Settings: Output files: "MCKidney16b/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: MCKidney16b/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 3989554 Using parameters --bmax 2992166 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2992166 --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 7; 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: 2.27974e+06 (target: 2992165) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2992166) 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 2327399 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2327400 Getting block 2 of 7 Reserving size (2992166) 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 1946535 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1946536 Getting block 3 of 7 Reserving size (2992166) 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 2923095 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2923096 Getting block 4 of 7 Reserving size (2992166) 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 1397005 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1397006 Getting block 5 of 7 Reserving size (2992166) 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 1946598 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1946599 Getting block 6 of 7 Reserving size (2992166) 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 2923739 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2923740 Getting block 7 of 7 Reserving size (2992166) 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 2493841 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2493842 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3870954 fchr[G]: 8019541 fchr[T]: 11934345 fchr[$]: 15958218 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 30209712 bytes to primary EBWT file: MCKidney16b/tmp/segment_juncs.1.bt2 Wrote 3989560 bytes to secondary EBWT file: MCKidney16b/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 15958218 bwtLen: 15958219 sz: 3989555 bwtSz: 3989555 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 997389 offsSz: 3989556 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 83116 numLines: 83116 ebwtTotLen: 5319424 ebwtTotSz: 5319424 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:11 Reading reference sizes Time reading reference sizes: 00:00:00 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: 3989554 Using parameters --bmax 2992166 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2992166 --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 Avg bucket size: 2.27974e+06 (target: 2992165) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2992166) 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 1282541 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1282542 Getting block 2 of 7 Reserving size (2992166) 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 2890247 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2890248 Getting block 3 of 7 Reserving size (2992166) 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 2648628 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2648629 Getting block 4 of 7 Reserving size (2992166) 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 2814286 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2814287 Getting block 5 of 7 Reserving size (2992166) 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 2465623 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2465624 Getting block 6 of 7 Reserving size (2992166) 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 1484815 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1484816 Getting block 7 of 7 Reserving size (2992166) 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 2372072 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2372073 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3870954 fchr[G]: 8019541 fchr[T]: 11934345 fchr[$]: 15958218 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 30209712 bytes to primary EBWT file: MCKidney16b/tmp/segment_juncs.rev.1.bt2 Wrote 3989560 bytes to secondary EBWT file: MCKidney16b/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 15958218 bwtLen: 15958219 sz: 3989555 bwtSz: 3989555 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 997389 offsSz: 3989556 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 83116 numLines: 83116 ebwtTotLen: 5319424 ebwtTotSz: 5319424 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:10