Settings: Output files: "Rsch_4_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: Rsch_4_R1//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: 00:00:07 bmax according to bmaxDivN setting: 21914355 Using parameters --bmax 16435767 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 16435767 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:04 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: 1.25225e+07 (target: 16435766) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (16435767) 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 13207845 (Using difference cover) Sorting block time: 00:00:07 Returning block of 13207846 Getting block 2 of 7 Reserving size (16435767) 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 13116263 (Using difference cover) Sorting block time: 00:00:13 Returning block of 13116264 Getting block 3 of 7 Reserving size (16435767) 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 13713603 (Using difference cover) Sorting block time: 00:00:09 Returning block of 13713604 Getting block 4 of 7 Reserving size (16435767) 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 10689156 (Using difference cover) Sorting block time: 00:00:06 Returning block of 10689157 Getting block 5 of 7 Reserving size (16435767) 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 11072279 (Using difference cover) Sorting block time: 00:00:05 Returning block of 11072280 Getting block 6 of 7 Reserving size (16435767) 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 15435374 (Using difference cover) Sorting block time: 00:00:08 Returning block of 15435375 Getting block 7 of 7 Reserving size (16435767) 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 10422895 (Using difference cover) Sorting block time: 00:00:05 Returning block of 10422896 Exited Ebwt loop fchr[A]: 0 fchr[C]: 25404870 fchr[G]: 43596960 fchr[T]: 62135934 fchr[$]: 87657421 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 156710973 bytes to primary EBWT file: Rsch_4_R1//tmp/segment_juncs.1.ebwt Wrote 10957184 bytes to secondary EBWT file: Rsch_4_R1//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 87657421 bwtLen: 87657422 sz: 21914356 bwtSz: 21914356 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2739295 offsSz: 10957180 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 195664 numSides: 391328 numLines: 391328 ebwtTotLen: 25044992 ebwtTotSz: 25044992 reverse: 0 Total time for call to driver() for forward index: 00:01:47 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: 21914355 Using parameters --bmax 16435767 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 16435767 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:04 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: 00:00:01 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 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: 1.09572e+07 (target: 16435766) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (16435767) 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 15761580 (Using difference cover) Sorting block time: 00:00:09 Returning block of 15761581 Getting block 2 of 8 Reserving size (16435767) 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 10770202 (Using difference cover) Sorting block time: 00:00:05 Returning block of 10770203 Getting block 3 of 8 Reserving size (16435767) 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 9144231 (Using difference cover) Sorting block time: 00:00:04 Returning block of 9144232 Getting block 4 of 8 Reserving size (16435767) 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 8960207 (Using difference cover) Sorting block time: 00:00:04 Returning block of 8960208 Getting block 5 of 8 Reserving size (16435767) 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 12457972 (Using difference cover) Sorting block time: 00:00:05 Returning block of 12457973 Getting block 6 of 8 Reserving size (16435767) 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 13593892 (Using difference cover) Sorting block time: 00:00:06 Returning block of 13593893 Getting block 7 of 8 Reserving size (16435767) 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 11504173 (Using difference cover) Sorting block time: 00:00:05 Returning block of 11504174 Getting block 8 of 8 Reserving size (16435767) 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 5465157 (Using difference cover) Sorting block time: 00:00:03 Returning block of 5465158 Exited Ebwt loop fchr[A]: 0 fchr[C]: 25404870 fchr[G]: 43596960 fchr[T]: 62135934 fchr[$]: 87657421 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 156710973 bytes to primary EBWT file: Rsch_4_R1//tmp/segment_juncs.rev.1.ebwt Wrote 10957184 bytes to secondary EBWT file: Rsch_4_R1//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 87657421 bwtLen: 87657422 sz: 21914356 bwtSz: 21914356 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2739295 offsSz: 10957180 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 195664 numSides: 391328 numLines: 391328 ebwtTotLen: 25044992 ebwtTotSz: 25044992 reverse: 0 Total time for backward call to driver() for mirror index: 00:01:34