Settings:
  Output files: "IRThyroidIR122/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:
  IRThyroidIR122/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: 00:00:02
bmax according to bmaxDivN setting: 5210751
Using parameters --bmax 3908064 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 3908064 --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: 00:00:01
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: 00:00:01
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: 00:00:01
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: 00:00:01
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: 00:00:01
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.60537e+06 (target: 3908063)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (3908064) 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 1953730
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1953731
Getting block 2 of 8
  Reserving size (3908064) 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 2741367
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 2741368
Getting block 3 of 8
  Reserving size (3908064) 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 1830571
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 1830572
Getting block 4 of 8
  Reserving size (3908064) 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 2525734
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 2525735
Getting block 5 of 8
  Reserving size (3908064) 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 3807167
  (Using difference cover)
  Sorting block time: 00:00:03
Returning block of 3807168
Getting block 6 of 8
  Reserving size (3908064) 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 3778991
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 3778992
Getting block 7 of 8
  Reserving size (3908064) 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 3731938
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 3731939
Getting block 8 of 8
  Reserving size (3908064) 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 473499
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 473500
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 4904816
fchr[G]: 10551462
fchr[T]: 15718811
fchr[$]: 20843004
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 38151701 bytes to primary EBWT file: IRThyroidIR122/tmp/segment_juncs.1.bt2
Wrote 5210756 bytes to secondary EBWT file: IRThyroidIR122/tmp/segment_juncs.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 20843004
    bwtLen: 20843005
    sz: 5210751
    bwtSz: 5210752
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 1302688
    offsSz: 5210752
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 108558
    numLines: 108558
    ebwtTotLen: 6947712
    ebwtTotSz: 6947712
    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: 5210751
Using parameters --bmax 3908064 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 3908064 --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
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:01
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
  Binary sorting into buckets
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  20%
  30%
  40%
  50%
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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
Avg bucket size: 2.97757e+06 (target: 3908063)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (3908064) 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 3203138
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 3203139
Getting block 2 of 7
  Reserving size (3908064) 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 2661354
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 2661355
Getting block 3 of 7
  Reserving size (3908064) 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 3084245
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 3084246
Getting block 4 of 7
  Reserving size (3908064) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
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  Block accumulator loop time: 00:00:00
  Sorting block of length 1811232
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1811233
Getting block 5 of 7
  Reserving size (3908064) 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 3563876
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 3563877
Getting block 6 of 7
  Reserving size (3908064) 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 2921034
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 2921035
Getting block 7 of 7
  Reserving size (3908064) 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 3598119
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 3598120
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 4904816
fchr[G]: 10551462
fchr[T]: 15718811
fchr[$]: 20843004
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 38151701 bytes to primary EBWT file: IRThyroidIR122/tmp/segment_juncs.rev.1.bt2
Wrote 5210756 bytes to secondary EBWT file: IRThyroidIR122/tmp/segment_juncs.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 20843004
    bwtLen: 20843005
    sz: 5210751
    bwtSz: 5210752
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 1302688
    offsSz: 5210752
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 108558
    numLines: 108558
    ebwtTotLen: 6947712
    ebwtTotSz: 6947712
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:24