870) 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 2761296 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2761297 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3680944 fchr[G]: 7731350 fchr[T]: 11602060 fchr[$]: 15460639 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 29399544 bytes to primary EBWT file: CB_Heart_tp1/tmp/segment_juncs.1.bt2 Wrote 3865164 bytes to secondary EBWT file: CB_Heart_tp1/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 15460639 bwtLen: 15460640 sz: 3865160 bwtSz: 3865160 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 966290 offsSz: 3865160 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 80525 numLines: 80525 ebwtTotLen: 5153600 ebwtTotSz: 5153600 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:12 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: 3865159 Using parameters --bmax 2898870 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2898870 --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 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: 1.93258e+06 (target: 2898869) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2898870) 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 2351652 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2351653 Getting block 2 of 8 Reserving size (2898870) 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 2370463 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2370464 Getting block 3 of 8 Reserving size (2898870) 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 1318016 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1318017 Getting block 4 of 8 Reserving size (2898870) 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 1794220 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1794221 Getting block 5 of 8 Reserving size (2898870) 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 2515120 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2515121 Getting block 6 of 8 Reserving size (2898870) 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 2118940 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2118941 Getting block 7 of 8 Reserving size (2898870) 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 2298932 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2298933 Getting block 8 of 8 Reserving size (2898870) 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 693289 (Using difference cover) Sorting block time: 00:00:01 Returning block of 693290 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3680944 fchr[G]: 7731350 fchr[T]: 11602060 fchr[$]: 15460639 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 29399544 bytes to primary EBWT file: CB_Heart_tp1/tmp/segment_juncs.rev.1.bt2 Wrote 3865164 bytes to secondary EBWT file: CB_Heart_tp1/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 15460639 bwtLen: 15460640 sz: 3865160 bwtSz: 3865160 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 966290 offsSz: 3865160 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 80525 numLines: 80525 ebwtTotLen: 5153600 ebwtTotSz: 5153600 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:12