Settings: Output files: "Sf_2//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//tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:06 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:10 bmax according to bmaxDivN setting: 26043604 Using parameters --bmax 19532703 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 19532703 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:06 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: 00:00:03 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: 00:00:17 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: 00:00:14 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.30218e+07 (target: 19532702) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (19532703) 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 13948882 (Using difference cover) Sorting block time: 00:00:13 Returning block of 13948883 Getting block 2 of 8 Reserving size (19532703) 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: 00:00:04 Sorting block of length 8008977 (Using difference cover) Sorting block time: 00:00:09 Returning block of 8008978 Getting block 3 of 8 Reserving size (19532703) 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: 00:00:05 Sorting block of length 13371763 (Using difference cover) Sorting block time: 00:00:16 Returning block of 13371764 Getting block 4 of 8 Reserving size (19532703) 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: 00:00:05 Sorting block of length 9256644 (Using difference cover) Sorting block time: 00:00:09 Returning block of 9256645 Getting block 5 of 8 Reserving size (19532703) 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: 00:00:05 Sorting block of length 19170637 (Using difference cover) Sorting block time: 00:00:22 Returning block of 19170638 Getting block 6 of 8 Reserving size (19532703) 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: 00:00:05 Sorting block of length 11793166 (Using difference cover) Sorting block time: 00:00:08 Returning block of 11793167 Getting block 7 of 8 Reserving size (19532703) 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: 00:00:05 Sorting block of length 14123411 (Using difference cover) Sorting block time: 00:00:13 Returning block of 14123412 Getting block 8 of 8 Reserving size (19532703) 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 14500929 (Using difference cover) Sorting block time: 00:00:15 Returning block of 14500930 Exited Ebwt loop fchr[A]: 0 fchr[C]: 31553126 fchr[G]: 52091904 fchr[T]: 72706965 fchr[$]: 104174416 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 185411327 bytes to primary EBWT file: Sf_2//tmp/segment_juncs.1.ebwt Wrote 13021808 bytes to secondary EBWT file: Sf_2//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 104174416 bwtLen: 104174417 sz: 26043604 bwtSz: 26043605 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3255451 offsSz: 13021804 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 232533 numSides: 465066 numLines: 465066 ebwtTotLen: 29764224 ebwtTotSz: 29764224 reverse: 0 Total time for call to driver() for forward index: 00:03:46 Reading reference sizes Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:09 bmax according to bmaxDivN setting: 26043604 Using parameters --bmax 19532703 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 19532703 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:05 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 Split 1, merged 5; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:07 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.30218e+07 (target: 19532702) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (19532703) 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 4033524 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4033525 Getting block 2 of 8 Reserving size (19532703) 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 16566768 (Using difference cover) Sorting block time: 00:00:10 Returning block of 16566769 Getting block 3 of 8 Reserving size (19532703) 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 13649771 (Using difference cover) Sorting block time: 00:00:07 Returning block of 13649772 Getting block 4 of 8 Reserving size (19532703) 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 16353878 (Using difference cover) Sorting block time: 00:00:13 Returning block of 16353879 Getting block 5 of 8 Reserving size (19532703) 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 5165905 (Using difference cover) Sorting block time: 00:00:04 Returning block of 5165906 Getting block 6 of 8 Reserving size (19532703) 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 15394499 (Using difference cover) Sorting block time: 00:00:13 Returning block of 15394500 Getting block 7 of 8 Reserving size (19532703) 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: 00:00:06 Sorting block of length 17597708 (Using difference cover) Sorting block time: 00:00:13 Returning block of 17597709 Getting block 8 of 8 Reserving size (19532703) 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 15412356 (Using difference cover) Sorting block time: 00:00:08 Returning block of 15412357 Exited Ebwt loop fchr[A]: 0 fchr[C]: 31553126 fchr[G]: 52091904 fchr[T]: 72706965 fchr[$]: 104174416 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 185411327 bytes to primary EBWT file: Sf_2//tmp/segment_juncs.rev.1.ebwt Wrote 13021808 bytes to secondary EBWT file: Sf_2//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 104174416 bwtLen: 104174417 sz: 26043604 bwtSz: 26043605 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3255451 offsSz: 13021804 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 232533 numSides: 465066 numLines: 465066 ebwtTotLen: 29764224 ebwtTotSz: 29764224 reverse: 0 Total time for backward call to driver() for mirror index: 00:02:31