Settings: Output files: "MCBrainF1B/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: MCBrainF1B/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: 4393777 Using parameters --bmax 3295333 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3295333 --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 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 Split 1, merged 2; 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 Split 1, merged 1; 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: 2.19689e+06 (target: 3295332) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3295333) 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 2616438 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2616439 Getting block 2 of 8 Reserving size (3295333) 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 3172828 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3172829 Getting block 3 of 8 Reserving size (3295333) 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 1310362 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1310363 Getting block 4 of 8 Reserving size (3295333) 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 2016203 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2016204 Getting block 5 of 8 Reserving size (3295333) 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 1872333 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1872334 Getting block 6 of 8 Reserving size (3295333) 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 3277177 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3277178 Getting block 7 of 8 Reserving size (3295333) 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 898249 (Using difference cover) Sorting block time: 00:00:00 Returning block of 898250 Getting block 8 of 8 Reserving size (3295333) 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 2411514 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2411515 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4233187 fchr[G]: 8791287 fchr[T]: 13185090 fchr[$]: 17575111 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 32846572 bytes to primary EBWT file: MCBrainF1B/tmp/segment_juncs.1.bt2 Wrote 4393784 bytes to secondary EBWT file: MCBrainF1B/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17575111 bwtLen: 17575112 sz: 4393778 bwtSz: 4393778 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1098445 offsSz: 4393780 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 91538 numLines: 91538 ebwtTotLen: 5858432 ebwtTotSz: 5858432 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:15 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: 4393777 Using parameters --bmax 3295333 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3295333 --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 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: 00:00:01 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.19689e+06 (target: 3295332) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3295333) 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 1866534 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1866535 Getting block 2 of 8 Reserving size (3295333) 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 3258438 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3258439 Getting block 3 of 8 Reserving size (3295333) 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 3274655 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3274656 Getting block 4 of 8 Reserving size (3295333) 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 708979 (Using difference cover) Sorting block time: 00:00:00 Returning block of 708980 Getting block 5 of 8 Reserving size (3295333) 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 2665516 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2665517 Getting block 6 of 8 Reserving size (3295333) 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 1830853 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1830854 Getting block 7 of 8 Reserving size (3295333) 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 3103037 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3103038 Getting block 8 of 8 Reserving size (3295333) 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 867092 (Using difference cover) Sorting block time: 00:00:00 Returning block of 867093 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4233187 fchr[G]: 8791287 fchr[T]: 13185090 fchr[$]: 17575111 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 32846572 bytes to primary EBWT file: MCBrainF1B/tmp/segment_juncs.rev.1.bt2 Wrote 4393784 bytes to secondary EBWT file: MCBrainF1B/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17575111 bwtLen: 17575112 sz: 4393778 bwtSz: 4393778 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1098445 offsSz: 4393780 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 91538 numLines: 91538 ebwtTotLen: 5858432 ebwtTotSz: 5858432 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:15