Settings:
  Output files: "A7DE_13064_GATCAG/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:
  A7DE_13064_GATCAG/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:05
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: 64954589
Using parameters --bmax 48715942 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 48715942 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:07
  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: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.71169e+07 (target: 48715941)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (48715942) 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 20431525
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 20431526
Getting block 2 of 7
  Reserving size (48715942) 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 41386986
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 41386987
Getting block 3 of 7
  Reserving size (48715942) 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 39333963
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 39333964
Getting block 4 of 7
  Reserving size (48715942) 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 42279793
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 42279794
Getting block 5 of 7
  Reserving size (48715942) 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 41302441
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 41302442
Getting block 6 of 7
  Reserving size (48715942) 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 45927520
  (Using difference cover)
  Sorting block time: 00:00:40
Returning block of 45927521
Getting block 7 of 7
  Reserving size (48715942) 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 29156122
  (Using difference cover)
  Sorting block time: 00:00:13
Returning block of 29156123
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 78680517
fchr[G]: 130532300
fchr[T]: 182234465
fchr[$]: 259818356
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 425759676 bytes to primary EBWT file: A7DE_13064_GATCAG/tmp/segment_juncs.1.bt2
Wrote 64954596 bytes to secondary EBWT file: A7DE_13064_GATCAG/tmp/segment_juncs.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 259818356
    bwtLen: 259818357
    sz: 64954589
    bwtSz: 64954590
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 16238648
    offsSz: 64954592
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1353221
    numLines: 1353221
    ebwtTotLen: 86606144
    ebwtTotSz: 86606144
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:04:03
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: 00:00:06
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 64954589
Using parameters --bmax 48715942 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 48715942 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:06
  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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  100%
  Binary sorting into buckets time: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
  Binary sorting into buckets
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  100%
  Binary sorting into buckets time: 00:00:08
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.71169e+07 (target: 48715941)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (48715942) 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 48585620
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 48585621
Getting block 2 of 7
  Reserving size (48715942) 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 47898986
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 47898987
Getting block 3 of 7
  Reserving size (48715942) 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 25126484
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 25126485
Getting block 4 of 7
  Reserving size (48715942) 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 45879700
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 45879701
Getting block 5 of 7
  Reserving size (48715942) 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 36800983
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 36800984
Getting block 6 of 7
  Reserving size (48715942) 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 25760299
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 25760300
Getting block 7 of 7
  Reserving size (48715942) 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 29766278
  (Using difference cover)
  Sorting block time: 00:00:13
Returning block of 29766279
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 78680517
fchr[G]: 130532300
fchr[T]: 182234465
fchr[$]: 259818356
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 425759676 bytes to primary EBWT file: A7DE_13064_GATCAG/tmp/segment_juncs.rev.1.bt2
Wrote 64954596 bytes to secondary EBWT file: A7DE_13064_GATCAG/tmp/segment_juncs.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 259818356
    bwtLen: 259818357
    sz: 64954589
    bwtSz: 64954590
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 16238648
    offsSz: 64954592
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1353221
    numLines: 1353221
    ebwtTotLen: 86606144
    ebwtTotSz: 86606144
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:04:11