Settings: Output files: "C_rub_R1//tmp/segment_juncs.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) 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: C_rub_R1//tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:03 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:04 bmax according to bmaxDivN setting: 19204108 Using parameters --bmax 14403081 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 14403081 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:03 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: 00:00:01 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: 00:00:05 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 8; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:05 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: 00:00:06 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: 00:00:09 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 9.60205e+06 (target: 14403080) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (14403081) 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: 00:00:02 Sorting block of length 3482717 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3482718 Getting block 2 of 8 Reserving size (14403081) 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: 00:00:03 Sorting block of length 13356607 (Using difference cover) Sorting block time: 00:00:13 Returning block of 13356608 Getting block 3 of 8 Reserving size (14403081) 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: 00:00:02 Sorting block of length 11962982 (Using difference cover) Sorting block time: 00:00:07 Returning block of 11962983 Getting block 4 of 8 Reserving size (14403081) 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 11998327 (Using difference cover) Sorting block time: 00:00:09 Returning block of 11998328 Getting block 5 of 8 Reserving size (14403081) 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 2474011 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2474012 Getting block 6 of 8 Reserving size (14403081) 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: 00:00:02 Sorting block of length 14187135 (Using difference cover) Sorting block time: 00:00:13 Returning block of 14187136 Getting block 7 of 8 Reserving size (14403081) 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 11591494 (Using difference cover) Sorting block time: 00:00:08 Returning block of 11591495 Getting block 8 of 8 Reserving size (14403081) 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: 00:00:02 Sorting block of length 7763152 (Using difference cover) Sorting block time: 00:00:04 Returning block of 7763153 Exited Ebwt loop fchr[A]: 0 fchr[C]: 22218609 fchr[G]: 38321417 fchr[T]: 54577311 fchr[$]: 76816432 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 137877312 bytes to primary EBWT file: C_rub_R1//tmp/segment_juncs.1.ebwt Wrote 9602060 bytes to secondary EBWT file: C_rub_R1//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 76816432 bwtLen: 76816433 sz: 19204108 bwtSz: 19204109 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2400514 offsSz: 9602056 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 171466 numSides: 342932 numLines: 342932 ebwtTotLen: 21947648 ebwtTotSz: 21947648 reverse: 0 Total time for call to driver() for forward index: 00:02:06 Reading reference sizes Time reading reference sizes: 00:00:03 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:05 bmax according to bmaxDivN setting: 19204108 Using parameters --bmax 14403081 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 14403081 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:03 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: 00:00:02 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: 00:00:06 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 5; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:06 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: 00:00:05 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 8.53516e+06 (target: 14403080) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (14403081) 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 11078562 (Using difference cover) Sorting block time: 00:00:06 Returning block of 11078563 Getting block 2 of 9 Reserving size (14403081) 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 6089923 (Using difference cover) Sorting block time: 00:00:04 Returning block of 6089924 Getting block 3 of 9 Reserving size (14403081) 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 10666548 (Using difference cover) Sorting block time: 00:00:04 Returning block of 10666549 Getting block 4 of 9 Reserving size (14403081) 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: 00:00:02 Sorting block of length 8170914 (Using difference cover) Sorting block time: 00:00:06 Returning block of 8170915 Getting block 5 of 9 Reserving size (14403081) 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 6715718 (Using difference cover) Sorting block time: 00:00:05 Returning block of 6715719 Getting block 6 of 9 Reserving size (14403081) 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 9857969 (Using difference cover) Sorting block time: 00:00:05 Returning block of 9857970 Getting block 7 of 9 Reserving size (14403081) 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: 00:00:02 Sorting block of length 8550132 (Using difference cover) Sorting block time: 00:00:05 Returning block of 8550133 Getting block 8 of 9 Reserving size (14403081) 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: 00:00:02 Sorting block of length 13205039 (Using difference cover) Sorting block time: 00:00:10 Returning block of 13205040 Getting block 9 of 9 Reserving size (14403081) 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 2481619 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2481620 Exited Ebwt loop fchr[A]: 0 fchr[C]: 22218609 fchr[G]: 38321417 fchr[T]: 54577311 fchr[$]: 76816432 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 137877312 bytes to primary EBWT file: C_rub_R1//tmp/segment_juncs.rev.1.ebwt Wrote 9602060 bytes to secondary EBWT file: C_rub_R1//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 76816432 bwtLen: 76816433 sz: 19204108 bwtSz: 19204109 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2400514 offsSz: 9602056 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 171466 numSides: 342932 numLines: 342932 ebwtTotLen: 21947648 ebwtTotSz: 21947648 reverse: 0 Total time for backward call to driver() for mirror index: 00:01:40