Settings: Output files: "CB_Lung_tp3a2/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_tp3a2/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: 4914416 Using parameters --bmax 3685812 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3685812 --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: 00:00:01 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 Avg bucket size: 2.45721e+06 (target: 3685811) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3685812) 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 1111350 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1111351 Getting block 2 of 8 Reserving size (3685812) 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 3037023 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3037024 Getting block 3 of 8 Reserving size (3685812) 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 1609841 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1609842 Getting block 4 of 8 Reserving size (3685812) 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 3402542 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3402543 Getting block 5 of 8 Reserving size (3685812) 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 3187848 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3187849 Getting block 6 of 8 Reserving size (3685812) 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 2334973 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2334974 Getting block 7 of 8 Reserving size (3685812) 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 3233725 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3233726 Getting block 8 of 8 Reserving size (3685812) 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 1740355 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1740356 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4720906 fchr[G]: 9838621 fchr[T]: 14735505 fchr[$]: 19657664 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 36298304 bytes to primary EBWT file: CB_Lung_tp3a2/tmp/segment_juncs.1.bt2 Wrote 4914424 bytes to secondary EBWT file: CB_Lung_tp3a2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19657664 bwtLen: 19657665 sz: 4914416 bwtSz: 4914417 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1228605 offsSz: 4914420 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 102384 numLines: 102384 ebwtTotLen: 6552576 ebwtTotSz: 6552576 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:14 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: 4914416 Using parameters --bmax 3685812 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3685812 --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: 2.80824e+06 (target: 3685811) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3685812) 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 3020713 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3020714 Getting block 2 of 7 Reserving size (3685812) 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 3492135 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3492136 Getting block 3 of 7 Reserving size (3685812) 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 3399141 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3399142 Getting block 4 of 7 Reserving size (3685812) 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 1448764 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1448765 Getting block 5 of 7 Reserving size (3685812) 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 3315248 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3315249 Getting block 6 of 7 Reserving size (3685812) 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 2862520 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2862521 Getting block 7 of 7 Reserving size (3685812) 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 2119137 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2119138 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4720906 fchr[G]: 9838621 fchr[T]: 14735505 fchr[$]: 19657664 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 36298304 bytes to primary EBWT file: CB_Lung_tp3a2/tmp/segment_juncs.rev.1.bt2 Wrote 4914424 bytes to secondary EBWT file: CB_Lung_tp3a2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19657664 bwtLen: 19657665 sz: 4914416 bwtSz: 4914417 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1228605 offsSz: 4914420 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 102384 numLines: 102384 ebwtTotLen: 6552576 ebwtTotSz: 6552576 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:14