Settings: Output files: "index/db.*.cf" Line rate: 7 (line is 128 bytes) Lines per side: 1 (side is 128 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Local offset rate: 3 (one in 8) Local fTable chars: 6 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: input/reference.fa 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: 00:00:00 bmax according to bmaxDivN setting: 202546 Using parameters --bmax 151910 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 151910 --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 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 115740 (target: 151909) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (151910) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: Getting block 2 of 7 Reserving size (151910) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 1: 10% bucket 2: 10% bucket 1: 20% bucket 2: 20% bucket 1: 30% bucket 2: 30% bucket 1: 40% bucket 1: 50% bucket 2: 40% bucket 1: 60% bucket 2: 50% bucket 1: 70% bucket 2: 60% bucket 1: 80% bucket 1: 90% bucket 2: 70% bucket 1: 100% Sorting block of length 109984 for bucket 1 (Using difference cover) bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 79486 for bucket 2 (Using difference cover) Sorting block time: 00:00:00 Returning block of 79487 for bucket 2 Getting block 3 of 7 Reserving size (151910) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% Sorting block time: 00:00:00 Returning block of 109985 for bucket 1 bucket 3: 50% bucket 3: 60% bucket 3: 70% Getting block 4 of 7 Reserving size (151910) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 3: 80% bucket 4: 10% bucket 3: 90% bucket 4: 20% bucket 3: 100% Sorting block of length 139734 for bucket 3 (Using difference cover) bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 131212 for bucket 4 (Using difference cover) Sorting block time: 00:00:00 Returning block of 139735 for bucket 3 Getting block 5 of 7 Reserving size (151910) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 10% Sorting block time: 00:00:00 Returning block of 131213 for bucket 4 bucket 5: 20% bucket 5: 30% bucket 5: 40% bucket 5: 50% Getting block 6 of 7 Reserving size (151910) for bucket 6 Calculating Z arrays for bucket 6 bucket 5: 60% Entering block accumulator loop for bucket 6: bucket 6: 10% bucket 5: 70% bucket 6: 20% bucket 5: 80% bucket 6: 30% bucket 5: 90% bucket 6: 40% bucket 5: 100% Sorting block of length 123163 for bucket 5 (Using difference cover) bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 144075 for bucket 6 (Using difference cover) Sorting block time: 00:00:01 Returning block of 123164 for bucket 5 Getting block 7 of 7 Reserving size (151910) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% Sorting block time: 00:00:01 Returning block of 144076 for bucket 6 bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 82524 for bucket 7 (Using difference cover) Sorting block time: 00:00:00 Returning block of 82525 for bucket 7 Exited Ebwt loop fchr[A]: 0 fchr[C]: 229251 fchr[G]: 454426 fchr[T]: 593137 fchr[$]: 810184 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 8666192 bytes to primary EBWT file: index/db.1.cf Wrote 101278 bytes to secondary EBWT file: index/db.2.cf Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 810184 bwtLen: 810185 sz: 202546 bwtSz: 202547 lineRate: 7 offRate: 4 offMask: 0xfffffffffffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 160 ftabLen: 1048577 ftabSz: 8388616 offsLen: 50637 offsSz: 405096 lineSz: 128 sideSz: 128 sideBwtSz: 96 sideBwtLen: 384 numSides: 2110 numLines: 2110 ebwtTotLen: 270080 ebwtTotSz: 270080 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:01:07