nohup: ignoring input Settings: Output files: "GCA_009914755.4.*.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: 32 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: GCA_009914755.4.fa Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:27 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:21 bmax according to bmaxDivN setting: 97415377 Using parameters --bmax 73061533 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 73061533 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:38 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:26 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:41 Sanity-checking and returning Building samples Reserving space for 86 sample suffixes Generating random suffixes QSorting 86 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 86 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 13, merged 36; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 9, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 5, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 4, merged 4; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 3; iterating... Avg bucket size: 4.94808e+07 (target: 73061532) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 2 of 63 Getting block 1 of 63 Reserving size (73061533) for bucket 2 Reserving size (73061533) for bucket 1 Getting block 3 of 63 Getting block 4 of 63 Getting block 5 of 63 Getting block 6 of 63 Getting block 7 of 63 Reserving size (73061533) for bucket 3 Reserving size (73061533) for bucket 4 Getting block 8 of 63 Calculating Z arrays for bucket 1 Reserving size (73061533) for bucket 5 Reserving size (73061533) for bucket 6 Reserving size (73061533) for bucket 7 Reserving size (73061533) for bucket 8 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 8 Entering block accumulator loop for bucket 2: Entering block accumulator loop for bucket 8: Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 5: bucket 1: 10% bucket 2: 10% bucket 3: 10% bucket 4: 10% bucket 5: 10% bucket 6: 10% bucket 8: 10% bucket 7: 10% bucket 1: 20% bucket 2: 20% bucket 3: 20% bucket 4: 20% bucket 5: 20% bucket 6: 20% bucket 8: 20% bucket 7: 20% bucket 1: 30% bucket 3: 30% bucket 2: 30% bucket 5: 30% bucket 6: 30% bucket 4: 30% bucket 8: 30% bucket 1: 40% bucket 7: 30% bucket 3: 40% bucket 2: 40% bucket 5: 40% bucket 6: 40% bucket 1: 50% bucket 4: 40% bucket 8: 40% bucket 7: 40% bucket 2: 50% bucket 3: 50% bucket 5: 50% bucket 1: 60% bucket 4: 50% bucket 6: 50% bucket 8: 50% bucket 7: 50% bucket 2: 60% bucket 3: 60% bucket 1: 70% bucket 5: 60% bucket 4: 60% bucket 6: 60% bucket 8: 60% bucket 2: 70% bucket 3: 70% bucket 7: 60% bucket 1: 80% bucket 5: 70% bucket 4: 70% bucket 6: 70% bucket 2: 80% bucket 8: 70% bucket 3: 80% bucket 7: 70% bucket 1: 90% bucket 5: 80% bucket 4: 80% bucket 6: 80% bucket 2: 90% bucket 3: 90% bucket 8: 80% bucket 1: 100% Sorting block of length 39841499 for bucket 1 (Using difference cover) bucket 7: 80% bucket 5: 90% bucket 4: 90% bucket 2: 100% Sorting block of length 45750114 for bucket 2 (Using difference cover) bucket 6: 90% bucket 3: 100% Sorting block of length 47729641 for bucket 3 (Using difference cover) bucket 8: 90% bucket 5: 100% Sorting block of length 59356211 for bucket 5 (Using difference cover) bucket 7: 90% bucket 4: 100% Sorting block of length 47146750 for bucket 4 (Using difference cover) bucket 6: 100% Sorting block of length 31575258 for bucket 6 (Using difference cover) bucket 8: 100% Sorting block of length 36519317 for bucket 8 (Using difference cover) bucket 7: 100% Sorting block of length 54211430 for bucket 7 (Using difference cover) Sorting block time: 00:00:23 Returning block of 39841500 for bucket 1 Getting block 9 of 63 Reserving size (73061533) for bucket 9 Calculating Z arrays for bucket 9 Entering block accumulator loop for bucket 9: bucket 9: 10% bucket 9: 20% Sorting block time: 00:00:27 Returning block of 36519318 for bucket 8 Sorting block time: 00:00:32 Returning block of 47729642 for bucket 3 Sorting block time: 00:00:33 Returning block of 45750115 for bucket 2 Getting block 10 of 63 Reserving size (73061533) for bucket 10 Calculating Z arrays for bucket 10 Entering block accumulator loop for bucket 10: Getting block 11 of 63 Reserving size (73061533) for bucket 11 Calculating Z arrays for bucket 11 Entering block accumulator loop for bucket 11: bucket 9: 30% Getting block 12 of 63 Reserving size (73061533) for bucket 12 Calculating Z arrays for bucket 12 Entering block accumulator loop for bucket 12: Sorting block time: 00:00:34 Returning block of 47146751 for bucket 4 Sorting block time: 00:00:34 Returning block of 31575259 for bucket 6 bucket 10: 10% Getting block 13 of 63 Reserving size (73061533) for bucket 13 Calculating Z arrays for bucket 13 Entering block accumulator loop for bucket 13: Getting block 14 of 63 Reserving size (73061533) for bucket 14 Calculating Z arrays for bucket 14 Entering block accumulator loop for bucket 14: bucket 11: 10% bucket 9: 40% bucket 12: 10% Sorting block time: 00:00:40 Returning block of 59356212 for bucket 5 bucket 10: 20% bucket 9: 50% bucket 11: 20% bucket 13: 10% bucket 14: 10% bucket 12: 20% Getting block 15 of 63 Reserving size (73061533) for bucket 15 Calculating Z arrays for bucket 15 Entering block accumulator loop for bucket 15: bucket 10: 30% Sorting block time: 00:00:42 Returning block of 54211431 for bucket 7 bucket 9: 60% bucket 11: 30% bucket 13: 20% bucket 14: 20% bucket 12: 30% bucket 15: 10% Getting block 16 of 63 Reserving size (73061533) for bucket 16 Calculating Z arrays for bucket 16 Entering block accumulator loop for bucket 16: bucket 10: 40% bucket 9: 70% bucket 11: 40% bucket 13: 30% bucket 14: 30% bucket 12: 40% bucket 15: 20% bucket 16: 10% bucket 10: 50% bucket 9: 80% bucket 11: 50% bucket 13: 40% bucket 12: 50% bucket 14: 40% bucket 16: 20% bucket 15: 30% bucket 10: 60% bucket 9: 90% bucket 11: 60% bucket 13: 50% bucket 14: 50% bucket 12: 60% bucket 15: 40% bucket 16: 30% bucket 10: 70% bucket 9: 100% Sorting block of length 67357268 for bucket 9 (Using difference cover) bucket 11: 70% bucket 14: 60% bucket 15: 50% bucket 16: 40% bucket 13: 60% bucket 12: 70% bucket 10: 80% bucket 11: 80% bucket 15: 60% bucket 16: 50% bucket 14: 70% bucket 12: 80% bucket 13: 70% bucket 10: 90% bucket 11: 90% bucket 16: 60% bucket 15: 70% bucket 14: 80% bucket 12: 90% bucket 10: 100% Sorting block of length 51477260 for bucket 10 (Using difference cover) bucket 13: 80% bucket 11: 100% Sorting block of length 33596021 for bucket 11 (Using difference cover) bucket 16: 70% bucket 15: 80% bucket 14: 90% bucket 12: 