Settings: Output files: "MCTestisE1b/tmp/segment_juncs.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) 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: MCTestisE1b/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:01 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 bmax according to bmaxDivN setting: 6718802 Using parameters --bmax 5039102 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 5039102 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 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: 00:00:00 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: 00:00:02 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.3594e+06 (target: 5039101) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (5039102) 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: 00:00:00 Sorting block of length 4763846 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4763847 Getting block 2 of 8 Reserving size (5039102) 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 3668453 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3668454 Getting block 3 of 8 Reserving size (5039102) 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: 00:00:00 Sorting block of length 5036857 (Using difference cover) Sorting block time: 00:00:02 Returning block of 5036858 Getting block 4 of 8 Reserving size (5039102) 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: 00:00:00 Sorting block of length 2222294 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2222295 Getting block 5 of 8 Reserving size (5039102) 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: 00:00:00 Sorting block of length 5032188 (Using difference cover) Sorting block time: 00:00:02 Returning block of 5032189 Getting block 6 of 8 Reserving size (5039102) 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: 00:00:00 Sorting block of length 514028 (Using difference cover) Sorting block time: 00:00:01 Returning block of 514029 Getting block 7 of 8 Reserving size (5039102) 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: 00:00:00 Sorting block of length 4557585 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4557586 Getting block 8 of 8 Reserving size (5039102) 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: 00:00:00 Sorting block of length 1079950 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1079951 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6629853 fchr[G]: 13482723 fchr[T]: 20026493 fchr[$]: 26875208 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 47960880 bytes to primary EBWT file: MCTestisE1b/tmp/segment_juncs.1.bt2 Wrote 6718808 bytes to secondary EBWT file: MCTestisE1b/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 26875208 bwtLen: 26875209 sz: 6718802 bwtSz: 6718803 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1679701 offsSz: 6718804 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 139976 numLines: 139976 ebwtTotLen: 8958464 ebwtTotSz: 8958464 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:25 Reading reference sizes Time reading reference sizes: 00:00:01 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 6718802 Using parameters --bmax 5039102 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 5039102 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.83931e+06 (target: 5039101) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (5039102) 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 4215990 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4215991 Getting block 2 of 7 Reserving size (5039102) 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: 00:00:00 Sorting block of length 4517712 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4517713 Getting block 3 of 7 Reserving size (5039102) 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: 00:00:00 Sorting block of length 2310825 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2310826 Getting block 4 of 7 Reserving size (5039102) 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 4087985 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4087986 Getting block 5 of 7 Reserving size (5039102) 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 3296389 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3296390 Getting block 6 of 7 Reserving size (5039102) 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 4794996 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4794997 Getting block 7 of 7 Reserving size (5039102) 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: 00:00:00 Sorting block of length 3651305 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3651306 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6629853 fchr[G]: 13482723 fchr[T]: 20026493 fchr[$]: 26875208 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 47960880 bytes to primary EBWT file: MCTestisE1b/tmp/segment_juncs.rev.1.bt2 Wrote 6718808 bytes to secondary EBWT file: MCTestisE1b/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 26875208 bwtLen: 26875209 sz: 6718802 bwtSz: 6718803 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1679701 offsSz: 6718804 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 139976 numLines: 139976 ebwtTotLen: 8958464 ebwtTotSz: 8958464 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:23