Settings: Output files: "MCKidneyE1b/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: MCKidneyE1b/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: 4422847 Using parameters --bmax 3317136 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3317136 --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: 00:00:00 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: 00:00:01 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.21142e+06 (target: 3317135) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3317136) 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 1315579 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1315580 Getting block 2 of 8 Reserving size (3317136) 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 2370177 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2370178 Getting block 3 of 8 Reserving size (3317136) 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 3229820 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3229821 Getting block 4 of 8 Reserving size (3317136) 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 481036 (Using difference cover) Sorting block time: 00:00:00 Returning block of 481037 Getting block 5 of 8 Reserving size (3317136) 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 2848710 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2848711 Getting block 6 of 8 Reserving size (3317136) 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 2227676 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2227677 Getting block 7 of 8 Reserving size (3317136) 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 3001937 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3001938 Getting block 8 of 8 Reserving size (3317136) 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 2216446 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2216447 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4273118 fchr[G]: 8866050 fchr[T]: 13236899 fchr[$]: 17691388 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 33032583 bytes to primary EBWT file: MCKidneyE1b/tmp/segment_juncs.1.bt2 Wrote 4422852 bytes to secondary EBWT file: MCKidneyE1b/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17691388 bwtLen: 17691389 sz: 4422847 bwtSz: 4422848 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1105712 offsSz: 4422848 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 92143 numLines: 92143 ebwtTotLen: 5897152 ebwtTotSz: 5897152 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:14 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: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 4422847 Using parameters --bmax 3317136 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3317136 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:01 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: 00:00:00 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: 00:00:01 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.21142e+06 (target: 3317135) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3317136) 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 2877437 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2877438 Getting block 2 of 8 Reserving size (3317136) 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 2544805 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2544806 Getting block 3 of 8 Reserving size (3317136) 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 1441356 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1441357 Getting block 4 of 8 Reserving size (3317136) 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 2496946 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2496947 Getting block 5 of 8 Reserving size (3317136) 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 2366012 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2366013 Getting block 6 of 8 Reserving size (3317136) 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 1510337 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1510338 Getting block 7 of 8 Reserving size (3317136) 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 2874663 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2874664 Getting block 8 of 8 Reserving size (3317136) 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 1579825 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1579826 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4273118 fchr[G]: 8866050 fchr[T]: 13236899 fchr[$]: 17691388 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 33032583 bytes to primary EBWT file: MCKidneyE1b/tmp/segment_juncs.rev.1.bt2 Wrote 4422852 bytes to secondary EBWT file: MCKidneyE1b/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17691388 bwtLen: 17691389 sz: 4422847 bwtSz: 4422848 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1105712 offsSz: 4422848 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 92143 numLines: 92143 ebwtTotLen: 5897152 ebwtTotSz: 5897152 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:14