100% Sorting block of length 72687885 for bucket 12 (Using difference cover) bucket 13: 90% bucket 15: 90% bucket 16: 80% bucket 14: 100% Sorting block of length 27407245 for bucket 14 (Using difference cover) bucket 13: 100% Sorting block of length 57813395 for bucket 13 (Using difference cover) bucket 15: 100% Sorting block of length 48310489 for bucket 15 (Using difference cover) bucket 16: 90% bucket 16: 100% Sorting block of length 31560353 for bucket 16 (Using difference cover) Sorting block time: 00:00:24 Returning block of 33596022 for bucket 11 Sorting block time: 00:00:18 Returning block of 27407246 for bucket 14 Getting block 17 of 63 Reserving size (73061533) for bucket 17 Calculating Z arrays for bucket 17 Entering block accumulator loop for bucket 17: Getting block 18 of 63 Reserving size (73061533) for bucket 18 Calculating Z arrays for bucket 18 Entering block accumulator loop for bucket 18: bucket 17: 10% bucket 18: 10% Sorting block time: 00:00:34 Returning block of 51477261 for bucket 10 Sorting block time: 00:00:45 Returning block of 67357269 for bucket 9 bucket 17: 20% Getting block 19 of 63 Reserving size (73061533) for bucket 19 Calculating Z arrays for bucket 19 Entering block accumulator loop for bucket 19: bucket 18: 20% Getting block 20 of 63 Reserving size (73061533) for bucket 20 Calculating Z arrays for bucket 20 Entering block accumulator loop for bucket 20: bucket 17: 30% bucket 19: 10% bucket 18: 30% bucket 20: 10% Sorting block time: 00:00:26 Returning block of 31560354 for bucket 16 bucket 17: 40% Sorting block time: 00:00:34 Returning block of 57813396 for bucket 13 bucket 19: 20% bucket 18: 40% Getting block 21 of 63 Reserving size (73061533) for bucket 21 Calculating Z arrays for bucket 21 Entering block accumulator loop for bucket 21: Sorting block time: 00:00:34 Returning block of 48310490 for bucket 15 bucket 20: 20% Getting block 22 of 63 Reserving size (73061533) for bucket 22 Calculating Z arrays for bucket 22 Entering block accumulator loop for bucket 22: bucket 17: 50% Sorting block time: 00:00:43 Returning block of 72687886 for bucket 12 bucket 18: 50% bucket 19: 30% Getting block 23 of 63 Reserving size (73061533) for bucket 23 Calculating Z arrays for bucket 23 Entering block accumulator loop for bucket 23: bucket 21: 10% bucket 20: 30% bucket 22: 10% Getting block 24 of 63 Reserving size (73061533) for bucket 24 Calculating Z arrays for bucket 24 Entering block accumulator loop for bucket 24: bucket 17: 60% bucket 19: 40% bucket 18: 60% bucket 23: 10% bucket 21: 20% bucket 22: 20% bucket 20: 40% bucket 24: 10% bucket 17: 70% bucket 19: 50% bucket 18: 70% bucket 21: 30% bucket 23: 20% bucket 22: 30% bucket 24: 20% bucket 20: 50% bucket 17: 80% bucket 19: 60% bucket 18: 80% bucket 23: 30% bucket 21: 40% bucket 22: 40% bucket 24: 30% bucket 20: 60% bucket 17: 90% bucket 19: 70% bucket 18: 90% bucket 21: 50% bucket 23: 40% bucket 22: 50% bucket 24: 40% bucket 17: 100% Sorting block of length 72255361 for bucket 17 (Using difference cover) bucket 19: 80% bucket 18: 100% Sorting block of length 30350216 for bucket 18 (Using difference cover) bucket 20: 70% bucket 23: 50% bucket 21: 60% bucket 22: 60% bucket 24: 50% bucket 19: 90% bucket 20: 80% bucket 21: 70% bucket 23: 60% bucket 22: 70% bucket 24: 60% bucket 19: 100% Sorting block of length 49964059 for bucket 19 (Using difference cover) bucket 20: 90% bucket 21: 80% bucket 23: 70% bucket 22: 80% bucket 24: 70% bucket 20: 100% Sorting block of length 44970677 for bucket 20 (Using difference cover) bucket 21: 90% bucket 23: 80% bucket 22: 90% bucket 24: 80% bucket 21: 100% Sorting block of length 67489329 for bucket 21 (Using difference cover) Sorting block time: 00:00:21 Returning block of 30350217 for bucket 18 bucket 23: 90% bucket 22: 100% Sorting block of length 15127015 for bucket 22 (Using difference cover) Getting block 25 of 63 Reserving size (73061533) for bucket 25 Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 25: bucket 24: 90% bucket 23: 100% Sorting block of length 69689112 for bucket 23 (Using difference cover) bucket 25: 10% bucket 24: 100% Sorting block of length 71022513 for bucket 24 (Using difference cover) bucket 25: 20% Sorting block time: 00:00:12 Returning block of 15127016 for bucket 22 Getting block 26 of 63 Reserving size (73061533) for bucket 26 Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 26: bucket 25: 30% bucket 26: 10% bucket 25: 40% bucket 26: 20% bucket 25: 50% Sorting block time: 00:00:34 Returning block of 44970678 for bucket 20 bucket 26: 30% bucket 25: 60% Getting block 27 of 63 Reserving size (73061533) for bucket 27 Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 27: bucket 26: 40% bucket 25: 70% bucket 27: 10% bucket 26: 50% Sorting block time: 00:00:51 Returning block of 49964060 for bucket 19 bucket 25: 80% bucket 27: 20% Getting block 28 of 63 Reserving size (73061533) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 26: 60% bucket 25: 90% bucket 27: 30% bucket 28: 10% Sorting block time: 00:00:48 Returning block of 67489330 for bucket 21 Sorting block time: 00:01:09 Returning block of 72255362 for bucket 17 bucket 26: 70% bucket 25: 100% Sorting block of length 36534849 for bucket 25 (Using difference cover) Getting block 29 of 63 Reserving size (73061533) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 27: 40% Getting block 30 of 63 Reserving size (73061533) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: Sorting block time: 00:00:47 Returning block of 69689113 for bucket 23 bucket 28: 20% bucket 26: 80% Getting block 31 of 63 Reserving size (73061533) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: bucket 29: 10% bucket 27: 50% bucket 30: 10% bucket 28: 30% bucket 26: 90% bucket 31: 10% bucket 29: 20% bucket 27: 60% bucket 26: 100% Sorting block of length 39167379 for bucket 26 (Using difference cover) bucket 30: 20% bucket 28: 40% bucket 29: 30% bucket 27: 70% bucket 31: 20% Sorting block time: 00:01:00 Returning block of 71022514 for bucket 24 bucket 28: 50% bucket 30: 30% bucket 27: 80% bucket 29: 40% Getting block 32 of 63 Reserving size (73061533) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: bucket 31: 30% bucket 28: 60% bucket 30: 40% bucket 29: 50% bucket 27: 90% bucket 32: 10% bucket 31: 40% bucket 28: 70% bucket 30: 50% bucket 27: 100% Sorting block of length 66300509 for bucket 27 (Using difference cover) bucket 29: 60% Sorting block time: 00:00:31 Returning block of 36534850 for bucket 25 bucket 31: 50% bucket 32: 20% bucket 28: 80% bucket 30: 60% Getting block 33 of 63 Reserving size (73061533) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: bucket 29: 70% bucket 32: 30% bucket 31: 60% Sorting block time: 00:00:24 Returning block of 39167380 for bucket 26 bucket 28: 90% bucket 30: 70% Getting block 34 of 63 Reserving size (73061533) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: bucket 33: 10% bucket 29: 80% bucket 28: 100% Sorting block of length 67922256 for bucket 28 (Using difference cover) bucket 31: 70% bucket 32: 40% bucket 30: 80% bucket 34: 10% bucket 29: 90% bucket 33: 20% bucket 31: 80% bucket 32: 50% bucket 30: 90% bucket 34: 20% bucket 29: 100% Sorting block of length 33179705 for bucket 29 (Using difference cover) bucket 33: 30% bucket 31: 90% bucket 32: 60% bucket 30: 100% Sorting block of length 56969780 for bucket 30 (Using difference cover) bucket 34: 30% bucket 31: 100% Sorting block of length 39668086 for bucket 31 (Using difference cover) bucket 32: 70% bucket 33: 40% bucket 34: 40% bucket 32: 80% bucket 33: 50% bucket 34: 50% bucket 32: 90% bucket 34: 60% bucket 33: 60% Sorting block time: 00:00:21 Returning block of 33179706 for bucket 29 bucket 32: 100% Sorting block of length 44464046 for bucket 32 (Using difference cover) Getting block 35 of 63 Reserving size (73061533) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: bucket 34: 70% bucket 33: 70% Sorting block time: 00:00:43 Returning block of 66300510 for bucket 27 bucket 35: 10% bucket 34: 80% Getting block 36 of 63 Reserving size (73061533) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: Sorting block time: 00:00:23 Returning block of 39668087 for bucket 31 bucket 33: 80% Getting block 37 of 63 Reserving size (73061533) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: bucket 35: 20% bucket 34: 90% bucket 36: 10% bucket 33: 90% bucket 37: 10% bucket 35: 30% bucket 34: 100% Sorting block of length 45502179 for bucket 34 (Using difference cover) Sorting block time: 00:00:35 Returning block of 56969781 for bucket 30 bucket 36: 20% Getting block 38 of 63 Reserving size (73061533) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: bucket 37: 20% bucket 33: 100% Sorting block of length 70715608 for bucket 33 (Using difference cover) Sorting block time: 00:00:48 Returning block of 67922257 for bucket 28 bucket 35: 40% bucket 36: 30% Getting block 39 of 63 Reserving size (73061533) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: bucket 38: 10% bucket 37: 30% bucket 35: 50% bucket 36: 40% bucket 39: 10% bucket 38: 20% Sorting block time: 00:00:29 Returning block of 44464047 for bucket 32 bucket 35: 60% bucket 37: 40% Getting block 40 of 63 Reserving size (73061533) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: bucket 36: 50% bucket 39: 20% bucket 38: 30% bucket 37: 50% bucket 35: 70% bucket 40: 10% bucket 36: 60% bucket 39: 30% bucket 38: 40% bucket 37: 60% bucket 40: 20% bucket 35: 80% bucket 36: 70% bucket 39: 40% bucket 38: 50% Sorting block time: 00:00:29 Returning block of 45502180 for bucket 34 bucket 37: 70% bucket 40: 30% bucket 35: 90% bucket 36: 80% Getting block 41 of 63 Reserving size (73061533) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: bucket 39: 50% bucket 38: 60% bucket 40: 40% bucket 37: 80% bucket 35: 100% Sorting block of length 36811975 for bucket 35 (Using difference cover) bucket 41: 10% bucket 36: 90% bucket 39: 60% bucket 38: 70% bucket 40: 50% bucket 37: 90% bucket 41: 20% bucket 36: 100% Sorting block of length 51877539 for bucket 36 (Using difference cover) bucket 39: 70% bucket 38: 80% bucket 40: 60% bucket 37: 100% Sorting block of length 53946516 for bucket 37 (Using difference cover) bucket 41: 30% bucket 39: 80% bucket 38: 90% bucket 40: 70% bucket 41: 40% bucket 39: 90% bucket 38: 100% Sorting block of length 69539475 for bucket 38 (Using difference cover) bucket 40: 80% bucket 41: 50% bucket 39: 100% Sorting block of length 44102403 for bucket 39 (Using difference cover) bucket 40: 90% Sorting block time: 00:00:22 Returning block of 36811976 for bucket 35 bucket 41: 60% Getting block 42 of 63 Reserving size (73061533) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: bucket 40: 100% Sorting block of length 69441406 for bucket 40 (Using difference cover) bucket 41: 70% bucket 42: 10% Sorting block time: 00:01:00 Returning block of 70715609 for bucket 33 bucket 41: 80% bucket 42: 20% Getting block 43 of 63 Reserving size (73061533) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: bucket 41: 90% bucket 42: 30% bucket 43: 10% bucket 41: 100% Sorting block of length 17875947 for bucket 41 (Using difference cover) Sorting block time: 00:00:32 Returning block of 53946517 for bucket 37 bucket 43: 20% bucket 42: 40% Getting block 44 of 63 Reserving size (73061533) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: Sorting block time: 00:00:39 Returning block of 51877540 for bucket 36 Getting block 45 of 63 Reserving size (73061533) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: bucket 43: 30% bucket 42: 50% bucket 44: 10% Sorting block time: 00:00:11 Returning block of 17875948 for bucket 41 Getting block 46 of 63 Reserving size (73061533) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: bucket 43: 40% bucket 45: 10% bucket 42: 60% bucket 44: 20% bucket 46: 10% bucket 43: 50% bucket 42: 70% bucket 45: 20% bucket 44: 30% Sorting block time: 00:00:39 Returning block of 44102404 for bucket 39 Sorting block time: 00:00:43 Returning block of 69539476 for bucket 38 Getting block 47 of 63 Reserving size (73061533) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: bucket 46: 20% bucket 43: 60% bucket 42: 80% bucket 44: 40% bucket 45: 30% Getting block 48 of 63 Reserving size (73061533) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: bucket 47: 10% bucket 46: 30% Sorting block time: 00:00:40 Returning block of 69441407 for bucket 40 bucket 43: 70% bucket 42: 90% bucket 44: 50% bucket 48: 10% bucket 45: 40% Getting block 49 of 63 Reserving size (73061533) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: bucket 47: 20% bucket 46: 40% bucket 43: 80% bucket 42: 100% Sorting block of length 70098261 for bucket 42 (Using difference cover) bucket 48: 20% bucket 44: 60% bucket 47: 30% bucket 46: 50% bucket 49: 10% bucket 45: 50% bucket 48: 30% bucket 43: 90% bucket 44: 70% bucket 47: 40% bucket 46: 60% bucket 49: 20% bucket 45: 60% bucket 48: 40% bucket 43: 100% Sorting block of length 23217924 for bucket 43 (Using difference cover) bucket 44: 80% bucket 47: 50% bucket 46: 70% bucket 49: 30% bucket 48: 50% bucket 45: 70% bucket 47: 60% bucket 44: 90% bucket 46: 80% bucket 49: 40% bucket 48: 60% bucket 47: 70% bucket 44: 