Settings:
  Output files: "Kn_0_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:
  Kn_0_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: 28744643
Using parameters --bmax 21558483 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 21558483 --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: 00:00:02
  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: 00:00:08
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, 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 0; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:08
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.64255e+07 (target: 21558482)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (21558483) 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 16118762
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 16118763
Getting block 2 of 7
  Reserving size (21558483) 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 12695784
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 12695785
Getting block 3 of 7
  Reserving size (21558483) 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 15769937
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 15769938
Getting block 4 of 7
  Reserving size (21558483) 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 9536402
  (Using difference cover)
  Sorting block time: 00:00:04
Returning block of 9536403
Getting block 5 of 7
  Reserving size (21558483) 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 20341930
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 20341931
Getting block 6 of 7
  Reserving size (21558483) 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 19281192
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 19281193
Getting block 7 of 7
  Reserving size (21558483) 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 21234560
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 21234561
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 33452742
fchr[G]: 57313108
fchr[T]: 81415216
fchr[$]: 114978573
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 204194078 bytes to primary EBWT file: Kn_0_R1//tmp/segment_juncs.1.ebwt
Wrote 14372328 bytes to secondary EBWT file: Kn_0_R1//tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 114978573
    bwtLen: 114978574
    sz: 28744644
    bwtSz: 28744644
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 3593081
    offsSz: 14372324
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 256649
    numSides: 513298
    numLines: 513298
    ebwtTotLen: 32851072
    ebwtTotSz: 32851072
    reverse: 0
Total time for call to driver() for forward index: 00:02:09
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: 00:00:06
bmax according to bmaxDivN setting: 28744643
Using parameters --bmax 21558483 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 21558483 --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: 00:00:01
  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
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:08
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: 00:00:06
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
  Binary sorting into buckets
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  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:06
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.64255e+07 (target: 21558482)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (21558483) 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 20906773
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 20906774
Getting block 2 of 7
  Reserving size (21558483) 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 19194550
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 19194551
Getting block 3 of 7
  Reserving size (21558483) 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 13031054
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 13031055
Getting block 4 of 7
  Reserving size (21558483) 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 15634787
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 15634788
Getting block 5 of 7
  Reserving size (21558483) 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 12688764
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 12688765
Getting block 6 of 7
  Reserving size (21558483) 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 13522183
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 13522184
Getting block 7 of 7
  Reserving size (21558483) 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 20000456
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 20000457
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 33452742
fchr[G]: 57313108
fchr[T]: 81415216
fchr[$]: 114978573
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 204194078 bytes to primary EBWT file: Kn_0_R1//tmp/segment_juncs.rev.1.ebwt
Wrote 14372328 bytes to secondary EBWT file: Kn_0_R1//tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 114978573
    bwtLen: 114978574
    sz: 28744644
    bwtSz: 28744644
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 3593081
    offsSz: 14372324
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 256649
    numSides: 513298
    numLines: 513298
    ebwtTotLen: 32851072
    ebwtTotSz: 32851072
    reverse: 0
Total time for backward call to driver() for mirror index: 00:02:18