Settings: Output files: "Sf_2_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: Sf_2_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: 28136521 Using parameters --bmax 21102391 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 21102391 --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: 00:00:00 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: 00:00:08 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 8; 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: 00:00:08 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.6078e+07 (target: 21102390) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (21102391) 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 19492739 (Using difference cover) Sorting block time: 00:00:12 Returning block of 19492740 Getting block 2 of 7 Reserving size (21102391) 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 17229071 (Using difference cover) Sorting block time: 00:00:12 Returning block of 17229072 Getting block 3 of 7 Reserving size (21102391) 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 8474205 (Using difference cover) Sorting block time: 00:00:05 Returning block of 8474206 Getting block 4 of 7 Reserving size (21102391) 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 13544752 (Using difference cover) Sorting block time: 00:00:12 Returning block of 13544753 Getting block 5 of 7 Reserving size (21102391) 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 15779496 (Using difference cover) Sorting block time: 00:00:11 Returning block of 15779497 Getting block 6 of 7 Reserving size (21102391) 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 17244933 (Using difference cover) Sorting block time: 00:00:11 Returning block of 17244934 Getting block 7 of 7 Reserving size (21102391) 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 20780883 (Using difference cover) Sorting block time: 00:00:13 Returning block of 20780884 Exited Ebwt loop fchr[A]: 0 fchr[C]: 32793024 fchr[G]: 56127394 fchr[T]: 79703371 fchr[$]: 112546085 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 199997603 bytes to primary EBWT file: Sf_2_R1//tmp/segment_juncs.1.ebwt Wrote 14068268 bytes to secondary EBWT file: Sf_2_R1//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 112546085 bwtLen: 112546086 sz: 28136522 bwtSz: 28136522 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3517066 offsSz: 14068264 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 251219 numSides: 502438 numLines: 502438 ebwtTotLen: 32156032 ebwtTotSz: 32156032 reverse: 0 Total time for call to driver() for forward index: 00:02:32 Reading reference sizes Time reading reference sizes: 00:00:04 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:11 bmax according to bmaxDivN setting: 28136521 Using parameters --bmax 21102391 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 21102391 --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: 00:00:02 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: 00:00:14 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: 00:00:13 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.40683e+07 (target: 21102390) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (21102391) 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 13979780 (Using difference cover) Sorting block time: 00:00:11 Returning block of 13979781 Getting block 2 of 8 Reserving size (21102391) 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 7921743 (Using difference cover) Sorting block time: 00:00:06 Returning block of 7921744 Getting block 3 of 8 Reserving size (21102391) 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 19014719 (Using difference cover) Sorting block time: 00:00:17 Returning block of 19014720 Getting block 4 of 8 Reserving size (21102391) 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 9441701 (Using difference cover) Sorting block time: 00:00:05 Returning block of 9441702 Getting block 5 of 8 Reserving size (21102391) 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 20570160 (Using difference cover) Sorting block time: 00:00:12 Returning block of 20570161 Getting block 6 of 8 Reserving size (21102391) 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 10322335 (Using difference cover) Sorting block time: 00:00:07 Returning block of 10322336 Getting block 7 of 8 Reserving size (21102391) 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 18939185 (Using difference cover) Sorting block time: 00:00:09 Returning block of 18939186 Getting block 8 of 8 Reserving size (21102391) 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 12356455 (Using difference cover) Sorting block time: 00:00:06 Returning block of 12356456 Exited Ebwt loop fchr[A]: 0 fchr[C]: 32793024 fchr[G]: 56127394 fchr[T]: 79703371 fchr[$]: 112546085 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 199997603 bytes to primary EBWT file: Sf_2_R1//tmp/segment_juncs.rev.1.ebwt Wrote 14068268 bytes to secondary EBWT file: Sf_2_R1//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 112546085 bwtLen: 112546086 sz: 28136522 bwtSz: 28136522 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3517066 offsSz: 14068264 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 251219 numSides: 502438 numLines: 502438 ebwtTotLen: 32156032 ebwtTotSz: 32156032 reverse: 0 Total time for backward call to driver() for mirror index: 00:02:48