100% Sorting block of length 54186686 for bucket 44 (Using difference cover) bucket 45: 80% bucket 46: 90% bucket 49: 50% bucket 48: 70% Sorting block time: 00:00:13 Returning block of 23217925 for bucket 43 bucket 47: 80% Getting block 50 of 63 Reserving size (73061533) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: bucket 46: 100% Sorting block of length 69123827 for bucket 46 (Using difference cover) bucket 45: 90% bucket 49: 60% bucket 48: 80% bucket 47: 90% bucket 50: 10% bucket 49: 70% bucket 48: 90% bucket 45: 100% Sorting block of length 33297176 for bucket 45 (Using difference cover) bucket 47: 100% Sorting block of length 54999862 for bucket 47 (Using difference cover) bucket 50: 20% bucket 48: 100% Sorting block of length 58918039 for bucket 48 (Using difference cover) bucket 49: 80% bucket 50: 30% bucket 49: 90% Sorting block time: 00:00:40 Returning block of 70098262 for bucket 42 bucket 50: 40% bucket 49: 100% Sorting block of length 35227925 for bucket 49 (Using difference cover) Getting block 51 of 63 Reserving size (73061533) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: bucket 50: 50% bucket 51: 10% bucket 50: 60% Sorting block time: 00:00:21 Returning block of 33297177 for bucket 45 Sorting block time: 00:00:32 Returning block of 54186687 for bucket 44 Getting block 52 of 63 Reserving size (73061533) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: bucket 51: 20% Getting block 53 of 63 Reserving size (73061533) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 50: 70% bucket 52: 10% bucket 51: 30% bucket 53: 10% bucket 50: 80% bucket 52: 20% Sorting block time: 00:00:37 Returning block of 69123828 for bucket 46 bucket 51: 40% bucket 53: 20% Getting block 54 of 63 Reserving size (73061533) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: Sorting block time: 00:00:32 Returning block of 54999863 for bucket 47 bucket 50: 90% bucket 52: 30% bucket 51: 50% Getting block 55 of 63 Reserving size (73061533) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: Sorting block time: 00:00:23 Returning block of 35227926 for bucket 49 bucket 53: 30% Getting block 56 of 63 Reserving size (73061533) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: bucket 50: 100% Sorting block of length 56591646 for bucket 50 (Using difference cover) bucket 54: 10% bucket 52: 40% bucket 51: 60% bucket 55: 10% bucket 53: 40% bucket 56: 10% Sorting block time: 00:00:39 Returning block of 58918040 for bucket 48 bucket 54: 20% bucket 52: 50% bucket 51: 70% bucket 55: 20% Getting block 57 of 63 Reserving size (73061533) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 56: 20% bucket 53: 50% bucket 52: 60% bucket 54: 30% bucket 51: 80% bucket 57: 10% bucket 55: 30% bucket 56: 30% bucket 52: 70% bucket 53: 60% bucket 54: 40% bucket 51: 90% bucket 57: 20% bucket 55: 40% bucket 56: 40% bucket 52: 80% bucket 54: 50% bucket 53: 70% bucket 51: 100% Sorting block of length 51664587 for bucket 51 (Using difference cover) bucket 57: 30% bucket 55: 50% bucket 56: 50% bucket 52: 90% bucket 54: 60% bucket 53: 80% bucket 57: 40% bucket 55: 60% bucket 52: 100% Sorting block of length 40503967 for bucket 52 (Using difference cover) bucket 56: 60% bucket 54: 70% bucket 53: 90% bucket 57: 50% bucket 55: 70% bucket 56: 70% bucket 54: 80% bucket 53: 100% Sorting block of length 57807797 for bucket 53 (Using difference cover) bucket 57: 60% bucket 55: 80% Sorting block time: 00:00:36 Returning block of 56591647 for bucket 50 bucket 56: 80% bucket 54: 90% Getting block 58 of 63 Reserving size (73061533) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: bucket 57: 70% bucket 55: 90% bucket 56: 90% bucket 54: 100% Sorting block of length 58611397 for bucket 54 (Using difference cover) bucket 58: 10% bucket 57: 80% bucket 55: 100% Sorting block of length 29577643 for bucket 55 (Using difference cover) bucket 56: 100% Sorting block of length 59645600 for bucket 56 (Using difference cover) bucket 58: 20% bucket 57: 90% bucket 58: 30% bucket 57: 100% Sorting block of length 17369491 for bucket 57 (Using difference cover) Sorting block time: 00:00:26 Returning block of 40503968 for bucket 52 Getting block 59 of 63 Reserving size (73061533) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 58: 40% bucket 59: 10% bucket 58: 50% Sorting block time: 00:00:42 Returning block of 51664588 for bucket 51 Sorting block time: 00:00:11 Returning block of 17369492 for bucket 57 bucket 59: 20% Getting block 60 of 63 Reserving size (73061533) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: Getting block 61 of 63 Reserving size (73061533) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: bucket 58: 60% Sorting block time: 00:00:34 Returning block of 57807798 for bucket 53 bucket 59: 30% bucket 60: 10% bucket 61: 10% bucket 58: 70% Getting block 62 of 63 Reserving size (73061533) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: bucket 59: 40% bucket 60: 20% Sorting block time: 00:00:28 Returning block of 29577644 for bucket 55 bucket 61: 20% Getting block 63 of 63 Reserving size (73061533) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 58: 80% bucket 62: 10% bucket 59: 50% bucket 60: 30% bucket 63: 10% bucket 61: 30% bucket 62: 20% Sorting block time: 00:00:33 Returning block of 59645601 for bucket 56 bucket 58: 90% Sorting block time: 00:00:37 Returning block of 58611398 for bucket 54 bucket 63: 20% bucket 59: 60% bucket 60: 40% bucket 61: 40% bucket 62: 30% bucket 58: 100% Sorting block of length 54867705 for bucket 58 (Using difference cover) bucket 63: 30% bucket 59: 70% bucket 60: 50% bucket 61: 50% bucket 62: 40% bucket 63: 40% bucket 59: 80% bucket 60: 60% bucket 63: 50% bucket 61: 60% bucket 62: 50% bucket 63: 60% bucket 59: 90% bucket 60: 70% bucket 61: 70% bucket 62: 60% bucket 63: 70% bucket 59: 100% Sorting block of length 66017867 for bucket 59 (Using difference cover) bucket 60: 80% bucket 62: 70% bucket 61: 80% bucket 63: 80% bucket 60: 90% bucket 63: 90% bucket 62: 80% bucket 61: 90% bucket 63: 100% Sorting block of length 22522733 for bucket 63 (Using difference cover) bucket 60: 100% Sorting block of length 60780494 for bucket 60 (Using difference cover) bucket 62: 90% bucket 61: 100% Sorting block of length 60317285 for bucket 61 (Using difference cover) Sorting block time: 00:00:28 Returning block of 54867706 for bucket 58 bucket 62: 100% Sorting block of length 64716020 for bucket 62 (Using difference cover) Sorting block time: 00:00:12 Returning block of 22522734 for bucket 63 Sorting block time: 00:00:33 Returning block of 60317286 for bucket 61 Sorting block time: 00:00:45 Returning block of 66017868 for bucket 59 Sorting block time: 00:00:42 Returning block of 60780495 for bucket 60 Sorting block time: 00:00:39 Returning block of 64716021 for bucket 62 Exited Ebwt loop fchr[A]: 0 fchr[C]: 923878813 fchr[G]: 1557575547 fchr[T]: 2194298091 fchr[$]: 3117292070 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 1043292532 bytes to primary EBWT file: GCA_009914755.4.1.bt2 Wrote 779323024 bytes to secondary EBWT file: GCA_009914755.4.