Settings: Output files: "Edi_0_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: Edi_0_R1//tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:02 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:06 bmax according to bmaxDivN setting: 26894978 Using parameters --bmax 20171234 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 20171234 --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: 00:00:07 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.34475e+07 (target: 20171233) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (20171234) 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 12818813 (Using difference cover) Sorting block time: 00:00:06 Returning block of 12818814 Getting block 2 of 8 Reserving size (20171234) 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 19335078 (Using difference cover) Sorting block time: 00:00:08 Returning block of 19335079 Getting block 3 of 8 Reserving size (20171234) 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 18239967 (Using difference cover) Sorting block time: 00:00:11 Returning block of 18239968 Getting block 4 of 8 Reserving size (20171234) 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 11990526 (Using difference cover) Sorting block time: 00:00:06 Returning block of 11990527 Getting block 5 of 8 Reserving size (20171234) 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 8308996 (Using difference cover) Sorting block time: 00:00:05 Returning block of 8308997 Getting block 6 of 8 Reserving size (20171234) 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 13400678 (Using difference cover) Sorting block time: 00:00:07 Returning block of 13400679 Getting block 7 of 8 Reserving size (20171234) 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 13381688 (Using difference cover) Sorting block time: 00:00:08 Returning block of 13381689 Getting block 8 of 8 Reserving size (20171234) 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 10104159 (Using difference cover) Sorting block time: 00:00:06 Returning block of 10104160 Exited Ebwt loop fchr[A]: 0 fchr[C]: 31285646 fchr[G]: 53585611 fchr[T]: 76156568 fchr[$]: 107579912 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 191406569 bytes to primary EBWT file: Edi_0_R1//tmp/segment_juncs.1.ebwt Wrote 13447496 bytes to secondary EBWT file: Edi_0_R1//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 107579912 bwtLen: 107579913 sz: 26894978 bwtSz: 26894979 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3361873 offsSz: 13447492 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 240134 numSides: 480268 numLines: 480268 ebwtTotLen: 30737152 ebwtTotSz: 30737152 reverse: 0 Total time for call to driver() for forward index: 00:01:55 Reading reference sizes Time reading reference sizes: 00:00:02 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: 26894978 Using parameters --bmax 20171234 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 20171234 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:04 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: 00:00:06 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: 00:00:05 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 Split 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:06 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.34475e+07 (target: 20171233) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (20171234) 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 6143024 (Using difference cover) Sorting block time: 00:00:03 Returning block of 6143025 Getting block 2 of 8 Reserving size (20171234) 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 19060963 (Using difference cover) Sorting block time: 00:00:11 Returning block of 19060964 Getting block 3 of 8 Reserving size (20171234) 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 16767405 (Using difference cover) Sorting block time: 00:00:09 Returning block of 16767406 Getting block 4 of 8 Reserving size (20171234) 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 15556866 (Using difference cover) Sorting block time: 00:00:08 Returning block of 15556867 Getting block 5 of 8 Reserving size (20171234) 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 9094755 (Using difference cover) Sorting block time: 00:00:06 Returning block of 9094756 Getting block 6 of 8 Reserving size (20171234) 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 11212547 (Using difference cover) Sorting block time: 00:00:06 Returning block of 11212548 Getting block 7 of 8 Reserving size (20171234) 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 9953868 (Using difference cover) Sorting block time: 00:00:05 Returning block of 9953869 Getting block 8 of 8 Reserving size (20171234) 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 19790477 (Using difference cover) Sorting block time: 00:00:10 Returning block of 19790478 Exited Ebwt loop fchr[A]: 0 fchr[C]: 31285646 fchr[G]: 53585611 fchr[T]: 76156568 fchr[$]: 107579912 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 191406569 bytes to primary EBWT file: Edi_0_R1//tmp/segment_juncs.rev.1.ebwt Wrote 13447496 bytes to secondary EBWT file: Edi_0_R1//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 107579912 bwtLen: 107579913 sz: 26894978 bwtSz: 26894979 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3361873 offsSz: 13447492 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 240134 numSides: 480268 numLines: 480268 ebwtTotLen: 30737152 ebwtTotSz: 30737152 reverse: 0 Total time for backward call to driver() for mirror index: 00:02:11