Settings: Output files: "CB_Liver_tp710/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_Liver_tp710/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: 5244369 Using parameters --bmax 3933277 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3933277 --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 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 Split 1, merged 2; 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: 2.99678e+06 (target: 3933276) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3933277) 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 1679712 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1679713 Getting block 2 of 7 Reserving size (3933277) 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 3577411 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3577412 Getting block 3 of 7 Reserving size (3933277) 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 3155551 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3155552 Getting block 4 of 7 Reserving size (3933277) 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 3479478 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3479479 Getting block 5 of 7 Reserving size (3933277) 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 3777691 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3777692 Getting block 6 of 7 Reserving size (3933277) 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 2685291 (Using difference cover) Sorting block time: 00:00:04 Returning block of 2685292 Getting block 7 of 7 Reserving size (3933277) 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 2622336 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2622337 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5293232 fchr[G]: 10337969 fchr[T]: 15178870 fchr[$]: 20977476 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 38253454 bytes to primary EBWT file: CB_Liver_tp710/tmp/segment_juncs.1.bt2 Wrote 5244376 bytes to secondary EBWT file: CB_Liver_tp710/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20977476 bwtLen: 20977477 sz: 5244369 bwtSz: 5244370 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1311093 offsSz: 5244372 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 109258 numLines: 109258 ebwtTotLen: 6992512 ebwtTotSz: 6992512 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:33 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: 5244369 Using parameters --bmax 3933277 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3933277 --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: 00:00:01 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 Avg bucket size: 2.62218e+06 (target: 3933276) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3933277) 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 1600373 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1600374 Getting block 2 of 8 Reserving size (3933277) 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 3923441 (Using difference cover) Sorting block time: 00:00:05 Returning block of 3923442 Getting block 3 of 8 Reserving size (3933277) 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 3851112 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3851113 Getting block 4 of 8 Reserving size (3933277) 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 2207744 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2207745 Getting block 5 of 8 Reserving size (3933277) 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 1733974 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1733975 Getting block 6 of 8 Reserving size (3933277) 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 3215303 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3215304 Getting block 7 of 8 Reserving size (3933277) 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 3483444 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3483445 Getting block 8 of 8 Reserving size (3933277) 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 962078 (Using difference cover) Sorting block time: 00:00:01 Returning block of 962079 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5293232 fchr[G]: 10337969 fchr[T]: 15178870 fchr[$]: 20977476 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 38253454 bytes to primary EBWT file: CB_Liver_tp710/tmp/segment_juncs.rev.1.bt2 Wrote 5244376 bytes to secondary EBWT file: CB_Liver_tp710/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20977476 bwtLen: 20977477 sz: 5244369 bwtSz: 5244370 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1311093 offsSz: 5244372 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 109258 numLines: 109258 ebwtTotLen: 6992512 ebwtTotSz: 6992512 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:34