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 3117292070 bwtLen: 3117292071 sz: 779323018 bwtSz: 779323018 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 194830755 offsSz: 779323020 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 16235897 numLines: 16235897 ebwtTotLen: 1039097408 ebwtTotSz: 1039097408 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:16:47 Reading reference sizes Time reading reference sizes: 00:00:24 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:02:08 Time to reverse reference sequence: 00:00:03 bmax according to bmaxDivN setting: 97415377 Using parameters --bmax 73061533 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 73061533 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:42 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:25 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:41 Sanity-checking and returning Building samples Reserving space for 86 sample suffixes Generating random suffixes QSorting 86 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 86 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 9, merged 39; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 5, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 5, merged 2; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 2; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Avg bucket size: 5.28355e+07 (target: 73061532) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 59 Reserving size (73061533) for bucket 1 Getting block 2 of 59 Reserving size (73061533) for bucket 2 Getting block 3 of 59 Getting block 4 of 59 Getting block 5 of 59 Getting block 6 of 59 Getting block 7 of 59 Getting block 8 of 59 Calculating Z arrays for bucket 1 Reserving size (73061533) for bucket 3 Calculating Z arrays for bucket 2 Reserving size (73061533) for bucket 4 Reserving size (73061533) for bucket 5 Reserving size (73061533) for bucket 6 Reserving size (73061533) for bucket 7 Reserving size (73061533) for bucket 8 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 2: Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 8 Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 6: Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 2: 10% bucket 1: 10% bucket 3: 10% bucket 5: 10% bucket 4: 10% bucket 8: 10% bucket 7: 10% bucket 6: 10% bucket 2: 20% bucket 1: 20% bucket 3: 20% bucket 5: 20% bucket 4: 20% bucket 6: 20% bucket 7: 20% bucket 8: 20% bucket 1: 30% bucket 2: 30% bucket 3: 30% bucket 5: 30% bucket 4: 30% bucket 6: 30% bucket 7: 30% bucket 8: 30% bucket 1: 40% bucket 2: 40% bucket 3: 40% bucket 5: 40% bucket 4: 40% bucket 1: 50% bucket 2: 50% bucket 6: 40% bucket 7: 40% bucket 8: 40% bucket 3: 50% bucket 5: 50% bucket 4: 50% bucket 1: 60% bucket 2: 60% bucket 6: 50% bucket 7: 50% bucket 8: 50% bucket 3: 60% bucket 5: 60% bucket 4: 60% bucket 1: 70% bucket 2: 70% bucket 6: 60% bucket 7: 60% bucket 3: 70% bucket 8: 60% bucket 5: 70% bucket 1: 80% bucket 4: 70% bucket 2: 80% bucket 6: 70% bucket 1: 90% bucket 3: 80% bucket 5: 80% bucket 7: 70% bucket 2: 90% bucket 4: 80% bucket 8: 70% bucket 1: 100% Sorting block of length 61135380 for bucket 1 (Using difference cover) bucket 3: 90% bucket 5: 90% bucket 6: 80% bucket 2: 100% Sorting block of length 47566633 for bucket 2 (Using difference cover) bucket 7: 80% bucket 4: 90% bucket 8: 80% bucket 3: 100% Sorting block of length 57226607 for bucket 3 (Using difference cover) bucket 5: 100% Sorting block of length 20489490 for bucket 5 (Using difference cover) bucket 6: 90% bucket 4: 100% Sorting block of length 70231503 for bucket 4 (Using difference cover) bucket 7: 90% bucket 8: 90% bucket 6: 100% Sorting block of length 59377120 for bucket 6 (Using difference cover) bucket 7: 100% Sorting block of length 68440970 for bucket 7 (Using difference cover) bucket 8: 100% Sorting block of length 69973728 for bucket 8 (Using difference cover) Sorting block time: 00:00:13 Returning block of 20489491 for bucket 5 Getting block 9 of 59 Reserving size (73061533) for bucket 9 Calculating Z arrays for bucket 9 Entering block accumulator loop for bucket 9: bucket 9: 10% bucket 9: 20% bucket 9: 30% Sorting block time: 00:00:31 Returning block of 47566634 for bucket 2 bucket 9: 40% Sorting block time: 00:00:32 Returning block of 61135381 for bucket 1 Getting block 10 of 59 Reserving size (73061533) for bucket 10 Calculating Z arrays for bucket 10 Entering block accumulator loop for bucket 10: Sorting block time: 00:00:31 Returning block of 57226608 for bucket 3 Getting block 11 of 59 Reserving size (73061533) for bucket 11 Calculating Z arrays for bucket 11 Entering block accumulator loop for bucket 11: bucket 9: 50% Sorting block time: 00:00:29 Returning block of 59377121 for bucket 6 bucket 10: 10% Getting block 12 of 59 Reserving size (73061533) for bucket 12 Calculating Z arrays for bucket 12 Entering block accumulator loop for bucket 12: bucket 11: 10% bucket 9: 60% Getting block 13 of 59 Reserving size (73061533) for bucket 13 Calculating Z arrays for bucket 13 Entering block accumulator loop for bucket 13: bucket 12: 10% bucket 10: 20% bucket 11: 20% bucket 9: 70% bucket 13: 10% bucket 12: 20% bucket 10: 30% Sorting block time: 00:00:38 Returning block of 68440971 for bucket 7 bucket 11: 30% bucket 9: 80% bucket 13: 20% bucket 12: 30% bucket 10: 40% Getting block 14 of 59 Reserving size (73061533) for bucket 14 Calculating Z arrays for bucket 14 Entering block accumulator loop for bucket 14: bucket 11: 40% bucket 9: 90% bucket 13: 30% Sorting block time: 00:00:43 Returning block of 69973729 for bucket 8 bucket 10: 50% bucket 12: 40% bucket 14: 10% bucket 9: 100% Sorting block of length 65424881 for bucket 9 (Using difference cover) bucket 11: 50% bucket 13: 40% Getting block 15 of 59 Reserving size (73061533) for bucket 15 Calculating Z arrays for bucket 15 Entering block accumulator loop for bucket 15: bucket 10: 60% bucket 12: 50% bucket 14: 20% bucket 11: 60% bucket 15: 10% bucket 13: 50% bucket 10: 70% bucket 12: 60% Sorting block time: 00:00:55 Returning block of 70231504 for bucket 4 bucket 14: 30% bucket 11: 70% bucket 15: 20% bucket 13: 60% Getting block 16 of 59 