Settings: Output files: "MCKidneyB2C/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: MCKidneyB2C/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: 00:00:01 bmax according to bmaxDivN setting: 4339254 Using parameters --bmax 3254441 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3254441 --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: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.47957e+06 (target: 3254440) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3254441) 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 2762126 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2762127 Getting block 2 of 7 Reserving size (3254441) 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 2150701 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2150702 Getting block 3 of 7 Reserving size (3254441) 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 3040726 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3040727 Getting block 4 of 7 Reserving size (3254441) 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 3181329 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3181330 Getting block 5 of 7 Reserving size (3254441) 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 1986807 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1986808 Getting block 6 of 7 Reserving size (3254441) 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 3162755 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3162756 Getting block 7 of 7 Reserving size (3254441) 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 1072569 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1072570 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4200499 fchr[G]: 8701584 fchr[T]: 12997457 fchr[$]: 17357019 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 32491795 bytes to primary EBWT file: MCKidneyB2C/tmp/segment_juncs.1.bt2 Wrote 4339260 bytes to secondary EBWT file: MCKidneyB2C/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17357019 bwtLen: 17357020 sz: 4339255 bwtSz: 4339255 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1084814 offsSz: 4339256 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 90402 numLines: 90402 ebwtTotLen: 5785728 ebwtTotSz: 5785728 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:13 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 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 4339254 Using parameters --bmax 3254441 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3254441 --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: 00:00:01 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 Avg bucket size: 2.16963e+06 (target: 3254440) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3254441) 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 2471402 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2471403 Getting block 2 of 8 Reserving size (3254441) 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 2851947 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2851948 Getting block 3 of 8 Reserving size (3254441) 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 2430421 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2430422 Getting block 4 of 8 Reserving size (3254441) 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 936667 (Using difference cover) Sorting block time: 00:00:00 Returning block of 936668 Getting block 5 of 8 Reserving size (3254441) 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 2730856 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2730857 Getting block 6 of 8 Reserving size (3254441) 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 2289089 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2289090 Getting block 7 of 8 Reserving size (3254441) 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 1603605 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1603606 Getting block 8 of 8 Reserving size (3254441) 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 2043025 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2043026 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4200499 fchr[G]: 8701584 fchr[T]: 12997457 fchr[$]: 17357019 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 32491795 bytes to primary EBWT file: MCKidneyB2C/tmp/segment_juncs.rev.1.bt2 Wrote 4339260 bytes to secondary EBWT file: MCKidneyB2C/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17357019 bwtLen: 17357020 sz: 4339255 bwtSz: 4339255 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1084814 offsSz: 4339256 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 90402 numLines: 90402 ebwtTotLen: 5785728 ebwtTotSz: 5785728 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:13