Settings: Output files: "Mt_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: Mt_0_R1//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: 00:00:09 bmax according to bmaxDivN setting: 26695437 Using parameters --bmax 20021578 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 20021578 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:06 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: 00:00:13 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.52545e+07 (target: 20021577) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (20021578) 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 13213843 (Using difference cover) Sorting block time: 00:00:12 Returning block of 13213844 Getting block 2 of 7 Reserving size (20021578) 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 17130320 (Using difference cover) Sorting block time: 00:00:15 Returning block of 17130321 Getting block 3 of 7 Reserving size (20021578) 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 12978953 (Using difference cover) Sorting block time: 00:00:12 Returning block of 12978954 Getting block 4 of 7 Reserving size (20021578) 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 19117088 (Using difference cover) Sorting block time: 00:00:09 Returning block of 19117089 Getting block 5 of 7 Reserving size (20021578) 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 15167134 (Using difference cover) Sorting block time: 00:00:07 Returning block of 15167135 Getting block 6 of 7 Reserving size (20021578) 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 9863982 (Using difference cover) Sorting block time: 00:00:07 Returning block of 9863983 Getting block 7 of 7 Reserving size (20021578) 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 19310424 (Using difference cover) Sorting block time: 00:00:17 Returning block of 19310425 Exited Ebwt loop fchr[A]: 0 fchr[C]: 31076041 fchr[G]: 53267245 fchr[T]: 75606309 fchr[$]: 106781750 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 190006154 bytes to primary EBWT file: Mt_0_R1//tmp/segment_juncs.1.ebwt Wrote 13347724 bytes to secondary EBWT file: Mt_0_R1//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 106781750 bwtLen: 106781751 sz: 26695438 bwtSz: 26695438 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3336930 offsSz: 13347720 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 238353 numSides: 476706 numLines: 476706 ebwtTotLen: 30509184 ebwtTotSz: 30509184 reverse: 0 Total time for call to driver() for forward index: 00:02:46 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: 00:00:10 bmax according to bmaxDivN setting: 26695437 Using parameters --bmax 20021578 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 20021578 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:05 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: 00:00:10 Splitting and merging Splitting and merging time: 00:00:00 Split 1, 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 Avg bucket size: 1.52545e+07 (target: 20021577) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (20021578) 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 17314976 (Using difference cover) Sorting block time: 00:00:07 Returning block of 17314977 Getting block 2 of 7 Reserving size (20021578) 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 19762158 (Using difference cover) Sorting block time: 00:00:14 Returning block of 19762159 Getting block 3 of 7 Reserving size (20021578) 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 16828932 (Using difference cover) Sorting block time: 00:00:13 Returning block of 16828933 Getting block 4 of 7 Reserving size (20021578) 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 13381882 (Using difference cover) Sorting block time: 00:00:10 Returning block of 13381883 Getting block 5 of 7 Reserving size (20021578) 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 16709507 (Using difference cover) Sorting block time: 00:00:09 Returning block of 16709508 Getting block 6 of 7 Reserving size (20021578) 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 19844512 (Using difference cover) Sorting block time: 00:00:10 Returning block of 19844513 Getting block 7 of 7 Reserving size (20021578) 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 2939777 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2939778 Exited Ebwt loop fchr[A]: 0 fchr[C]: 31076041 fchr[G]: 53267245 fchr[T]: 75606309 fchr[$]: 106781750 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 190006154 bytes to primary EBWT file: Mt_0_R1//tmp/segment_juncs.rev.1.ebwt Wrote 13347724 bytes to secondary EBWT file: Mt_0_R1//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 106781750 bwtLen: 106781751 sz: 26695438 bwtSz: 26695438 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3336930 offsSz: 13347720 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 238353 numSides: 476706 numLines: 476706 ebwtTotLen: 30509184 ebwtTotSz: 30509184 reverse: 0 Total time for backward call to driver() for mirror index: 00:02:30