Settings: Output files: "CB_Lung_tp51/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_tp51/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: 5125767 Using parameters --bmax 3844326 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3844326 --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 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 Avg bucket size: 2.56288e+06 (target: 3844325) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3844326) 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 2157769 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2157770 Getting block 2 of 8 Reserving size (3844326) 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 3243648 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3243649 Getting block 3 of 8 Reserving size (3844326) 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 1293565 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1293566 Getting block 4 of 8 Reserving size (3844326) 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 3482305 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3482306 Getting block 5 of 8 Reserving size (3844326) 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 2510557 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2510558 Getting block 6 of 8 Reserving size (3844326) 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 2742613 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2742614 Getting block 7 of 8 Reserving size (3844326) 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 1759663 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1759664 Getting block 8 of 8 Reserving size (3844326) 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 3312944 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3312945 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4912212 fchr[G]: 10316399 fchr[T]: 15374098 fchr[$]: 20503071 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37707413 bytes to primary EBWT file: CB_Lung_tp51/tmp/segment_juncs.1.bt2 Wrote 5125772 bytes to secondary EBWT file: CB_Lung_tp51/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20503071 bwtLen: 20503072 sz: 5125768 bwtSz: 5125768 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1281442 offsSz: 5125768 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 106787 numLines: 106787 ebwtTotLen: 6834368 ebwtTotSz: 6834368 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:16 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: 5125767 Using parameters --bmax 3844326 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3844326 --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 1, merged 8; 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 Split 1, merged 0; 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 0; 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: 2.56288e+06 (target: 3844325) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3844326) 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 1874336 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1874337 Getting block 2 of 8 Reserving size (3844326) 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 2775963 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2775964 Getting block 3 of 8 Reserving size (3844326) 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 1681431 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1681432 Getting block 4 of 8 Reserving size (3844326) 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 2502544 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2502545 Getting block 5 of 8 Reserving size (3844326) 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 3832656 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3832657 Getting block 6 of 8 Reserving size (3844326) 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 3053458 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3053459 Getting block 7 of 8 Reserving size (3844326) 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 3202973 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3202974 Getting block 8 of 8 Reserving size (3844326) 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 1579703 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1579704 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4912212 fchr[G]: 10316399 fchr[T]: 15374098 fchr[$]: 20503071 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37707413 bytes to primary EBWT file: CB_Lung_tp51/tmp/segment_juncs.rev.1.bt2 Wrote 5125772 bytes to secondary EBWT file: CB_Lung_tp51/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20503071 bwtLen: 20503072 sz: 5125768 bwtSz: 5125768 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1281442 offsSz: 5125768 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 106787 numLines: 106787 ebwtTotLen: 6834368 ebwtTotSz: 6834368 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:17