Settings: Output files: "Rsch_4//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//tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:09 bmax according to bmaxDivN setting: 42178986 Using parameters --bmax 31634240 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 31634240 --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: 00:00:02 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:04 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: 00:00:15 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: 00:00:11 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: 00:00:10 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.10895e+07 (target: 31634239) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (31634240) 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 23001048 (Using difference cover) Sorting block time: 00:00:18 Returning block of 23001049 Getting block 2 of 8 Reserving size (31634240) 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 24064722 (Using difference cover) Sorting block time: 00:00:22 Returning block of 24064723 Getting block 3 of 8 Reserving size (31634240) 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 13685566 (Using difference cover) Sorting block time: 00:00:12 Returning block of 13685567 Getting block 4 of 8 Reserving size (31634240) 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 24859023 (Using difference cover) Sorting block time: 00:00:23 Returning block of 24859024 Getting block 5 of 8 Reserving size (31634240) 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 30890821 (Using difference cover) Sorting block time: 00:00:24 Returning block of 30890822 Getting block 6 of 8 Reserving size (31634240) 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 15921291 (Using difference cover) Sorting block time: 00:00:11 Returning block of 15921292 Getting block 7 of 8 Reserving size (31634240) 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 30753360 (Using difference cover) Sorting block time: 00:00:31 Returning block of 30753361 Getting block 8 of 8 Reserving size (31634240) 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 5540106 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5540107 Exited Ebwt loop fchr[A]: 0 fchr[C]: 52254711 fchr[G]: 84337950 fchr[T]: 116501185 fchr[$]: 168715944 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 297772384 bytes to primary EBWT file: Rsch_4//tmp/segment_juncs.1.ebwt Wrote 21089500 bytes to secondary EBWT file: Rsch_4//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 168715944 bwtLen: 168715945 sz: 42178986 bwtSz: 42178987 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5272374 offsSz: 21089496 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 376599 numSides: 753198 numLines: 753198 ebwtTotLen: 48204672 ebwtTotSz: 48204672 reverse: 0 Total time for call to driver() for forward index: 00:04:43 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: 00:00:06 bmax according to bmaxDivN setting: 42178986 Using parameters --bmax 31634240 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 31634240 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:07 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: 00:00:14 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 5; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:16 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.10895e+07 (target: 31634239) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (31634240) 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 25219801 (Using difference cover) Sorting block time: 00:00:22 Returning block of 25219802 Getting block 2 of 8 Reserving size (31634240) 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 12612305 (Using difference cover) Sorting block time: 00:00:17 Returning block of 12612306 Getting block 3 of 8 Reserving size (31634240) 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 22019774 (Using difference cover) Sorting block time: 00:00:26 Returning block of 22019775 Getting block 4 of 8 Reserving size (31634240) 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 24486066 (Using difference cover) Sorting block time: 00:00:37 Returning block of 24486067 Getting block 5 of 8 Reserving size (31634240) 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: 00:00:07 Sorting block of length 28213518 (Using difference cover) Sorting block time: 00:00:35 Returning block of 28213519 Getting block 6 of 8 Reserving size (31634240) 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: 00:00:08 Sorting block of length 22544452 (Using difference cover) Sorting block time: 00:00:27 Returning block of 22544453 Getting block 7 of 8 Reserving size (31634240) 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: 00:00:08 Sorting block of length 31018505 (Using difference cover) Sorting block time: 00:00:42 Returning block of 31018506 Getting block 8 of 8 Reserving size (31634240) 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 2601516 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2601517 Exited Ebwt loop fchr[A]: 0 fchr[C]: 52254711 fchr[G]: 84337950 fchr[T]: 116501185 fchr[$]: 168715944 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 297772384 bytes to primary EBWT file: Rsch_4//tmp/segment_juncs.rev.1.ebwt Wrote 21089500 bytes to secondary EBWT file: Rsch_4//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 168715944 bwtLen: 168715945 sz: 42178986 bwtSz: 42178987 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5272374 offsSz: 21089496 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 376599 numSides: 753198 numLines: 753198 ebwtTotLen: 48204672 ebwtTotSz: 48204672 reverse: 0 Total time for backward call to driver() for mirror index: 00:06:04