Reserving size (73061533) for bucket 16 Calculating Z arrays for bucket 16 Entering block accumulator loop for bucket 16: bucket 10: 80% bucket 12: 70% bucket 14: 40% bucket 11: 80% bucket 15: 30% bucket 13: 70% bucket 10: 90% bucket 16: 10% bucket 12: 80% bucket 14: 50% bucket 11: 90% bucket 15: 40% bucket 13: 80% bucket 10: 100% Sorting block of length 46877066 for bucket 10 (Using difference cover) bucket 12: 90% bucket 16: 20% bucket 14: 60% bucket 11: 100% Sorting block of length 45535936 for bucket 11 (Using difference cover) bucket 15: 50% bucket 13: 90% bucket 12: 100% Sorting block of length 42307292 for bucket 12 (Using difference cover) bucket 16: 30% bucket 14: 70% bucket 15: 60% bucket 13: 100% Sorting block of length 50404622 for bucket 13 (Using difference cover) bucket 16: 40% bucket 14: 80% bucket 15: 70% bucket 16: 50% bucket 14: 90% bucket 15: 80% bucket 16: 60% bucket 14: 100% Sorting block of length 57766806 for bucket 14 (Using difference cover) bucket 15: 90% bucket 16: 70% bucket 15: 100% Sorting block of length 17377650 for bucket 15 (Using difference cover) bucket 16: 80% Sorting block time: 00:00:39 Returning block of 65424882 for bucket 9 bucket 16: 90% Getting block 17 of 59 Reserving size (73061533) for bucket 17 Calculating Z arrays for bucket 17 Entering block accumulator loop for bucket 17: Sorting block time: 00:00:27 Returning block of 46877067 for bucket 10 Getting block 18 of 59 Reserving size (73061533) for bucket 18 Calculating Z arrays for bucket 18 Entering block accumulator loop for bucket 18: bucket 16: 100% Sorting block of length 69295816 for bucket 16 (Using difference cover) bucket 17: 10% Sorting block time: 00:00:13 Returning block of 17377651 for bucket 15 Getting block 19 of 59 Reserving size (73061533) for bucket 19 Calculating Z arrays for bucket 19 Entering block accumulator loop for bucket 19: bucket 18: 10% bucket 17: 20% Sorting block time: 00:00:33 Returning block of 45535937 for bucket 11 bucket 19: 10% Getting block 20 of 59 Reserving size (73061533) for bucket 20 Calculating Z arrays for bucket 20 Entering block accumulator loop for bucket 20: bucket 17: 30% Sorting block time: 00:00:30 Returning block of 50404623 for bucket 13 bucket 18: 20% Sorting block time: 00:00:33 Returning block of 42307293 for bucket 12 Getting block 21 of 59 Reserving size (73061533) for bucket 21 Calculating Z arrays for bucket 21 Entering block accumulator loop for bucket 21: Getting block 22 of 59 Reserving size (73061533) for bucket 22 Calculating Z arrays for bucket 22 Entering block accumulator loop for bucket 22: bucket 19: 20% bucket 20: 10% bucket 17: 40% bucket 18: 30% bucket 21: 10% bucket 22: 10% bucket 19: 30% bucket 20: 20% bucket 17: 50% bucket 18: 40% bucket 21: 20% bucket 22: 20% bucket 19: 40% bucket 17: 60% bucket 20: 30% bucket 18: 50% bucket 21: 30% Sorting block time: 00:00:36 Returning block of 57766807 for bucket 14 bucket 22: 30% bucket 19: 50% bucket 17: 70% bucket 20: 40% Getting block 23 of 59 Reserving size (73061533) for bucket 23 Calculating Z arrays for bucket 23 Entering block accumulator loop for bucket 23: bucket 18: 60% bucket 21: 40% bucket 19: 60% bucket 22: 40% bucket 17: 80% bucket 20: 50% bucket 23: 10% bucket 18: 70% bucket 21: 50% bucket 17: 90% bucket 19: 70% bucket 22: 50% bucket 20: 60% bucket 23: 20% bucket 21: 60% bucket 18: 80% bucket 17: 100% Sorting block of length 45992616 for bucket 17 (Using difference cover) bucket 19: 80% bucket 22: 60% bucket 20: 70% Sorting block time: 00:00:36 Returning block of 69295817 for bucket 16 bucket 23: 30% bucket 21: 70% bucket 19: 90% bucket 18: 90% bucket 20: 80% bucket 22: 70% Getting block 24 of 59 Reserving size (73061533) for bucket 24 Calculating Z arrays for bucket 24 Entering block accumulator loop for bucket 24: bucket 23: 40% bucket 21: 80% bucket 19: 100% Sorting block of length 54247990 for bucket 19 (Using difference cover) bucket 18: 100% Sorting block of length 52970266 for bucket 18 (Using difference cover) bucket 20: 90% bucket 22: 80% bucket 24: 10% bucket 23: 50% bucket 21: 90% bucket 20: 100% Sorting block of length 27580145 for bucket 20 (Using difference cover) bucket 22: 90% bucket 23: 60% bucket 24: 20% bucket 21: 100% Sorting block of length 72772167 for bucket 21 (Using difference cover) bucket 22: 100% Sorting block of length 60502112 for bucket 22 (Using difference cover) bucket 23: 70% bucket 24: 30% bucket 23: 80% bucket 24: 40% Sorting block time: 00:00:24 Returning block of 45992617 for bucket 17 bucket 23: 90% Getting block 25 of 59 Reserving size (73061533) for bucket 25 Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 25: bucket 24: 50% Sorting block time: 00:00:16 Returning block of 27580146 for bucket 20 Getting block 26 of 59 Reserving size (73061533) for bucket 26 Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 26: bucket 23: 100% Sorting block of length 18841338 for bucket 23 (Using difference cover) bucket 24: 60% bucket 25: 10% bucket 26: 10% bucket 24: 70% bucket 25: 20% Sorting block time: 00:00:28 Returning block of 52970267 for bucket 18 bucket 26: 20% bucket 24: 80% Sorting block time: 00:00:31 Returning block of 54247991 for bucket 19 Getting block 27 of 59 Reserving size (73061533) for bucket 27 Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 27: bucket 25: 30% Sorting block time: 00:00:10 Returning block of 18841339 for bucket 23 Getting block 28 of 59 Reserving size (73061533) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: Getting block 29 of 59 Reserving size (73061533) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 24: 90% bucket 26: 30% bucket 27: 10% bucket 25: 40% bucket 28: 10% bucket 29: 10% bucket 24: 100% Sorting block of length 56632658 for bucket 24 (Using difference cover) bucket 26: 40% bucket 27: 20% bucket 25: 50% Sorting block time: 00:00:30 Returning block of 60502113 for bucket 22 bucket 28: 20% bucket 29: 20% Getting block 30 of 59 Reserving size (73061533) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: bucket 26: 50% bucket 25: 60% bucket 27: 30% bucket 28: 30% bucket 29: 30% bucket 30: 10% Sorting block time: 00:00:39 Returning block of 72772168 for bucket 21 bucket 26: 60% bucket 25: 70% bucket 27: 40% Getting block 31 of 59 Reserving size (73061533) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: bucket 28: 40% bucket 29: 40% bucket 30: 20% bucket 26: 70% bucket 25: 80% bucket 27: 50% bucket 28: 50% bucket 31: 10% bucket 29: 50% bucket 30: 30% bucket 25: 90% bucket 26: 80% bucket 27: 60% bucket 28: 60% bucket 29: 60% bucket 30: 40% bucket 31: 20% bucket 25: 100% Sorting