Settings:
  Output files: "A_lyr_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:
  A_lyr_R2//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: 00:00:08
bmax according to bmaxDivN setting: 39241274
Using parameters --bmax 29430956 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 29430956 --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: 00:00:03
  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: 00:00:15
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
  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 2, merged 1; iterating...
  Binary sorting into buckets
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  100%
  Binary sorting into buckets time: 00:00:10
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.24236e+07 (target: 29430955)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (29430956) 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 13812871
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 13812872
Getting block 2 of 7
  Reserving size (29430956) 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 29024559
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 29024560
Getting block 3 of 7
  Reserving size (29430956) 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 28650340
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 28650341
Getting block 4 of 7
  Reserving size (29430956) 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 18114838
  (Using difference cover)
  Sorting block time: 00:00:11
Returning block of 18114839
Getting block 5 of 7
  Reserving size (29430956) 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: 00:00:03
  Sorting block of length 24495595
  (Using difference cover)
  Sorting block time: 00:00:13
Returning block of 24495596
Getting block 6 of 7
  Reserving size (29430956) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 20993732
  (Using difference cover)
  Sorting block time: 00:00:16
Returning block of 20993733
Getting block 7 of 7
  Reserving size (29430956) 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 21873158
  (Using difference cover)
  Sorting block time: 00:00:13
Returning block of 21873159
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 45797774
fchr[G]: 78123927
fchr[T]: 110961124
fchr[$]: 156965099
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 277393248 bytes to primary EBWT file: A_lyr_R2//tmp/segment_juncs.1.ebwt
Wrote 19620644 bytes to secondary EBWT file: A_lyr_R2//tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 156965099
    bwtLen: 156965100
    sz: 39241275
    bwtSz: 39241275
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4905160
    offsSz: 19620640
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 350369
    numSides: 700738
    numLines: 700738
    ebwtTotLen: 44847232
    ebwtTotSz: 44847232
    reverse: 0
Total time for call to driver() for forward index: 00:03:25
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: 00:00:08
bmax according to bmaxDivN setting: 39241274
Using parameters --bmax 29430956 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 29430956 --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: 00:00:02
  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: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
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  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:07
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.96206e+07 (target: 29430955)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (29430956) 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 9311255
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 9311256
Getting block 2 of 8
  Reserving size (29430956) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 20978605
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 20978606
Getting block 3 of 8
  Reserving size (29430956) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  100%
  Block accumulator loop time: 00:00:06
  Sorting block of length 22950519
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 22950520
Getting block 4 of 8
  Reserving size (29430956) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
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  100%
  Block accumulator loop time: 00:00:05
  Sorting block of length 23484929
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 23484930
Getting block 5 of 8
  Reserving size (29430956) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  100%
  Block accumulator loop time: 00:00:10
  Sorting block of length 28193940
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 28193941
Getting block 6 of 8
  Reserving size (29430956) 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: 00:00:10
  Sorting block of length 13293667
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 13293668
Getting block 7 of 8
  Reserving size (29430956) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:10
  Sorting block of length 19468026
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 19468027
Getting block 8 of 8
  Reserving size (29430956) 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: 00:00:06
  Sorting block of length 19284151
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 19284152
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 45797774
fchr[G]: 78123927
fchr[T]: 110961124
fchr[$]: 156965099
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 277393248 bytes to primary EBWT file: A_lyr_R2//tmp/segment_juncs.rev.1.ebwt
Wrote 19620644 bytes to secondary EBWT file: A_lyr_R2//tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 156965099
    bwtLen: 156965100
    sz: 39241275
    bwtSz: 39241275
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4905160
    offsSz: 19620640
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 350369
    numSides: 700738
    numLines: 700738
    ebwtTotLen: 44847232
    ebwtTotSz: 44847232
    reverse: 0
Total time for backward call to driver() for mirror index: 00:05:18