Settings: Output files: "CB_Lung_tp172/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: CB_Lung_tp172/tmp/segment_juncs.fa 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 bmax according to bmaxDivN setting: 5455046 Using parameters --bmax 4091285 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4091285 --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 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 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: 3.11717e+06 (target: 4091284) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4091285) 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 2695493 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2695494 Getting block 2 of 7 Reserving size (4091285) 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 3830843 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3830844 Getting block 3 of 7 Reserving size (4091285) 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 2681472 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2681473 Getting block 4 of 7 Reserving size (4091285) 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 3165594 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3165595 Getting block 5 of 7 Reserving size (4091285) 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 3632271 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3632272 Getting block 6 of 7 Reserving size (4091285) 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 2979850 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2979851 Getting block 7 of 7 Reserving size (4091285) 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 2834658 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2834659 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5254445 fchr[G]: 11000950 fchr[T]: 16355547 fchr[$]: 21820187 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 39872460 bytes to primary EBWT file: CB_Lung_tp172/tmp/segment_juncs.1.bt2 Wrote 5455052 bytes to secondary EBWT file: CB_Lung_tp172/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 21820187 bwtLen: 21820188 sz: 5455047 bwtSz: 5455047 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1363762 offsSz: 5455048 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 113647 numLines: 113647 ebwtTotLen: 7273408 ebwtTotSz: 7273408 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: 5455046 Using parameters --bmax 4091285 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4091285 --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: 00:00:01 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 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: 3.11717e+06 (target: 4091284) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4091285) 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 3209750 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3209751 Getting block 2 of 7 Reserving size (4091285) 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 2475893 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2475894 Getting block 3 of 7 Reserving size (4091285) 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 2284525 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2284526 Getting block 4 of 7 Reserving size (4091285) 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 4008201 (Using difference cover) Sorting block time: 00:00:01 Returning block of 4008202 Getting block 5 of 7 Reserving size (4091285) 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 2547967 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2547968 Getting block 6 of 7 Reserving size (4091285) 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 3948977 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3948978 Getting block 7 of 7 Reserving size (4091285) 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 3344868 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3344869 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5254445 fchr[G]: 11000950 fchr[T]: 16355547 fchr[$]: 21820187 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 39872460 bytes to primary EBWT file: CB_Lung_tp172/tmp/segment_juncs.rev.1.bt2 Wrote 5455052 bytes to secondary EBWT file: CB_Lung_tp172/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 21820187 bwtLen: 21820188 sz: 5455047 bwtSz: 5455047 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1363762 offsSz: 5455048 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 113647 numLines: 113647 ebwtTotLen: 7273408 ebwtTotSz: 7273408 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:17