block of length 19666678 for bucket 25 (Using difference cover) bucket 26: 90% bucket 27: 70% bucket 28: 70% bucket 29: 70% bucket 30: 50% bucket 26: 100% Sorting block of length 72639097 for bucket 26 (Using difference cover) bucket 27: 80% bucket 31: 30% bucket 28: 80% bucket 29: 80% bucket 30: 60% bucket 27: 90% Sorting block time: 00:00:10 Returning block of 19666679 for bucket 25 Getting block 32 of 59 Reserving size (73061533) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: bucket 31: 40% bucket 28: 90% bucket 29: 90% bucket 30: 70% bucket 27: 100% Sorting block of length 35615825 for bucket 27 (Using difference cover) Sorting block time: 00:00:37 Returning block of 56632659 for bucket 24 bucket 32: 10% bucket 28: 100% Sorting block of length 72591177 for bucket 28 (Using difference cover) bucket 31: 50% bucket 29: 100% Sorting block of length 68582167 for bucket 29 (Using difference cover) Getting block 33 of 59 Reserving size (73061533) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: bucket 30: 80% bucket 32: 20% bucket 31: 60% bucket 33: 10% bucket 30: 90% bucket 32: 30% bucket 33: 20% bucket 30: 100% Sorting block of length 25759242 for bucket 30 (Using difference cover) bucket 31: 70% bucket 32: 40% bucket 33: 30% bucket 31: 80% bucket 32: 50% Sorting block time: 00:00:19 Returning block of 35615826 for bucket 27 Getting block 34 of 59 Reserving size (73061533) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: bucket 33: 40% bucket 32: 60% bucket 31: 90% bucket 34: 10% bucket 33: 50% bucket 32: 70% Sorting block time: 00:00:15 Returning block of 25759243 for bucket 30 bucket 34: 20% bucket 31: 100% Sorting block of length 61552086 for bucket 31 (Using difference cover) Getting block 35 of 59 Reserving size (73061533) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: Sorting block time: 00:00:39 Returning block of 72639098 for bucket 26 bucket 33: 60% bucket 32: 80% bucket 34: 30% Getting block 36 of 59 Reserving size (73061533) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: bucket 35: 10% bucket 33: 70% bucket 32: 90% bucket 36: 10% bucket 34: 40% bucket 35: 20% bucket 33: 80% bucket 32: 100% Sorting block of length 57432245 for bucket 32 (Using difference cover) bucket 36: 20% bucket 34: 50% bucket 35: 30% bucket 33: 90% bucket 36: 30% bucket 34: 60% bucket 35: 40% bucket 33: 100% Sorting block of length 64389779 for bucket 33 (Using difference cover) Sorting block time: 00:00:47 Returning block of 72591178 for bucket 28 bucket 36: 40% bucket 34: 70% Getting block 37 of 59 Reserving size (73061533) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: bucket 35: 50% Sorting block time: 00:00:50 Returning block of 68582168 for bucket 29 bucket 36: 50% bucket 34: 80% bucket 37: 10% Getting block 38 of 59 Reserving size (73061533) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: bucket 35: 60% bucket 36: 60% bucket 34: 90% bucket 37: 20% bucket 38: 10% bucket 35: 70% bucket 36: 70% bucket 34: 100% Sorting block of length 59066616 for bucket 34 (Using difference cover) bucket 37: 30% bucket 35: 80% bucket 38: 20% Sorting block time: 00:00:39 Returning block of 61552087 for bucket 31 bucket 36: 80% bucket 37: 40% bucket 35: 90% bucket 38: 30% Getting block 39 of 59 Reserving size (73061533) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: Sorting block time: 00:00:31 Returning block of 57432246 for bucket 32 bucket 36: 90% bucket 37: 50% bucket 35: 100% Sorting block of length 61678638 for bucket 35 (Using difference cover) Getting block 40 of 59 Reserving size (73061533) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: bucket 38: 40% bucket 39: 10% bucket 36: 100% Sorting block of length 13940627 for bucket 36 (Using difference cover) bucket 37: 60% bucket 40: 10% bucket 38: 50% bucket 39: 20% bucket 37: 70% bucket 40: 20% Sorting block time: 00:00:07 Returning block of 13940628 for bucket 36 Getting block 41 of 59 Reserving size (73061533) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: bucket 38: 60% bucket 39: 30% Sorting block time: 00:00:37 Returning block of 64389780 for bucket 33 bucket 37: 80% Getting block 42 of 59 Reserving size (73061533) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: bucket 40: 30% bucket 38: 70% bucket 41: 10% bucket 39: 40% bucket 37: 90% bucket 40: 40% bucket 42: 10% bucket 38: 80% bucket 41: 20% bucket 39: 50% bucket 37: 100% Sorting block of length 68272344 for bucket 37 (Using difference cover) bucket 40: 50% bucket 38: 90% bucket 41: 30% bucket 42: 20% bucket 39: 60% Sorting block time: 00:00:34 Returning block of 59066617 for bucket 34 bucket 40: 60% Getting block 43 of 59 Reserving size (73061533) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: bucket 38: 100% Sorting block of length 71390673 for bucket 38 (Using difference cover) bucket 41: 40% bucket 39: 70% bucket 42: 30% bucket 43: 10% bucket 40: 70% bucket 41: 50% bucket 39: 80% bucket 42: 40% bucket 43: 20% bucket 40: 80% bucket 41: 60% bucket 39: 90% bucket 42: 50% bucket 43: 30% bucket 40: 90% bucket 41: 70% bucket 39: 100% Sorting block of length 64852052 for bucket 39 (Using difference cover) Sorting block time: 00:00:45 Returning block of 61678639 for bucket 35 bucket 43: 40% bucket 42: 60% Getting block 44 of 59 Reserving size (73061533) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: bucket 40: 100% Sorting block of length 59439881 for bucket 40 (Using difference cover) bucket 41: 80% bucket 43: 50% bucket 44: 10% bucket 42: 70% bucket 41: 90% bucket 43: 60% bucket 44: 20% bucket 42: 80% bucket 41: 100% Sorting block of length 32120240 for bucket 41 (Using difference cover) bucket 43: 70% bucket 44: 30% bucket 42: 90% bucket 43: 80% bucket 44: 40% bucket 43: 90% bucket 42: 100% Sorting block of length 47218374 for bucket 42 (Using difference cover) bucket 44: 50% Sorting block time: 00:00:50 Returning block of 68272345 for bucket 37 bucket 43: 100% Sorting block of length 67212272 for bucket 43 (Using difference cover) bucket 44: 60% Getting block 45 of 59 Reserving size (73061533) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: bucket 45: 10% Sorting block time: 00:00:22 Returning block of 32120241 for bucket 41 bucket 44: 70% Getting block 46 of 59 Reserving size (73061533) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: Sorting block time: 00:00:54 Returning block of 71390674 for bucket 38 Sorting block time: 00:00:36 Returning block of 59439882 for bucket 40 Sorting block time: 00:00:39 Returning block of 64852053 for bucket 39 bucket 44: 80% bucket 45: 20% bucket 46: 10% Getting block 47 of 59 Reserving size (73061533) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: Getting block 48 of 59 Reserving size (73061533) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: Getting block 49 of 59 Reserving size (73061533) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: bucket 44: 90% bucket 45: 30% bucket 46: 20% bucket 47: 10% bucket 48: 10% bucket 49: 10% bucket 44: 100% Sorting block of length 70781936 for bucket 44 (Using difference cover) bucket 45: 40% bucket 46: 30% bucket 47: 20% bucket 48: 20% bucket 49: 20% bucket 45: 50% bucket 46: 40% Sorting block time: 00:00:30 Returning block of 47218375 for bucket 42 bucket 47: 30% bucket 49: 30% bucket 48: 30% Getting block 50 of 59 Reserving size (73061533) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: bucket 45: 60% bucket 46: 50% bucket 47: 40% bucket 48: 40% bucket 49: 40% bucket 50: 10% bucket 45: 70% bucket 46: 60% bucket 47: 50% bucket 48: 50% bucket 49: 50% bucket 50: 20% bucket 45: 80% bucket 46: 70% bucket 47: 60% bucket 48: 60% bucket 49: 60% bucket 50: 30% bucket 45: 90% bucket 46: 80% bucket 47: 70% bucket 48: 70% bucket 49: 70% bucket 46: 90% bucket 45: 100% Sorting block of length 62440570 for bucket 45 (Using difference cover) bucket 50: 40% bucket 47: 80% bucket 46: 100% Sorting block of length 45272198 for bucket 46 (Using difference cover) bucket 48: 80% bucket 49: 80% bucket 50: 50% Sorting block time: 00:00:55 Returning block of 67212273 for bucket 43 bucket 47: 90% bucket 49: 90% bucket 48: 90% bucket 50: 60% Getting block 51 of 59 Reserving size (73061533) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: bucket 47: 100% Sorting block of length 62419983 for bucket 47 (Using difference cover) bucket 49: 100% Sorting block of length 29465220 for bucket 49 (Using difference cover) bucket 48: 100% Sorting block of length 54224365 for bucket 48 (Using difference cover) bucket 50: 70% bucket 51: 10% bucket 50: 80% bucket 51: 20% Sorting block time: 00:00:49 Returning block of 70781937 for bucket 44 bucket 50: 90% Getting block 52 of 59 Reserving size (73061533) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: bucket 51: 30% bucket 50: 100% Sorting block of length 57542245 for bucket 50 (Using difference cover) bucket 52: 10% Sorting block time: 00:00:16 Returning block of 29465221 for bucket 49 bucket 51: 40% Getting block 53 of 59 Reserving size (73061533) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: Sorting block time: 00:00:29 Returning block of 45272199 for bucket 46 bucket 52: 20% Getting block 54 of 59 Reserving size (73061533) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 51: 50% bucket 53: 10% bucket 52: 30% bucket 54: 10% bucket 51: 60% bucket 53: 20% Sorting block time: 00:00:29 Returning block of 54224366 for bucket 48 bucket 52: 40% bucket 54: 20% bucket 51: 70% Getting block 55 of 59 Reserving size (73061533) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: Sorting block time: 00:00:45 Returning block of 62440571 for bucket 45 bucket 53: 30% bucket 52: 50% Getting block 56 of 59 Reserving size (73061533) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: bucket 54: 30% bucket 55: 10% Sorting block time: 00:00:37 Returning block of 62419984 for bucket 47 bucket 51: 80% bucket 53: 40% bucket 52: 60% bucket 56: 10% bucket 54: 40% Getting block 57 of 59 Reserving size (73061533) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 55: 20% bucket 51: 90% bucket 53: 50% bucket 57: 10% bucket 52: 70% bucket 54: 50% bucket 56: 20% bucket 55: 30% bucket 51: 100% Sorting block of length 68704561 for bucket 51 (Using difference cover) bucket 53: 60% bucket 54: 60% bucket 56: 30% bucket 57: 20% bucket 52: 80% Sorting block time: 00:00:35 Returning block of 57542246 for bucket 50 bucket 55: 40% bucket 53: 70% bucket 54: 70% bucket 56: 40% bucket 52: 90% Getting block 58 of 59 Reserving size (73061533) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: bucket 57: 30% bucket 55: 50% bucket 53: 80% bucket 54: 80% bucket 58: 10% bucket 52: 100% Sorting block of length 55999998 for bucket 52 (Using difference cover) bucket 57: 40% bucket 56: 50% bucket 55: 60% bucket 53: 90% bucket 54: 90% bucket 58: 20% bucket 56: 60% bucket 57: 50% bucket 55: 70% bucket 53: 100% Sorting block of length 61840887 for bucket 53 (Using difference cover) bucket 54: 100% Sorting block of length 28693855 for bucket 54 (Using difference cover) bucket 58: 30% bucket 57: 60% bucket 56: 70% bucket 55: 80% bucket 58: 40% bucket 57: 70% bucket 56: 80% bucket 55: 90% bucket 58: 50% bucket 57: 80% bucket 56: 90% bucket 55: 100% Sorting block of length 58520972 for bucket 55 (Using difference cover) bucket 58: 60% bucket 57: 90% bucket 56: 100% Sorting block of length 64897257 for bucket 56 (Using difference cover) bucket 58: 70% bucket 57: 100% Sorting block of length 52968816 for bucket 57 (Using difference cover) Sorting block time: 00:00:43 Returning block of 68704562 for bucket 51 bucket 58: 80% Sorting block time: 00:00:26 Returning block of 28693856 for bucket 54 Sorting block time: 00:00:34 Returning block of 55999999 for bucket 52 Getting block 59 of 59 Reserving size (73061533) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 58: 90% bucket 59: 10% bucket 58: 100% Sorting block of length 48629766 for bucket 58 (Using difference cover) bucket 59: 20% bucket 59: 30% bucket 59: 40% Sorting block time: 00:00:39 Returning block of 61840888 for bucket 53 bucket 59: 50% bucket 59: 60% bucket 59: 70% Sorting block time: 00:00:29 Returning block of 52968817 for bucket 57 Sorting block time: 00:00:37 Returning block of 58520973 for bucket 55 bucket 59: 80% Sorting block time: 00:00:39 Returning block of 64897258 for bucket 56 bucket 59: 90% bucket 59: 100% Sorting block of length 32498578 for bucket 59 (Using difference cover) Sorting block time: 00:00:28 Returning block of 48629767 for bucket 58 Sorting block time: 00:00:17 Returning block of 32498579 for bucket 59 Exited Ebwt loop fchr[A]: 0 fchr[C]: 923878813 fchr[G]: 1557575547 fchr[T]: 2194298091 fchr[$]: 3117292070 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 1043292532 bytes to primary EBWT file: GCA_009914755.4.rev.1.bt2 Wrote 779323024 bytes to secondary EBWT file: GCA_009914755.4.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 3117292070 bwtLen: 3117292071 sz: 779323018 bwtSz: 779323018 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 194830755 offsSz: 779323020 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 16235897 numLines: 16235897 ebwtTotLen: 1039097408 ebwtTotSz: 1039097408 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:17:00