Settings: Output files: "MC_ThyroidF1B_/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: MC_ThyroidF1B_/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: 4593004 Using parameters --bmax 3444753 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3444753 --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 Avg bucket size: 2.2965e+06 (target: 3444752) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3444753) 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 2884325 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2884326 Getting block 2 of 8 Reserving size (3444753) 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 2083501 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2083502 Getting block 3 of 8 Reserving size (3444753) 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 3349531 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3349532 Getting block 4 of 8 Reserving size (3444753) 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 411529 (Using difference cover) Sorting block time: 00:00:01 Returning block of 411530 Getting block 5 of 8 Reserving size (3444753) 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 3177777 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3177778 Getting block 6 of 8 Reserving size (3444753) 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 2356968 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2356969 Getting block 7 of 8 Reserving size (3444753) 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 2662474 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2662475 Getting block 8 of 8 Reserving size (3444753) 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 1445904 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1445905 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4372653 fchr[G]: 9315280 fchr[T]: 13855935 fchr[$]: 18372016 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 34129240 bytes to primary EBWT file: MC_ThyroidF1B_/tmp/segment_juncs.1.bt2 Wrote 4593012 bytes to secondary EBWT file: MC_ThyroidF1B_/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18372016 bwtLen: 18372017 sz: 4593004 bwtSz: 4593005 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1148252 offsSz: 4593008 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 95688 numLines: 95688 ebwtTotLen: 6124032 ebwtTotSz: 6124032 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:18 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: 4593004 Using parameters --bmax 3444753 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3444753 --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 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: 2.62457e+06 (target: 3444752) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3444753) 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 3123523 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3123524 Getting block 2 of 7 Reserving size (3444753) 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 3368123 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3368124 Getting block 3 of 7 Reserving size (3444753) 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 2587085 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2587086 Getting block 4 of 7 Reserving size (3444753) 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 1657823 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1657824 Getting block 5 of 7 Reserving size (3444753) 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 3093270 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3093271 Getting block 6 of 7 Reserving size (3444753) 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 1400437 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1400438 Getting block 7 of 7 Reserving size (3444753) 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 3141749 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3141750 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4372653 fchr[G]: 9315280 fchr[T]: 13855935 fchr[$]: 18372016 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 34129240 bytes to primary EBWT file: MC_ThyroidF1B_/tmp/segment_juncs.rev.1.bt2 Wrote 4593012 bytes to secondary EBWT file: MC_ThyroidF1B_/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18372016 bwtLen: 18372017 sz: 4593004 bwtSz: 4593005 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1148252 offsSz: 4593008 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 95688 numLines: 95688 ebwtTotLen: 6124032 ebwtTotSz: 6124032 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:20