Settings: Output files: "MCLiver18b/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: MCLiver18b/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: 6019751 Using parameters --bmax 4514814 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4514814 --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: 00:00:01 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 Avg bucket size: 3.43986e+06 (target: 4514813) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4514814) 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 3635368 (Using difference cover) Sorting block time: 00:00:06 Returning block of 3635369 Getting block 2 of 7 Reserving size (4514814) 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 2727266 (Using difference cover) Sorting block time: 00:00:06 Returning block of 2727267 Getting block 3 of 7 Reserving size (4514814) 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 3948054 (Using difference cover) Sorting block time: 00:00:06 Returning block of 3948055 Getting block 4 of 7 Reserving size (4514814) 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 3881685 (Using difference cover) Sorting block time: 00:00:06 Returning block of 3881686 Getting block 5 of 7 Reserving size (4514814) 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 3262785 (Using difference cover) Sorting block time: 00:00:06 Returning block of 3262786 Getting block 6 of 7 Reserving size (4514814) 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 3945346 (Using difference cover) Sorting block time: 00:00:08 Returning block of 3945347 Getting block 7 of 7 Reserving size (4514814) 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 2678495 (Using difference cover) Sorting block time: 00:00:05 Returning block of 2678496 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6181883 fchr[G]: 11864632 fchr[T]: 17233389 fchr[$]: 24079005 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 43214430 bytes to primary EBWT file: MCLiver18b/tmp/segment_juncs.1.bt2 Wrote 6019756 bytes to secondary EBWT file: MCLiver18b/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 24079005 bwtLen: 24079006 sz: 6019752 bwtSz: 6019752 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1504938 offsSz: 6019752 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 125412 numLines: 125412 ebwtTotLen: 8026368 ebwtTotSz: 8026368 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:54 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: 00:00:01 bmax according to bmaxDivN setting: 6019751 Using parameters --bmax 4514814 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4514814 --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: 00:00:01 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 2, merged 6; 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 Split 1, merged 3; 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 1; 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: 3.43986e+06 (target: 4514813) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4514814) 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 2483458 (Using difference cover) Sorting block time: 00:00:04 Returning block of 2483459 Getting block 2 of 7 Reserving size (4514814) 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 4166952 (Using difference cover) Sorting block time: 00:00:07 Returning block of 4166953 Getting block 3 of 7 Reserving size (4514814) 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 1209068 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1209069 Getting block 4 of 7 Reserving size (4514814) 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 4422539 (Using difference cover) Sorting block time: 00:00:07 Returning block of 4422540 Getting block 5 of 7 Reserving size (4514814) 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 4096301 (Using difference cover) Sorting block time: 00:00:06 Returning block of 4096302 Getting block 6 of 7 Reserving size (4514814) 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 3921293 (Using difference cover) Sorting block time: 00:00:08 Returning block of 3921294 Getting block 7 of 7 Reserving size (4514814) 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 3779388 (Using difference cover) Sorting block time: 00:00:08 Returning block of 3779389 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6181883 fchr[G]: 11864632 fchr[T]: 17233389 fchr[$]: 24079005 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 43214430 bytes to primary EBWT file: MCLiver18b/tmp/segment_juncs.rev.1.bt2 Wrote 6019756 bytes to secondary EBWT file: MCLiver18b/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 24079005 bwtLen: 24079006 sz: 6019752 bwtSz: 6019752 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1504938 offsSz: 6019752 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 125412 numLines: 125412 ebwtTotLen: 8026368 ebwtTotSz: 8026368 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:01:00