Settings: Output files: "CB_Lung_tp1/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_tp1/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: 4907003 Using parameters --bmax 3680253 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3680253 --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: 2.4535e+06 (target: 3680252) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3680253) 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 3338012 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3338013 Getting block 2 of 8 Reserving size (3680253) 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 2275293 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2275294 Getting block 3 of 8 Reserving size (3680253) 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 2613283 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2613284 Getting block 4 of 8 Reserving size (3680253) 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 2186847 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2186848 Getting block 5 of 8 Reserving size (3680253) 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 2560341 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2560342 Getting block 6 of 8 Reserving size (3680253) 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 1945140 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1945141 Getting block 7 of 8 Reserving size (3680253) 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 2205362 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2205363 Getting block 8 of 8 Reserving size (3680253) 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 2503730 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2503731 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4700833 fchr[G]: 9827941 fchr[T]: 14725831 fchr[$]: 19628015 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 36244813 bytes to primary EBWT file: CB_Lung_tp1/tmp/segment_juncs.1.bt2 Wrote 4907008 bytes to secondary EBWT file: CB_Lung_tp1/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19628015 bwtLen: 19628016 sz: 4907004 bwtSz: 4907004 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1226751 offsSz: 4907004 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 102230 numLines: 102230 ebwtTotLen: 6542720 ebwtTotSz: 6542720 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:15 Reading reference sizes Time reading reference sizes: 00:00:00 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: 4907003 Using parameters --bmax 3680253 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3680253 --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 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: 2.4535e+06 (target: 3680252) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3680253) 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 3152440 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3152441 Getting block 2 of 8 Reserving size (3680253) 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 3034687 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3034688 Getting block 3 of 8 Reserving size (3680253) 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 3455973 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3455974 Getting block 4 of 8 Reserving size (3680253) 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 2135036 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2135037 Getting block 5 of 8 Reserving size (3680253) 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 2482690 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2482691 Getting block 6 of 8 Reserving size (3680253) 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 1512025 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1512026 Getting block 7 of 8 Reserving size (3680253) 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 2237901 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2237902 Getting block 8 of 8 Reserving size (3680253) 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 1617256 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1617257 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4700833 fchr[G]: 9827941 fchr[T]: 14725831 fchr[$]: 19628015 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 36244813 bytes to primary EBWT file: CB_Lung_tp1/tmp/segment_juncs.rev.1.bt2 Wrote 4907008 bytes to secondary EBWT file: CB_Lung_tp1/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19628015 bwtLen: 19628016 sz: 4907004 bwtSz: 4907004 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1226751 offsSz: 4907004 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 102230 numLines: 102230 ebwtTotLen: 6542720 ebwtTotSz: 6542720 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:16