Settings:
  Output files: "2M-HS/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-HS/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:01
bmax according to bmaxDivN setting: 5762201
Using parameters --bmax 4321651 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 4321651 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  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: 00:00:01
  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: 00:00:01
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 5; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:02
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.8811e+06 (target: 4321650)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 4234497
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 4234498
Getting block 2 of 8
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 2865296
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 2865297
Getting block 3 of 8
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 2393465
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 2393466
Getting block 4 of 8
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 2422847
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 2422848
Getting block 5 of 8
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 1982028
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1982029
Getting block 6 of 8
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 3525704
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 3525705
Getting block 7 of 8
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 3657990
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 3657991
Getting block 8 of 8
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 1966970
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1966971
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 6631816
fchr[G]: 11590095
fchr[T]: 16336105
fchr[$]: 23048804
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 40281419 bytes to primary EBWT file: 2M-HS/tmp/segment_juncs.1.bt2
Wrote 5762208 bytes to secondary EBWT file: 2M-HS/tmp/segment_juncs.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 23048804
    bwtLen: 23048805
    sz: 5762201
    bwtSz: 5762202
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 1440551
    offsSz: 5762204
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 120046
    numLines: 120046
    ebwtTotLen: 7682944
    ebwtTotSz: 7682944
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:27
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:01
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 5762201
Using parameters --bmax 4321651 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 4321651 --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
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  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
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  20%
  30%
  40%
  50%
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  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
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  80%
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  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
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  100%
  Binary sorting into buckets time: 00:00:01
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.29269e+06 (target: 4321650)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 2936446
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 2936447
Getting block 2 of 7
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 2403866
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 2403867
Getting block 3 of 7
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 2690948
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 2690949
Getting block 4 of 7
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 3413412
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 3413413
Getting block 5 of 7
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 4061529
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 4061530
Getting block 6 of 7
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 4132612
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 4132613
Getting block 7 of 7
  Reserving size (4321651) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 3409985
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 3409986
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 6631816
fchr[G]: 11590095
fchr[T]: 16336105
fchr[$]: 23048804
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 40281419 bytes to primary EBWT file: 2M-HS/tmp/segment_juncs.rev.1.bt2
Wrote 5762208 bytes to secondary EBWT file: 2M-HS/tmp/segment_juncs.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 23048804
    bwtLen: 23048805
    sz: 5762201
    bwtSz: 5762202
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 1440551
    offsSz: 5762204
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 120046
    numLines: 120046
    ebwtTotLen: 7682944
    ebwtTotSz: 7682944
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:29