Settings: Output files: "MCLiverF1B/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: MCLiverF1B/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: 4933578 Using parameters --bmax 3700184 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3700184 --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: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 7; iterating... 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 Avg bucket size: 2.81919e+06 (target: 3700183) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3700184) 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 3232403 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3232404 Getting block 2 of 7 Reserving size (3700184) 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 2955342 (Using difference cover) Sorting block time: 00:00:04 Returning block of 2955343 Getting block 3 of 7 Reserving size (3700184) 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 2512727 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2512728 Getting block 4 of 7 Reserving size (3700184) 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 2730882 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2730883 Getting block 5 of 7 Reserving size (3700184) 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 3618060 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3618061 Getting block 6 of 7 Reserving size (3700184) 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 1603891 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1603892 Getting block 7 of 7 Reserving size (3700184) 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 3081001 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3081002 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5004663 fchr[G]: 9769391 fchr[T]: 14310835 fchr[$]: 19734312 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 36238636 bytes to primary EBWT file: MCLiverF1B/tmp/segment_juncs.1.bt2 Wrote 4933584 bytes to secondary EBWT file: MCLiverF1B/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19734312 bwtLen: 19734313 sz: 4933578 bwtSz: 4933579 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1233395 offsSz: 4933580 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 102783 numLines: 102783 ebwtTotLen: 6578112 ebwtTotSz: 6578112 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:29 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: 4933578 Using parameters --bmax 3700184 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3700184 --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 Avg bucket size: 3.28905e+06 (target: 3700183) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (3700184) 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 3609335 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3609336 Getting block 2 of 6 Reserving size (3700184) 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 3101809 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3101810 Getting block 3 of 6 Reserving size (3700184) 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 3345537 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3345538 Getting block 4 of 6 Reserving size (3700184) 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 3115536 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3115537 Getting block 5 of 6 Reserving size (3700184) 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 3662922 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3662923 Getting block 6 of 6 Reserving size (3700184) 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 2899168 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2899169 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5004663 fchr[G]: 9769391 fchr[T]: 14310835 fchr[$]: 19734312 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 36238636 bytes to primary EBWT file: MCLiverF1B/tmp/segment_juncs.rev.1.bt2 Wrote 4933584 bytes to secondary EBWT file: MCLiverF1B/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19734312 bwtLen: 19734313 sz: 4933578 bwtSz: 4933579 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1233395 offsSz: 4933580 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 102783 numLines: 102783 ebwtTotLen: 6578112 ebwtTotSz: 6578112 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:28