Settings: Output files: "Rsch_4_R2//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: Rsch_4_R2//tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:03 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:04 bmax according to bmaxDivN setting: 27157790 Using parameters --bmax 20368343 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 20368343 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:02 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: 00:00:07 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: 00:00:08 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.55187e+07 (target: 20368342) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (20368343) 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 15052675 (Using difference cover) Sorting block time: 00:00:09 Returning block of 15052676 Getting block 2 of 7 Reserving size (20368343) 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 17667661 (Using difference cover) Sorting block time: 00:00:10 Returning block of 17667662 Getting block 3 of 7 Reserving size (20368343) 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 10253813 (Using difference cover) Sorting block time: 00:00:04 Returning block of 10253814 Getting block 4 of 7 Reserving size (20368343) 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 16285082 (Using difference cover) Sorting block time: 00:00:09 Returning block of 16285083 Getting block 5 of 7 Reserving size (20368343) 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 13962887 (Using difference cover) Sorting block time: 00:00:07 Returning block of 13962888 Getting block 6 of 7 Reserving size (20368343) 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 17446759 (Using difference cover) Sorting block time: 00:00:09 Returning block of 17446760 Getting block 7 of 7 Reserving size (20368343) 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 17962278 (Using difference cover) Sorting block time: 00:00:07 Returning block of 17962279 Exited Ebwt loop fchr[A]: 0 fchr[C]: 31579109 fchr[G]: 54143493 fchr[T]: 76939410 fchr[$]: 108631161 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 193231718 bytes to primary EBWT file: Rsch_4_R2//tmp/segment_juncs.1.ebwt Wrote 13578900 bytes to secondary EBWT file: Rsch_4_R2//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 108631161 bwtLen: 108631162 sz: 27157791 bwtSz: 27157791 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3394724 offsSz: 13578896 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 242481 numSides: 484962 numLines: 484962 ebwtTotLen: 31037568 ebwtTotSz: 31037568 reverse: 0 Total time for call to driver() for forward index: 00:01:55 Reading reference sizes Time reading reference sizes: 00:00:02 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:04 bmax according to bmaxDivN setting: 27157790 Using parameters --bmax 20368343 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 20368343 --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: 00:00:00 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: 00:00:08 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.81052e+07 (target: 20368342) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (20368343) 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 19969908 (Using difference cover) Sorting block time: 00:00:09 Returning block of 19969909 Getting block 2 of 6 Reserving size (20368343) 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 17969542 (Using difference cover) Sorting block time: 00:00:07 Returning block of 17969543 Getting block 3 of 6 Reserving size (20368343) 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 19202400 (Using difference cover) Sorting block time: 00:00:06 Returning block of 19202401 Getting block 4 of 6 Reserving size (20368343) 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 18122151 (Using difference cover) Sorting block time: 00:00:07 Returning block of 18122152 Getting block 5 of 6 Reserving size (20368343) 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 14105056 (Using difference cover) Sorting block time: 00:00:06 Returning block of 14105057 Getting block 6 of 6 Reserving size (20368343) 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 19262099 (Using difference cover) Sorting block time: 00:00:07 Returning block of 19262100 Exited Ebwt loop fchr[A]: 0 fchr[C]: 31579109 fchr[G]: 54143493 fchr[T]: 76939410 fchr[$]: 108631161 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 193231718 bytes to primary EBWT file: Rsch_4_R2//tmp/segment_juncs.rev.1.ebwt Wrote 13578900 bytes to secondary EBWT file: Rsch_4_R2//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 108631161 bwtLen: 108631162 sz: 27157791 bwtSz: 27157791 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3394724 offsSz: 13578896 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 242481 numSides: 484962 numLines: 484962 ebwtTotLen: 31037568 ebwtTotSz: 31037568 reverse: 0 Total time for backward call to driver() for mirror index: 00:01:27