Settings: Output files: "IRLiver132/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: IRLiver132/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: 4790409 Using parameters --bmax 3592807 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3592807 --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 Avg bucket size: 2.3952e+06 (target: 3592806) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3592807) 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 3418866 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3418867 Getting block 2 of 8 Reserving size (3592807) 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 1816642 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1816643 Getting block 3 of 8 Reserving size (3592807) 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 3060808 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3060809 Getting block 4 of 8 Reserving size (3592807) 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 1223269 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1223270 Getting block 5 of 8 Reserving size (3592807) 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 2725966 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2725967 Getting block 6 of 8 Reserving size (3592807) 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 3268311 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3268312 Getting block 7 of 8 Reserving size (3592807) 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 678441 (Using difference cover) Sorting block time: 00:00:01 Returning block of 678442 Getting block 8 of 8 Reserving size (3592807) 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 2969326 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2969327 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4795651 fchr[G]: 9494070 fchr[T]: 13955622 fchr[$]: 19161636 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 35356006 bytes to primary EBWT file: IRLiver132/tmp/segment_juncs.1.bt2 Wrote 4790416 bytes to secondary EBWT file: IRLiver132/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19161636 bwtLen: 19161637 sz: 4790409 bwtSz: 4790410 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1197603 offsSz: 4790412 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 99801 numLines: 99801 ebwtTotLen: 6387264 ebwtTotSz: 6387264 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:27 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: 4790409 Using parameters --bmax 3592807 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3592807 --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: 00:00:01 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: 3.19361e+06 (target: 3592806) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (3592807) 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 3115331 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3115332 Getting block 2 of 6 Reserving size (3592807) 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 3332329 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3332330 Getting block 3 of 6 Reserving size (3592807) 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 3046407 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3046408 Getting block 4 of 6 Reserving size (3592807) 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 3223794 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3223795 Getting block 5 of 6 Reserving size (3592807) 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 3086435 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3086436 Getting block 6 of 6 Reserving size (3592807) 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 3357335 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3357336 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4795651 fchr[G]: 9494070 fchr[T]: 13955622 fchr[$]: 19161636 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 35356006 bytes to primary EBWT file: IRLiver132/tmp/segment_juncs.rev.1.bt2 Wrote 4790416 bytes to secondary EBWT file: IRLiver132/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19161636 bwtLen: 19161637 sz: 4790409 bwtSz: 4790410 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1197603 offsSz: 4790412 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 99801 numLines: 99801 ebwtTotLen: 6387264 ebwtTotSz: 6387264 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:27