Settings: Output files: "IR_Gut_07F1C1/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: IR_Gut_07F1C1/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: 4542044 Using parameters --bmax 3406533 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3406533 --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: 2.59545e+06 (target: 3406532) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3406533) 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 2685871 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2685872 Getting block 2 of 7 Reserving size (3406533) 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 3101716 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3101717 Getting block 3 of 7 Reserving size (3406533) 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 2010244 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2010245 Getting block 4 of 7 Reserving size (3406533) 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 3050742 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3050743 Getting block 5 of 7 Reserving size (3406533) 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 2883071 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2883072 Getting block 6 of 7 Reserving size (3406533) 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 2987951 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2987952 Getting block 7 of 7 Reserving size (3406533) 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 1448575 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1448576 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4366308 fchr[G]: 9069234 fchr[T]: 13645832 fchr[$]: 18168176 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 33903617 bytes to primary EBWT file: IR_Gut_07F1C1/tmp/segment_juncs.1.bt2 Wrote 4542052 bytes to secondary EBWT file: IR_Gut_07F1C1/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18168176 bwtLen: 18168177 sz: 4542044 bwtSz: 4542045 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1135512 offsSz: 4542048 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 94626 numLines: 94626 ebwtTotLen: 6056064 ebwtTotSz: 6056064 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:17 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: 00:00:00 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 4542044 Using parameters --bmax 3406533 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3406533 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 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 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: 2.27102e+06 (target: 3406532) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3406533) 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 1763947 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1763948 Getting block 2 of 8 Reserving size (3406533) 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 3170054 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3170055 Getting block 3 of 8 Reserving size (3406533) 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 684471 (Using difference cover) Sorting block time: 00:00:01 Returning block of 684472 Getting block 4 of 8 Reserving size (3406533) 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 3299623 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3299624 Getting block 5 of 8 Reserving size (3406533) 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 3080486 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3080487 Getting block 6 of 8 Reserving size (3406533) 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 652935 (Using difference cover) Sorting block time: 00:00:01 Returning block of 652936 Getting block 7 of 8 Reserving size (3406533) 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 3046021 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3046022 Getting block 8 of 8 Reserving size (3406533) 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 2470632 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2470633 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4366308 fchr[G]: 9069234 fchr[T]: 13645832 fchr[$]: 18168176 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 33903617 bytes to primary EBWT file: IR_Gut_07F1C1/tmp/segment_juncs.rev.1.bt2 Wrote 4542052 bytes to secondary EBWT file: IR_Gut_07F1C1/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18168176 bwtLen: 18168177 sz: 4542044 bwtSz: 4542045 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1135512 offsSz: 4542048 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 94626 numLines: 94626 ebwtTotLen: 6056064 ebwtTotSz: 6056064 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:17