Settings:
  Output files: "Kn_0//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:
  Kn_0//tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:11
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:14
bmax according to bmaxDivN setting: 36208308
Using parameters --bmax 27156231 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 27156231 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:09
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:03
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:03
  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: 00:00:21
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 8; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:16
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:18
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.06905e+07 (target: 27156230)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (27156231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 20756349
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 20756350
Getting block 2 of 7
  Reserving size (27156231) 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 25392298
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 25392299
Getting block 3 of 7
  Reserving size (27156231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 22842356
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 22842357
Getting block 4 of 7
  Reserving size (27156231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:09
  Sorting block of length 21912464
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 21912465
Getting block 5 of 7
  Reserving size (27156231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:08
  Sorting block of length 9926264
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 9926265
Getting block 6 of 7
  Reserving size (27156231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:08
  Sorting block of length 22755211
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 22755212
Getting block 7 of 7
  Reserving size (27156231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 21248287
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 21248288
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 44860341
fchr[G]: 72551924
fchr[T]: 100191575
fchr[$]: 144833235
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 256116619 bytes to primary EBWT file: Kn_0//tmp/segment_juncs.1.ebwt
Wrote 18104160 bytes to secondary EBWT file: Kn_0//tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 144833235
    bwtLen: 144833236
    sz: 36208309
    bwtSz: 36208309
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4526039
    offsSz: 18104156
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 323289
    numSides: 646578
    numLines: 646578
    ebwtTotLen: 41380992
    ebwtTotSz: 41380992
    reverse: 0
Total time for call to driver() for forward index: 00:08:01
Reading reference sizes
  Time reading reference sizes: 00:00:08
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:25
bmax according to bmaxDivN setting: 36208308
Using parameters --bmax 27156231 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 27156231 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:10
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:02
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:03
  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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  90%
  100%
  Binary sorting into buckets time: 00:00:17
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
  Binary sorting into buckets
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  100%
  Binary sorting into buckets time: 00:00:15
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.06905e+07 (target: 27156230)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (27156231) 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 23105319
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 23105320
Getting block 2 of 7
  Reserving size (27156231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 26724025
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 26724026
Getting block 3 of 7
  Reserving size (27156231) 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 19542659
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 19542660
Getting block 4 of 7
  Reserving size (27156231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 18875548
  (Using difference cover)
  Sorting block time: 00:00:13
Returning block of 18875549
Getting block 5 of 7
  Reserving size (27156231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 24777301
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 24777302
Getting block 6 of 7
  Reserving size (27156231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 11537695
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 11537696
Getting block 7 of 7
  Reserving size (27156231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 20270682
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 20270683
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 44860341
fchr[G]: 72551924
fchr[T]: 100191575
fchr[$]: 144833235
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 256116619 bytes to primary EBWT file: Kn_0//tmp/segment_juncs.rev.1.ebwt
Wrote 18104160 bytes to secondary EBWT file: Kn_0//tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 144833235
    bwtLen: 144833236
    sz: 36208309
    bwtSz: 36208309
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4526039
    offsSz: 18104156
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 323289
    numSides: 646578
    numLines: 646578
    ebwtTotLen: 41380992
    ebwtTotSz: 41380992
    reverse: 0
Total time for backward call to driver() for mirror index: 00:05:18