Settings:
  Output files: "A_lyr_R1//tmp/segment_juncs.*.ebwt"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 5 (one in 32)
  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:
  A_lyr_R1//tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:03
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:05
bmax according to bmaxDivN setting: 32661211
Using parameters --bmax 24495909 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 24495909 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:04
  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: 00:00:02
  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
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  Binary sorting into buckets time: 00:00:07
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.86635e+07 (target: 24495908)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:02
  Sorting block of length 20580638
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 20580639
Getting block 2 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 19179001
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 19179002
Getting block 3 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 23212568
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 23212569
Getting block 4 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 18128296
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 18128297
Getting block 5 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 23978943
  (Using difference cover)
  Sorting block time: 00:00:11
Returning block of 23978944
Getting block 6 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:02
  Sorting block of length 10659835
  (Using difference cover)
  Sorting block time: 00:00:05
Returning block of 10659836
Getting block 7 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:02
  Sorting block of length 14905557
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 14905558
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 37929783
fchr[G]: 65033469
fchr[T]: 92587674
fchr[$]: 130644844
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 231562320 bytes to primary EBWT file: A_lyr_R1//tmp/segment_juncs.1.ebwt
Wrote 16330612 bytes to secondary EBWT file: A_lyr_R1//tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 130644844
    bwtLen: 130644845
    sz: 32661211
    bwtSz: 32661212
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4082652
    offsSz: 16330608
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 291618
    numSides: 583236
    numLines: 583236
    ebwtTotLen: 37327104
    ebwtTotSz: 37327104
    reverse: 0
Total time for call to driver() for forward index: 00:01:56
Reading reference sizes
  Time reading reference sizes: 00:00:02
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:05
bmax according to bmaxDivN setting: 32661211
Using parameters --bmax 24495909 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 24495909 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:03
  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: 00:00:02
  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
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  30%
  40%
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  60%
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  100%
  Binary sorting into buckets time: 00:00:08
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
  Binary sorting into buckets
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  100%
  Binary sorting into buckets time: 00:00:05
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
  Binary sorting into buckets
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  30%
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  100%
  Binary sorting into buckets time: 00:00:08
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.86635e+07 (target: 24495908)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:02
  Sorting block of length 13225422
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 13225423
Getting block 2 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 21592419
  (Using difference cover)
  Sorting block time: 00:00:11
Returning block of 21592420
Getting block 3 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:02
  Sorting block of length 15840970
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 15840971
Getting block 4 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 17275106
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 17275107
Getting block 5 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 18864202
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 18864203
Getting block 6 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 22044801
  (Using difference cover)
  Sorting block time: 00:00:11
Returning block of 22044802
Getting block 7 of 7
  Reserving size (24495909) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:02
  Sorting block of length 21801918
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 21801919
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 37929783
fchr[G]: 65033469
fchr[T]: 92587674
fchr[$]: 130644844
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 231562320 bytes to primary EBWT file: A_lyr_R1//tmp/segment_juncs.rev.1.ebwt
Wrote 16330612 bytes to secondary EBWT file: A_lyr_R1//tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 130644844
    bwtLen: 130644845
    sz: 32661211
    bwtSz: 32661212
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4082652
    offsSz: 16330608
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 291618
    numSides: 583236
    numLines: 583236
    ebwtTotLen: 37327104
    ebwtTotSz: 37327104
    reverse: 0
Total time for backward call to driver() for mirror index: 00:02:20