Settings: Output files: "Hi_0//tmp/segment_juncs.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) 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: Hi_0//tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:07 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:12 bmax according to bmaxDivN setting: 31852825 Using parameters --bmax 23889619 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 23889619 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:08 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: 00:00:03 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: 00:00:12 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: 00:00:10 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.82016e+07 (target: 23889618) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (23889619) 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: 00:00:03 Sorting block of length 18146476 (Using difference cover) Sorting block time: 00:00:16 Returning block of 18146477 Getting block 2 of 7 Reserving size (23889619) 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: 00:00:05 Sorting block of length 13452579 (Using difference cover) Sorting block time: 00:00:11 Returning block of 13452580 Getting block 3 of 7 Reserving size (23889619) 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: 00:00:02 Sorting block of length 19513734 (Using difference cover) Sorting block time: 00:00:14 Returning block of 19513735 Getting block 4 of 7 Reserving size (23889619) 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: 00:00:04 Sorting block of length 22649363 (Using difference cover) Sorting block time: 00:00:20 Returning block of 22649364 Getting block 5 of 7 Reserving size (23889619) 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: 00:00:03 Sorting block of length 14990866 (Using difference cover) Sorting block time: 00:00:08 Returning block of 14990867 Getting block 6 of 7 Reserving size (23889619) 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: 00:00:04 Sorting block of length 23242600 (Using difference cover) Sorting block time: 00:00:17 Returning block of 23242601 Getting block 7 of 7 Reserving size (23889619) 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: 00:00:03 Sorting block of length 15415677 (Using difference cover) Sorting block time: 00:00:10 Returning block of 15415678 Exited Ebwt loop fchr[A]: 0 fchr[C]: 39075025 fchr[G]: 63717789 fchr[T]: 88404082 fchr[$]: 127411301 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 225936499 bytes to primary EBWT file: Hi_0//tmp/segment_juncs.1.ebwt Wrote 15926420 bytes to secondary EBWT file: Hi_0//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 127411301 bwtLen: 127411302 sz: 31852826 bwtSz: 31852826 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3981604 offsSz: 15926416 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 284401 numSides: 568802 numLines: 568802 ebwtTotLen: 36403328 ebwtTotSz: 36403328 reverse: 0 Total time for call to driver() for forward index: 00:03:20 Reading reference sizes Time reading reference sizes: 00:00:04 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:07 bmax according to bmaxDivN setting: 31852825 Using parameters --bmax 23889619 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 23889619 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:03 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: 00:00:02 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: 00:00:13 Splitting and merging Splitting and merging time: 00:00:00 Split 3, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:14 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.12352e+07 (target: 23889618) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (23889619) 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: 00:00:03 Sorting block of length 22423552 (Using difference cover) Sorting block time: 00:00:16 Returning block of 22423553 Getting block 2 of 6 Reserving size (23889619) 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: 00:00:03 Sorting block of length 21680854 (Using difference cover) Sorting block time: 00:00:12 Returning block of 21680855 Getting block 3 of 6 Reserving size (23889619) 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: 00:00:03 Sorting block of length 23689820 (Using difference cover) Sorting block time: 00:00:18 Returning block of 23689821 Getting block 4 of 6 Reserving size (23889619) 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: 00:00:05 Sorting block of length 20609852 (Using difference cover) Sorting block time: 00:00:18 Returning block of 20609853 Getting block 5 of 6 Reserving size (23889619) 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: 00:00:06 Sorting block of length 19975181 (Using difference cover) Sorting block time: 00:00:21 Returning block of 19975182 Getting block 6 of 6 Reserving size (23889619) 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: 00:00:04 Sorting block of length 19032037 (Using difference cover) Sorting block time: 00:00:19 Returning block of 19032038 Exited Ebwt loop fchr[A]: 0 fchr[C]: 39075025 fchr[G]: 63717789 fchr[T]: 88404082 fchr[$]: 127411301 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 225936499 bytes to primary EBWT file: Hi_0//tmp/segment_juncs.rev.1.ebwt Wrote 15926420 bytes to secondary EBWT file: Hi_0//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 127411301 bwtLen: 127411302 sz: 31852826 bwtSz: 31852826 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3981604 offsSz: 15926416 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 284401 numSides: 568802 numLines: 568802 ebwtTotLen: 36403328 ebwtTotSz: 36403328 reverse: 0 Total time for backward call to driver() for mirror index: 00:03:22