Settings: Output files: "Bur_0_R1//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: Bur_0_R1//tmp/segment_juncs.fa 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: 00:00:05 bmax according to bmaxDivN setting: 29530278 Using parameters --bmax 22147709 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 22147709 --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: 00:00:09 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:06 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: 00:00:07 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.47651e+07 (target: 22147708) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (22147709) 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 13190053 (Using difference cover) Sorting block time: 00:00:05 Returning block of 13190054 Getting block 2 of 8 Reserving size (22147709) 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 14501392 (Using difference cover) Sorting block time: 00:00:10 Returning block of 14501393 Getting block 3 of 8 Reserving size (22147709) 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 14608143 (Using difference cover) Sorting block time: 00:00:08 Returning block of 14608144 Getting block 4 of 8 Reserving size (22147709) 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 14429504 (Using difference cover) Sorting block time: 00:00:09 Returning block of 14429505 Getting block 5 of 8 Reserving size (22147709) 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 21465384 (Using difference cover) Sorting block time: 00:00:10 Returning block of 21465385 Getting block 6 of 8 Reserving size (22147709) 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 1814878 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1814879 Getting block 7 of 8 Reserving size (22147709) 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 21056740 (Using difference cover) Sorting block time: 00:00:08 Returning block of 21056741 Getting block 8 of 8 Reserving size (22147709) 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 17055013 (Using difference cover) Sorting block time: 00:00:07 Returning block of 17055014 Exited Ebwt loop fchr[A]: 0 fchr[C]: 34268424 fchr[G]: 58792880 fchr[T]: 83700927 fchr[$]: 118121114 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 209749838 bytes to primary EBWT file: Bur_0_R1//tmp/segment_juncs.1.ebwt Wrote 14765144 bytes to secondary EBWT file: Bur_0_R1//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 118121114 bwtLen: 118121115 sz: 29530279 bwtSz: 29530279 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3691285 offsSz: 14765140 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 263664 numSides: 527328 numLines: 527328 ebwtTotLen: 33748992 ebwtTotSz: 33748992 reverse: 0 Total time for call to driver() for forward index: 00:02:08 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: 00:00:05 bmax according to bmaxDivN setting: 29530278 Using parameters --bmax 22147709 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 22147709 --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: 00:00:01 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: 00:00:06 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.68744e+07 (target: 22147708) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (22147709) 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 18231174 (Using difference cover) Sorting block time: 00:00:08 Returning block of 18231175 Getting block 2 of 7 Reserving size (22147709) 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 19959598 (Using difference cover) Sorting block time: 00:00:08 Returning block of 19959599 Getting block 3 of 7 Reserving size (22147709) 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 15247020 (Using difference cover) Sorting block time: 00:00:07 Returning block of 15247021 Getting block 4 of 7 Reserving size (22147709) 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 19147178 (Using difference cover) Sorting block time: 00:00:08 Returning block of 19147179 Getting block 5 of 7 Reserving size (22147709) 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 11931167 (Using difference cover) Sorting block time: 00:00:05 Returning block of 11931168 Getting block 6 of 7 Reserving size (22147709) 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 19565371 (Using difference cover) Sorting block time: 00:00:08 Returning block of 19565372 Getting block 7 of 7 Reserving size (22147709) 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 14039600 (Using difference cover) Sorting block time: 00:00:05 Returning block of 14039601 Exited Ebwt loop fchr[A]: 0 fchr[C]: 34268424 fchr[G]: 58792880 fchr[T]: 83700927 fchr[$]: 118121114 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 209749838 bytes to primary EBWT file: Bur_0_R1//tmp/segment_juncs.rev.1.ebwt Wrote 14765144 bytes to secondary EBWT file: Bur_0_R1//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 118121114 bwtLen: 118121115 sz: 29530279 bwtSz: 29530279 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3691285 offsSz: 14765140 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 263664 numSides: 527328 numLines: 527328 ebwtTotLen: 33748992 ebwtTotSz: 33748992 reverse: 0 Total time for backward call to driver() for mirror index: 00:01:35