Settings: Output files: "4M/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: 4M/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: 5578220 Using parameters --bmax 4183665 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4183665 --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 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 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: 3.18755e+06 (target: 4183664) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4183665) 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 3456336 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3456337 Getting block 2 of 7 Reserving size (4183665) 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 2460587 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2460588 Getting block 3 of 7 Reserving size (4183665) 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 3133170 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3133171 Getting block 4 of 7 Reserving size (4183665) 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 3018826 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3018827 Getting block 5 of 7 Reserving size (4183665) 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 4074011 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4074012 Getting block 6 of 7 Reserving size (4183665) 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 4061591 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4061592 Getting block 7 of 7 Reserving size (4183665) 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 2108354 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2108355 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6399515 fchr[G]: 11250678 fchr[T]: 15849663 fchr[$]: 22312881 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 39140334 bytes to primary EBWT file: 4M/tmp/segment_juncs.1.bt2 Wrote 5578228 bytes to secondary EBWT file: 4M/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 22312881 bwtLen: 22312882 sz: 5578221 bwtSz: 5578221 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1394556 offsSz: 5578224 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 116213 numLines: 116213 ebwtTotLen: 7437632 ebwtTotSz: 7437632 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: 5578220 Using parameters --bmax 4183665 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4183665 --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 Avg bucket size: 3.18755e+06 (target: 4183664) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4183665) 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 3923025 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3923026 Getting block 2 of 7 Reserving size (4183665) 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 3726321 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3726322 Getting block 3 of 7 Reserving size (4183665) 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 2507690 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2507691 Getting block 4 of 7 Reserving size (4183665) 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 3972525 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3972526 Getting block 5 of 7 Reserving size (4183665) 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 3382397 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3382398 Getting block 6 of 7 Reserving size (4183665) 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 2885549 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2885550 Getting block 7 of 7 Reserving size (4183665) 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 1915368 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1915369 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6399515 fchr[G]: 11250678 fchr[T]: 15849663 fchr[$]: 22312881 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 39140334 bytes to primary EBWT file: 4M/tmp/segment_juncs.rev.1.bt2 Wrote 5578228 bytes to secondary EBWT file: 4M/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 22312881 bwtLen: 22312882 sz: 5578221 bwtSz: 5578221 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1394556 offsSz: 5578224 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 116213 numLines: 116213 ebwtTotLen: 7437632 ebwtTotSz: 7437632 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:23