Settings: Output files: "MCTestisC12/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: MCTestisC12/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: 6535269 Using parameters --bmax 4901452 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4901452 --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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 5; iterating... 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 3; 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: 3.26763e+06 (target: 4901451) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (4901452) 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 2554388 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2554389 Getting block 2 of 8 Reserving size (4901452) 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 4091882 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4091883 Getting block 3 of 8 Reserving size (4901452) 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 1070968 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1070969 Getting block 4 of 8 Reserving size (4901452) 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 4696784 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4696785 Getting block 5 of 8 Reserving size (4901452) 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 2585714 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2585715 Getting block 6 of 8 Reserving size (4901452) 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 3545889 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3545890 Getting block 7 of 8 Reserving size (4901452) 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 4561809 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4561810 Getting block 8 of 8 Reserving size (4901452) 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 3033635 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3033636 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6466101 fchr[G]: 13111837 fchr[T]: 19483082 fchr[$]: 26141076 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 46773825 bytes to primary EBWT file: MCTestisC12/tmp/segment_juncs.1.bt2 Wrote 6535276 bytes to secondary EBWT file: MCTestisC12/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 26141076 bwtLen: 26141077 sz: 6535269 bwtSz: 6535270 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1633818 offsSz: 6535272 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 136152 numLines: 136152 ebwtTotLen: 8713728 ebwtTotSz: 8713728 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:27 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: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 6535269 Using parameters --bmax 4901452 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4901452 --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: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Split 2, 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 Split 1, merged 2; 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: 3.73444e+06 (target: 4901451) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4901452) 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 4726830 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4726831 Getting block 2 of 7 Reserving size (4901452) 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 3619260 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3619261 Getting block 3 of 7 Reserving size (4901452) 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 3306948 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3306949 Getting block 4 of 7 Reserving size (4901452) 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 4814968 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4814969 Getting block 5 of 7 Reserving size (4901452) 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 4198607 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4198608 Getting block 6 of 7 Reserving size (4901452) 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 2634337 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2634338 Getting block 7 of 7 Reserving size (4901452) 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 2840120 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2840121 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6466101 fchr[G]: 13111837 fchr[T]: 19483082 fchr[$]: 26141076 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 46773825 bytes to primary EBWT file: MCTestisC12/tmp/segment_juncs.rev.1.bt2 Wrote 6535276 bytes to secondary EBWT file: MCTestisC12/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 26141076 bwtLen: 26141077 sz: 6535269 bwtSz: 6535270 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1633818 offsSz: 6535272 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 136152 numLines: 136152 ebwtTotLen: 8713728 ebwtTotSz: 8713728 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:24