Settings: Output files: "MCMuscle18b/tmp/segment_juncs.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) 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: MCMuscle18b/tmp/segment_juncs.fa 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: 00:00:00 bmax according to bmaxDivN setting: 3218709 Using parameters --bmax 2414032 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2414032 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:01 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: 00:00:00 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: 00:00:00 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: 00:00:01 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.83926e+06 (target: 2414031) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2414032) 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: 00:00:00 Sorting block of length 2359499 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2359500 Getting block 2 of 7 Reserving size (2414032) 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: 00:00:00 Sorting block of length 2111949 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2111950 Getting block 3 of 7 Reserving size (2414032) 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: 00:00:00 Sorting block of length 1657991 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1657992 Getting block 4 of 7 Reserving size (2414032) 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: 00:00:00 Sorting block of length 1757510 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1757511 Getting block 5 of 7 Reserving size (2414032) 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: 00:00:00 Sorting block of length 2039802 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2039803 Getting block 6 of 7 Reserving size (2414032) 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: 00:00:00 Sorting block of length 563636 (Using difference cover) Sorting block time: 00:00:00 Returning block of 563637 Getting block 7 of 7 Reserving size (2414032) 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 2384443 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2384444 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3113147 fchr[G]: 6457792 fchr[T]: 9674652 fchr[$]: 12874836 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 25179136 bytes to primary EBWT file: MCMuscle18b/tmp/segment_juncs.1.bt2 Wrote 3218716 bytes to secondary EBWT file: MCMuscle18b/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 12874836 bwtLen: 12874837 sz: 3218709 bwtSz: 3218710 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 804678 offsSz: 3218712 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 67057 numLines: 67057 ebwtTotLen: 4291648 ebwtTotSz: 4291648 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:11 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 3218709 Using parameters --bmax 2414032 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2414032 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 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: 00:00:00 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 5; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.60935e+06 (target: 2414031) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2414032) 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: 00:00:00 Sorting block of length 1807524 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1807525 Getting block 2 of 8 Reserving size (2414032) 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: 00:00:00 Sorting block of length 2106549 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2106550 Getting block 3 of 8 Reserving size (2414032) 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: 00:00:00 Sorting block of length 834706 (Using difference cover) Sorting block time: 00:00:00 Returning block of 834707 Getting block 4 of 8 Reserving size (2414032) 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 2235519 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2235520 Getting block 5 of 8 Reserving size (2414032) 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: 00:00:00 Sorting block of length 1122595 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1122596 Getting block 6 of 8 Reserving size (2414032) 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 2174688 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2174689 Getting block 7 of 8 Reserving size (2414032) 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 1843672 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1843673 Getting block 8 of 8 Reserving size (2414032) 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 749576 (Using difference cover) Sorting block time: 00:00:00 Returning block of 749577 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3113147 fchr[G]: 6457792 fchr[T]: 9674652 fchr[$]: 12874836 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 25179136 bytes to primary EBWT file: MCMuscle18b/tmp/segment_juncs.rev.1.bt2 Wrote 3218716 bytes to secondary EBWT file: MCMuscle18b/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 12874836 bwtLen: 12874837 sz: 3218709 bwtSz: 3218710 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 804678 offsSz: 3218712 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 67057 numLines: 67057 ebwtTotLen: 4291648 ebwtTotSz: 4291648 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:10