Settings: Output files: "Ler_0//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: Ler_0//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: 00:00:07 bmax according to bmaxDivN setting: 27641843 Using parameters --bmax 20731383 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 20731383 --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: 00:00:13 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 7; 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: 1.38209e+07 (target: 20731382) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (20731383) 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 20074004 (Using difference cover) Sorting block time: 00:00:15 Returning block of 20074005 Getting block 2 of 8 Reserving size (20731383) 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 4837949 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4837950 Getting block 3 of 8 Reserving size (20731383) 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 17701776 (Using difference cover) Sorting block time: 00:00:17 Returning block of 17701777 Getting block 4 of 8 Reserving size (20731383) 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 17967136 (Using difference cover) Sorting block time: 00:00:17 Returning block of 17967137 Getting block 5 of 8 Reserving size (20731383) 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 10499755 (Using difference cover) Sorting block time: 00:00:08 Returning block of 10499756 Getting block 6 of 8 Reserving size (20731383) 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 18064774 (Using difference cover) Sorting block time: 00:00:15 Returning block of 18064775 Getting block 7 of 8 Reserving size (20731383) 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 6362171 (Using difference cover) Sorting block time: 00:00:06 Returning block of 6362172 Getting block 8 of 8 Reserving size (20731383) 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 15059800 (Using difference cover) Sorting block time: 00:00:12 Returning block of 15059801 Exited Ebwt loop fchr[A]: 0 fchr[C]: 33726917 fchr[G]: 55340112 fchr[T]: 76951815 fchr[$]: 110567372 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 196605836 bytes to primary EBWT file: Ler_0//tmp/segment_juncs.1.ebwt Wrote 13820928 bytes to secondary EBWT file: Ler_0//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 110567372 bwtLen: 110567373 sz: 27641843 bwtSz: 27641844 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3455231 offsSz: 13820924 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 246803 numSides: 493606 numLines: 493606 ebwtTotLen: 31590784 ebwtTotSz: 31590784 reverse: 0 Total time for call to driver() for forward index: 00:03:20 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: 27641843 Using parameters --bmax 20731383 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 20731383 --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: 00:00:02 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 Avg bucket size: 1.57953e+07 (target: 20731382) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (20731383) 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 18171264 (Using difference cover) Sorting block time: 00:00:14 Returning block of 18171265 Getting block 2 of 7 Reserving size (20731383) 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 20486125 (Using difference cover) Sorting block time: 00:00:20 Returning block of 20486126 Getting block 3 of 7 Reserving size (20731383) 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 20072319 (Using difference cover) Sorting block time: 00:00:18 Returning block of 20072320 Getting block 4 of 7 Reserving size (20731383) 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 8868781 (Using difference cover) Sorting block time: 00:00:12 Returning block of 8868782 Getting block 5 of 7 Reserving size (20731383) 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 18152954 (Using difference cover) Sorting block time: 00:00:18 Returning block of 18152955 Getting block 6 of 7 Reserving size (20731383) 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 16903402 (Using difference cover) Sorting block time: 00:00:16 Returning block of 16903403 Getting block 7 of 7 Reserving size (20731383) 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 7912521 (Using difference cover) Sorting block time: 00:00:09 Returning block of 7912522 Exited Ebwt loop fchr[A]: 0 fchr[C]: 33726917 fchr[G]: 55340112 fchr[T]: 76951815 fchr[$]: 110567372 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 196605836 bytes to primary EBWT file: Ler_0//tmp/segment_juncs.rev.1.ebwt Wrote 13820928 bytes to secondary EBWT file: Ler_0//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 110567372 bwtLen: 110567373 sz: 27641843 bwtSz: 27641844 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3455231 offsSz: 13820924 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 246803 numSides: 493606 numLines: 493606 ebwtTotLen: 31590784 ebwtTotSz: 31590784 reverse: 0 Total time for backward call to driver() for mirror index: 00:03:41