Settings: Output files: "4M-HS/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: 4M-HS/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: 3708042 Using parameters --bmax 2781032 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2781032 --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 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: 2.11888e+06 (target: 2781031) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2781032) 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 2558761 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2558762 Getting block 2 of 7 Reserving size (2781032) 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 2546844 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2546845 Getting block 3 of 7 Reserving size (2781032) 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 1636511 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1636512 Getting block 4 of 7 Reserving size (2781032) 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 1654403 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1654404 Getting block 5 of 7 Reserving size (2781032) 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 2670188 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2670189 Getting block 6 of 7 Reserving size (2781032) 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 2727255 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2727256 Getting block 7 of 7 Reserving size (2781032) 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 1038201 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1038202 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4296828 fchr[G]: 7474300 fchr[T]: 10483776 fchr[$]: 14832169 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 27395813 bytes to primary EBWT file: 4M-HS/tmp/segment_juncs.1.bt2 Wrote 3708048 bytes to secondary EBWT file: 4M-HS/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 14832169 bwtLen: 14832170 sz: 3708043 bwtSz: 3708043 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 927011 offsSz: 3708044 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 77251 numLines: 77251 ebwtTotLen: 4944064 ebwtTotSz: 4944064 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:15 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: 3708042 Using parameters --bmax 2781032 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2781032 --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 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: 2.11888e+06 (target: 2781031) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2781032) 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 1955760 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1955761 Getting block 2 of 7 Reserving size (2781032) 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 1719808 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1719809 Getting block 3 of 7 Reserving size (2781032) 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 1699769 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1699770 Getting block 4 of 7 Reserving size (2781032) 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 2278057 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2278058 Getting block 5 of 7 Reserving size (2781032) 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 2752193 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2752194 Getting block 6 of 7 Reserving size (2781032) 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 2563815 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2563816 Getting block 7 of 7 Reserving size (2781032) 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 1862761 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1862762 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4296828 fchr[G]: 7474300 fchr[T]: 10483776 fchr[$]: 14832169 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 27395813 bytes to primary EBWT file: 4M-HS/tmp/segment_juncs.rev.1.bt2 Wrote 3708048 bytes to secondary EBWT file: 4M-HS/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 14832169 bwtLen: 14832170 sz: 3708043 bwtSz: 3708043 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 927011 offsSz: 3708044 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 77251 numLines: 77251 ebwtTotLen: 4944064 ebwtTotSz: 4944064 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:16