Settings: Output files: "MCLiver16b/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: MCLiver16b/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: 5518500 Using parameters --bmax 4138875 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4138875 --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: 00:00:01 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 Split 1, merged 6; 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 Split 1, merged 1; 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: 3.15343e+06 (target: 4138874) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4138875) 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 3829105 (Using difference cover) Sorting block time: 00:00:05 Returning block of 3829106 Getting block 2 of 7 Reserving size (4138875) 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 3876190 (Using difference cover) Sorting block time: 00:00:05 Returning block of 3876191 Getting block 3 of 7 Reserving size (4138875) 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 3507024 (Using difference cover) Sorting block time: 00:00:05 Returning block of 3507025 Getting block 4 of 7 Reserving size (4138875) 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 3724620 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3724621 Getting block 5 of 7 Reserving size (4138875) 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 2667656 (Using difference cover) Sorting block time: 00:00:05 Returning block of 2667657 Getting block 6 of 7 Reserving size (4138875) 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 3667139 (Using difference cover) Sorting block time: 00:00:06 Returning block of 3667140 Getting block 7 of 7 Reserving size (4138875) 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 802260 (Using difference cover) Sorting block time: 00:00:01 Returning block of 802261 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5594827 fchr[G]: 10875747 fchr[T]: 15897657 fchr[$]: 22074000 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 40014659 bytes to primary EBWT file: MCLiver16b/tmp/segment_juncs.1.bt2 Wrote 5518508 bytes to secondary EBWT file: MCLiver16b/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 22074000 bwtLen: 22074001 sz: 5518500 bwtSz: 5518501 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1379626 offsSz: 5518504 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 114969 numLines: 114969 ebwtTotLen: 7358016 ebwtTotSz: 7358016 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:45 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: 5518500 Using parameters --bmax 4138875 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4138875 --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: 00:00:01 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: 2.75925e+06 (target: 4138874) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (4138875) 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 3480731 (Using difference cover) Sorting block time: 00:00:05 Returning block of 3480732 Getting block 2 of 8 Reserving size (4138875) 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 3059595 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3059596 Getting block 3 of 8 Reserving size (4138875) 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 3640072 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3640073 Getting block 4 of 8 Reserving size (4138875) 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 1987988 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1987989 Getting block 5 of 8 Reserving size (4138875) 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 2880833 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2880834 Getting block 6 of 8 Reserving size (4138875) 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 1895457 (Using difference cover) Sorting block time: 00:00:03 Returning block of 1895458 Getting block 7 of 8 Reserving size (4138875) 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 2782951 (Using difference cover) Sorting block time: 00:00:04 Returning block of 2782952 Getting block 8 of 8 Reserving size (4138875) 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 2346366 (Using difference cover) Sorting block time: 00:00:04 Returning block of 2346367 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5594827 fchr[G]: 10875747 fchr[T]: 15897657 fchr[$]: 22074000 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 40014659 bytes to primary EBWT file: MCLiver16b/tmp/segment_juncs.rev.1.bt2 Wrote 5518508 bytes to secondary EBWT file: MCLiver16b/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 22074000 bwtLen: 22074001 sz: 5518500 bwtSz: 5518501 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1379626 offsSz: 5518504 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 114969 numLines: 114969 ebwtTotLen: 7358016 ebwtTotSz: 7358016 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:40