Settings: Output files: "Sf_2_R2//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: Sf_2_R2//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: 00:00:03 bmax according to bmaxDivN setting: 22027360 Using parameters --bmax 16520520 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 16520520 --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: 00:00:06 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: 00:00:03 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: 00:00:04 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: 00:00:04 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.25871e+07 (target: 16520519) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (16520520) 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 16073276 (Using difference cover) Sorting block time: 00:00:10 Returning block of 16073277 Getting block 2 of 7 Reserving size (16520520) 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 9531921 (Using difference cover) Sorting block time: 00:00:06 Returning block of 9531922 Getting block 3 of 7 Reserving size (16520520) 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 7051655 (Using difference cover) Sorting block time: 00:00:04 Returning block of 7051656 Getting block 4 of 7 Reserving size (16520520) 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 16166581 (Using difference cover) Sorting block time: 00:00:09 Returning block of 16166582 Getting block 5 of 7 Reserving size (16520520) 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 10975581 (Using difference cover) Sorting block time: 00:00:05 Returning block of 10975582 Getting block 6 of 7 Reserving size (16520520) 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 16026433 (Using difference cover) Sorting block time: 00:00:09 Returning block of 16026434 Getting block 7 of 7 Reserving size (16520520) 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 12283988 (Using difference cover) Sorting block time: 00:00:06 Returning block of 12283989 Exited Ebwt loop fchr[A]: 0 fchr[C]: 25605199 fchr[G]: 43949423 fchr[T]: 62440649 fchr[$]: 88109441 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 157503780 bytes to primary EBWT file: Sf_2_R2//tmp/segment_juncs.1.ebwt Wrote 11013688 bytes to secondary EBWT file: Sf_2_R2//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 88109441 bwtLen: 88109442 sz: 22027361 bwtSz: 22027361 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2753421 offsSz: 11013684 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 196673 numSides: 393346 numLines: 393346 ebwtTotLen: 25174144 ebwtTotSz: 25174144 reverse: 0 Total time for call to driver() for forward index: 00:01:42 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: 00:00:04 bmax according to bmaxDivN setting: 22027360 Using parameters --bmax 16520520 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 16520520 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:02 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: 00:00:04 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: 00:00:04 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 Avg bucket size: 1.25871e+07 (target: 16520519) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (16520520) 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 16250004 (Using difference cover) Sorting block time: 00:00:10 Returning block of 16250005 Getting block 2 of 7 Reserving size (16520520) 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 13060950 (Using difference cover) Sorting block time: 00:00:07 Returning block of 13060951 Getting block 3 of 7 Reserving size (16520520) 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 15307283 (Using difference cover) Sorting block time: 00:00:08 Returning block of 15307284 Getting block 4 of 7 Reserving size (16520520) 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 12642722 (Using difference cover) Sorting block time: 00:00:06 Returning block of 12642723 Getting block 5 of 7 Reserving size (16520520) 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 8589572 (Using difference cover) Sorting block time: 00:00:06 Returning block of 8589573 Getting block 6 of 7 Reserving size (16520520) 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 8247789 (Using difference cover) Sorting block time: 00:00:05 Returning block of 8247790 Getting block 7 of 7 Reserving size (16520520) 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 14011115 (Using difference cover) Sorting block time: 00:00:08 Returning block of 14011116 Exited Ebwt loop fchr[A]: 0 fchr[C]: 25605199 fchr[G]: 43949423 fchr[T]: 62440649 fchr[$]: 88109441 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 157503780 bytes to primary EBWT file: Sf_2_R2//tmp/segment_juncs.rev.1.ebwt Wrote 11013688 bytes to secondary EBWT file: Sf_2_R2//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 88109441 bwtLen: 88109442 sz: 22027361 bwtSz: 22027361 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2753421 offsSz: 11013684 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 196673 numSides: 393346 numLines: 393346 ebwtTotLen: 25174144 ebwtTotSz: 25174144 reverse: 0 Total time for backward call to driver() for mirror index: 00:01:44