Settings: Output files: "CB_Brain_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_Brain_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: 4191235 Using parameters --bmax 3143427 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3143427 --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 7; 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 Avg bucket size: 2.39499e+06 (target: 3143426) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3143427) 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 1971761 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1971762 Getting block 2 of 7 Reserving size (3143427) 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 1657523 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1657524 Getting block 3 of 7 Reserving size (3143427) 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 2371350 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2371351 Getting block 4 of 7 Reserving size (3143427) 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 2993534 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2993535 Getting block 5 of 7 Reserving size (3143427) 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 2308227 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2308228 Getting block 6 of 7 Reserving size (3143427) 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 3125349 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3125350 Getting block 7 of 7 Reserving size (3143427) 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 2337192 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2337193 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4013730 fchr[G]: 8384894 fchr[T]: 12579266 fchr[$]: 16764942 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 31537777 bytes to primary EBWT file: CB_Brain_tp1/tmp/segment_juncs.1.bt2 Wrote 4191240 bytes to secondary EBWT file: CB_Brain_tp1/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16764942 bwtLen: 16764943 sz: 4191236 bwtSz: 4191236 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1047809 offsSz: 4191236 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 87318 numLines: 87318 ebwtTotLen: 5588352 ebwtTotSz: 5588352 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:12 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: 4191235 Using parameters --bmax 3143427 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3143427 --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 2, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.39499e+06 (target: 3143426) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3143427) 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 2211427 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2211428 Getting block 2 of 7 Reserving size (3143427) 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 2604741 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2604742 Getting block 3 of 7 Reserving size (3143427) 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 2830820 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2830821 Getting block 4 of 7 Reserving size (3143427) 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 2575537 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2575538 Getting block 5 of 7 Reserving size (3143427) 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 2279190 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2279191 Getting block 6 of 7 Reserving size (3143427) 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 1945688 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1945689 Getting block 7 of 7 Reserving size (3143427) 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 2317533 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2317534 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4013730 fchr[G]: 8384894 fchr[T]: 12579266 fchr[$]: 16764942 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 31537777 bytes to primary EBWT file: CB_Brain_tp1/tmp/segment_juncs.rev.1.bt2 Wrote 4191240 bytes to secondary EBWT file: CB_Brain_tp1/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16764942 bwtLen: 16764943 sz: 4191236 bwtSz: 4191236 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1047809 offsSz: 4191236 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 87318 numLines: 87318 ebwtTotLen: 5588352 ebwtTotSz: 5588352 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:13