Settings:
  Output files: "Kn_0_R2//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_R2//tmp/segment_juncs.fa
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: 00:00:04
bmax according to bmaxDivN setting: 31593612
Using parameters --bmax 23695209 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 23695209 --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: 00:00:01
  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: 00:00:07
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 6; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:06
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:06
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.80535e+07 (target: 23695208)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (23695209) 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 22594394
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 22594395
Getting block 2 of 7
  Reserving size (23695209) 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 17260859
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 17260860
Getting block 3 of 7
  Reserving size (23695209) 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 23349237
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 23349238
Getting block 4 of 7
  Reserving size (23695209) 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 17081094
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 17081095
Getting block 5 of 7
  Reserving size (23695209) 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 16204499
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 16204500
Getting block 6 of 7
  Reserving size (23695209) 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 8065651
  (Using difference cover)
  Sorting block time: 00:00:03
Returning block of 8065652
Getting block 7 of 7
  Reserving size (23695209) 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 21818710
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 21818711
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 36813583
fchr[G]: 63024765
fchr[T]: 89446514
fchr[$]: 126374450
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 224025944 bytes to primary EBWT file: Kn_0_R2//tmp/segment_juncs.1.ebwt
Wrote 15796812 bytes to secondary EBWT file: Kn_0_R2//tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 126374450
    bwtLen: 126374451
    sz: 31593613
    bwtSz: 31593613
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 3949202
    offsSz: 15796808
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 282086
    numSides: 564172
    numLines: 564172
    ebwtTotLen: 36107008
    ebwtTotSz: 36107008
    reverse: 0
Total time for call to driver() for forward index: 00:01:51
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: 00:00:03
bmax according to bmaxDivN setting: 31593612
Using parameters --bmax 23695209 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 23695209 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:02
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  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
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:07
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.80535e+07 (target: 23695208)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (23695209) 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 11924934
  (Using difference cover)
  Sorting block time: 00:00:05
Returning block of 11924935
Getting block 2 of 7
  Reserving size (23695209) 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 19475407
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 19475408
Getting block 3 of 7
  Reserving size (23695209) 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 19371759
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 19371760
Getting block 4 of 7
  Reserving size (23695209) 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 14522884
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 14522885
Getting block 5 of 7
  Reserving size (23695209) 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 20007347
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 20007348
Getting block 6 of 7
  Reserving size (23695209) 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 17890719
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 17890720
Getting block 7 of 7
  Reserving size (23695209) 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 23181394
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 23181395
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 36813583
fchr[G]: 63024765
fchr[T]: 89446514
fchr[$]: 126374450
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 224025944 bytes to primary EBWT file: Kn_0_R2//tmp/segment_juncs.rev.1.ebwt
Wrote 15796812 bytes to secondary EBWT file: Kn_0_R2//tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 126374450
    bwtLen: 126374451
    sz: 31593613
    bwtSz: 31593613
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 3949202
    offsSz: 15796808
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 282086
    numSides: 564172
    numLines: 564172
    ebwtTotLen: 36107008
    ebwtTotSz: 36107008
    reverse: 0
Total time for backward call to driver() for mirror index: 00:01:39