Settings:
  Output files: "Wil_2_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:
  Wil_2_R2//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: 00:00:04
bmax according to bmaxDivN setting: 24759255
Using parameters --bmax 18569442 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 18569442 --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
Avg bucket size: 1.41481e+07 (target: 18569441)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (18569442) 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 17336751
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 17336752
Getting block 2 of 7
  Reserving size (18569442) 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 13159062
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 13159063
Getting block 3 of 7
  Reserving size (18569442) 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 7681224
  (Using difference cover)
  Sorting block time: 00:00:04
Returning block of 7681225
Getting block 4 of 7
  Reserving size (18569442) 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 14114771
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 14114772
Getting block 5 of 7
  Reserving size (18569442) 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 18370516
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 18370517
Getting block 6 of 7
  Reserving size (18569442) 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 14210383
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 14210384
Getting block 7 of 7
  Reserving size (18569442) 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 14164308
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 14164309
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 28733042
fchr[G]: 49341238
fchr[T]: 70174807
fchr[$]: 99037021
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 176529774 bytes to primary EBWT file: Wil_2_R2//tmp/segment_juncs.1.ebwt
Wrote 12379632 bytes to secondary EBWT file: Wil_2_R2//tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 99037021
    bwtLen: 99037022
    sz: 24759256
    bwtSz: 24759256
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 3094907
    offsSz: 12379628
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 221065
    numSides: 442130
    numLines: 442130
    ebwtTotLen: 28296320
    ebwtTotSz: 28296320
    reverse: 0
Total time for call to driver() for forward index: 00:01:32
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: 24759255
Using parameters --bmax 18569442 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 18569442 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:05
  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: 00:00:10
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
Avg bucket size: 1.23796e+07 (target: 18569441)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (18569442) 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 9876963
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 9876964
Getting block 2 of 8
  Reserving size (18569442) 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 14143254
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 14143255
Getting block 3 of 8
  Reserving size (18569442) 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 10648900
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 10648901
Getting block 4 of 8
  Reserving size (18569442) 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 14227176
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 14227177
Getting block 5 of 8
  Reserving size (18569442) 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 9273348
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 9273349
Getting block 6 of 8
  Reserving size (18569442) 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 12541622
  (Using difference cover)
  Sorting block time: 00:00:11
Returning block of 12541623
Getting block 7 of 8
  Reserving size (18569442) 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 16600684
  (Using difference cover)
  Sorting block time: 00:00:11
Returning block of 16600685
Getting block 8 of 8
  Reserving size (18569442) 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 11725067
  (Using difference cover)
  Sorting block time: 00:00:05
Returning block of 11725068
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 28733042
fchr[G]: 49341238
fchr[T]: 70174807
fchr[$]: 99037021
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 176529774 bytes to primary EBWT file: Wil_2_R2//tmp/segment_juncs.rev.1.ebwt
Wrote 12379632 bytes to secondary EBWT file: Wil_2_R2//tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 99037021
    bwtLen: 99037022
    sz: 24759256
    bwtSz: 24759256
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 3094907
    offsSz: 12379628
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 221065
    numSides: 442130
    numLines: 442130
    ebwtTotLen: 28296320
    ebwtTotSz: 28296320
    reverse: 0
Total time for backward call to driver() for mirror index: 00:02:16