Settings: Output files: "CBLivertp121WH/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: CBLivertp121WH/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: 7768579 Using parameters --bmax 5826435 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 5826435 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:02 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: 00:00:02 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 2, merged 1; iterating... 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 Avg bucket size: 4.43919e+06 (target: 5826434) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (5826435) 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 4547647 (Using difference cover) Sorting block time: 00:00:08 Returning block of 4547648 Getting block 2 of 7 Reserving size (5826435) 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 3872945 (Using difference cover) Sorting block time: 00:00:08 Returning block of 3872946 Getting block 3 of 7 Reserving size (5826435) 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 5563693 (Using difference cover) Sorting block time: 00:00:10 Returning block of 5563694 Getting block 4 of 7 Reserving size (5826435) 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 5037151 (Using difference cover) Sorting block time: 00:00:08 Returning block of 5037152 Getting block 5 of 7 Reserving size (5826435) 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 5160837 (Using difference cover) Sorting block time: 00:00:10 Returning block of 5160838 Getting block 6 of 7 Reserving size (5826435) 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 4086947 (Using difference cover) Sorting block time: 00:00:08 Returning block of 4086948 Getting block 7 of 7 Reserving size (5826435) 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 2805090 (Using difference cover) Sorting block time: 00:00:06 Returning block of 2805091 Exited Ebwt loop fchr[A]: 0 fchr[C]: 7893568 fchr[G]: 15285263 fchr[T]: 22360506 fchr[$]: 31074316 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 54623097 bytes to primary EBWT file: CBLivertp121WH/tmp/segment_juncs.1.bt2 Wrote 7768584 bytes to secondary EBWT file: CBLivertp121WH/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 31074316 bwtLen: 31074317 sz: 7768579 bwtSz: 7768580 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1942145 offsSz: 7768580 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 161846 numLines: 161846 ebwtTotLen: 10358144 ebwtTotSz: 10358144 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:01:18 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: 7768579 Using parameters --bmax 5826435 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 5826435 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:03 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 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: 5.17905e+06 (target: 5826434) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (5826435) 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 5397975 (Using difference cover) Sorting block time: 00:00:09 Returning block of 5397976 Getting block 2 of 6 Reserving size (5826435) 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 5704710 (Using difference cover) Sorting block time: 00:00:10 Returning block of 5704711 Getting block 3 of 6 Reserving size (5826435) 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 5724689 (Using difference cover) Sorting block time: 00:00:10 Returning block of 5724690 Getting block 4 of 6 Reserving size (5826435) 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 5208288 (Using difference cover) Sorting block time: 00:00:08 Returning block of 5208289 Getting block 5 of 6 Reserving size (5826435) 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 3269371 (Using difference cover) Sorting block time: 00:00:07 Returning block of 3269372 Getting block 6 of 6 Reserving size (5826435) 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 5769278 (Using difference cover) Sorting block time: 00:00:12 Returning block of 5769279 Exited Ebwt loop fchr[A]: 0 fchr[C]: 7893568 fchr[G]: 15285263 fchr[T]: 22360506 fchr[$]: 31074316 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 54623097 bytes to primary EBWT file: CBLivertp121WH/tmp/segment_juncs.rev.1.bt2 Wrote 7768584 bytes to secondary EBWT file: CBLivertp121WH/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 31074316 bwtLen: 31074317 sz: 7768579 bwtSz: 7768580 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1942145 offsSz: 7768580 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 161846 numLines: 161846 ebwtTotLen: 10358144 ebwtTotSz: 10358144 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:01:11