Settings: Output files: "IRThyroid05F1C1/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: IRThyroid05F1C1/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: 5231070 Using parameters --bmax 3923303 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3923303 --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 Avg bucket size: 2.98918e+06 (target: 3923302) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3923303) 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 3222411 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3222412 Getting block 2 of 7 Reserving size (3923303) 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 3708830 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3708831 Getting block 3 of 7 Reserving size (3923303) 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 2053408 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2053409 Getting block 4 of 7 Reserving size (3923303) 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 2828659 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2828660 Getting block 5 of 7 Reserving size (3923303) 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 2691384 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2691385 Getting block 6 of 7 Reserving size (3923303) 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 3448681 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3448682 Getting block 7 of 7 Reserving size (3923303) 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 2970901 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2970902 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4941827 fchr[G]: 10530883 fchr[T]: 15733773 fchr[$]: 20924280 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 38359178 bytes to primary EBWT file: IRThyroid05F1C1/tmp/segment_juncs.1.bt2 Wrote 5231076 bytes to secondary EBWT file: IRThyroid05F1C1/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20924280 bwtLen: 20924281 sz: 5231070 bwtSz: 5231071 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1307768 offsSz: 5231072 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 108981 numLines: 108981 ebwtTotLen: 6974784 ebwtTotSz: 6974784 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:20 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: 00:00:01 bmax according to bmaxDivN setting: 5231070 Using parameters --bmax 3923303 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3923303 --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: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Split 2, 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: 2.61553e+06 (target: 3923302) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3923303) 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 2091262 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2091263 Getting block 2 of 8 Reserving size (3923303) 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 3282522 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3282523 Getting block 3 of 8 Reserving size (3923303) 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 2801177 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2801178 Getting block 4 of 8 Reserving size (3923303) 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 1766323 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1766324 Getting block 5 of 8 Reserving size (3923303) 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 3507572 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3507573 Getting block 6 of 8 Reserving size (3923303) 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 935866 (Using difference cover) Sorting block time: 00:00:01 Returning block of 935867 Getting block 7 of 8 Reserving size (3923303) 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 3005611 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3005612 Getting block 8 of 8 Reserving size (3923303) 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 3533940 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3533941 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4941827 fchr[G]: 10530883 fchr[T]: 15733773 fchr[$]: 20924280 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 38359178 bytes to primary EBWT file: IRThyroid05F1C1/tmp/segment_juncs.rev.1.bt2 Wrote 5231076 bytes to secondary EBWT file: IRThyroid05F1C1/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20924280 bwtLen: 20924281 sz: 5231070 bwtSz: 5231071 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1307768 offsSz: 5231072 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 108981 numLines: 108981 ebwtTotLen: 6974784 ebwtTotSz: 6974784 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:23