Settings: Output files: "MCGut18b/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: MCGut18b/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: 5062824 Using parameters --bmax 3797118 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3797118 --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: 2.89304e+06 (target: 3797117) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3797118) 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 2143432 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2143433 Getting block 2 of 7 Reserving size (3797118) 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 2989269 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2989270 Getting block 3 of 7 Reserving size (3797118) 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 3226498 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3226499 Getting block 4 of 7 Reserving size (3797118) 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 3617674 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3617675 Getting block 5 of 7 Reserving size (3797118) 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 3630558 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3630559 Getting block 6 of 7 Reserving size (3797118) 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 2367562 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2367563 Getting block 7 of 7 Reserving size (3797118) 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 2276297 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2276298 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4876749 fchr[G]: 10121906 fchr[T]: 15153306 fchr[$]: 20251296 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37281853 bytes to primary EBWT file: MCGut18b/tmp/segment_juncs.1.bt2 Wrote 5062832 bytes to secondary EBWT file: MCGut18b/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20251296 bwtLen: 20251297 sz: 5062824 bwtSz: 5062825 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1265707 offsSz: 5062828 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 105476 numLines: 105476 ebwtTotLen: 6750464 ebwtTotSz: 6750464 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:18 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: 5062824 Using parameters --bmax 3797118 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3797118 --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: 00:00:01 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 Avg bucket size: 2.89304e+06 (target: 3797117) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3797118) 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 3460487 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3460488 Getting block 2 of 7 Reserving size (3797118) 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 3521610 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3521611 Getting block 3 of 7 Reserving size (3797118) 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 3536649 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3536650 Getting block 4 of 7 Reserving size (3797118) 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 2463301 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2463302 Getting block 5 of 7 Reserving size (3797118) 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 3269655 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3269656 Getting block 6 of 7 Reserving size (3797118) 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 2720668 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2720669 Getting block 7 of 7 Reserving size (3797118) 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 1278920 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1278921 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4876749 fchr[G]: 10121906 fchr[T]: 15153306 fchr[$]: 20251296 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37281853 bytes to primary EBWT file: MCGut18b/tmp/segment_juncs.rev.1.bt2 Wrote 5062832 bytes to secondary EBWT file: MCGut18b/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20251296 bwtLen: 20251297 sz: 5062824 bwtSz: 5062825 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1265707 offsSz: 5062828 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 105476 numLines: 105476 ebwtTotLen: 6750464 ebwtTotSz: 6750464 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:17