Settings: Output files: "2M/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: 2M/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: 6016946 Using parameters --bmax 4512710 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4512710 --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 8; 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 1; 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 1; 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 1; 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: 3.43825e+06 (target: 4512709) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4512710) 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 4173933 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4173934 Getting block 2 of 7 Reserving size (4512710) 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 3517012 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3517013 Getting block 3 of 7 Reserving size (4512710) 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 4397357 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4397358 Getting block 4 of 7 Reserving size (4512710) 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 3401215 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3401216 Getting block 5 of 7 Reserving size (4512710) 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 1435264 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1435265 Getting block 6 of 7 Reserving size (4512710) 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 3086071 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3086072 Getting block 7 of 7 Reserving size (4512710) 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 4056927 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4056928 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6948981 fchr[G]: 12088305 fchr[T]: 17022059 fchr[$]: 24067785 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 41880870 bytes to primary EBWT file: 2M/tmp/segment_juncs.1.bt2 Wrote 6016952 bytes to secondary EBWT file: 2M/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 24067785 bwtLen: 24067786 sz: 6016947 bwtSz: 6016947 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1504237 offsSz: 6016948 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 125354 numLines: 125354 ebwtTotLen: 8022656 ebwtTotSz: 8022656 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:31 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 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 6016946 Using parameters --bmax 4512710 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4512710 --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 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: 3.00847e+06 (target: 4512709) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (4512710) 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 2630043 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2630044 Getting block 2 of 8 Reserving size (4512710) 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 2210012 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2210013 Getting block 3 of 8 Reserving size (4512710) 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 4261178 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4261179 Getting block 4 of 8 Reserving size (4512710) 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 2251001 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2251002 Getting block 5 of 8 Reserving size (4512710) 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 2831617 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2831618 Getting block 6 of 8 Reserving size (4512710) 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 3748518 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3748519 Getting block 7 of 8 Reserving size (4512710) 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 3861501 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3861502 Getting block 8 of 8 Reserving size (4512710) 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 2273908 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2273909 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6948981 fchr[G]: 12088305 fchr[T]: 17022059 fchr[$]: 24067785 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 41880870 bytes to primary EBWT file: 2M/tmp/segment_juncs.rev.1.bt2 Wrote 6016952 bytes to secondary EBWT file: 2M/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 24067785 bwtLen: 24067786 sz: 6016947 bwtSz: 6016947 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1504237 offsSz: 6016948 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 125354 numLines: 125354 ebwtTotLen: 8022656 ebwtTotSz: 8022656 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:28