Settings:
  Output files: "./tophat_out/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:
  ./tophat_out/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: 00:00:00
bmax according to bmaxDivN setting: 35310
Using parameters --bmax 26483 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 26483 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  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: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 20176.3 (target: 26482)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (26483) 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 21611
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 21612
Getting block 2 of 7
  Reserving size (26483) 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 22326
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 22327
Getting block 3 of 7
  Reserving size (26483) 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 22904
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 22905
Getting block 4 of 7
  Reserving size (26483) 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 21661
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 21662
Getting block 5 of 7
  Reserving size (26483) 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 14245
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 14246
Getting block 6 of 7
  Reserving size (26483) 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 25960
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 25961
Getting block 7 of 7
  Reserving size (26483) 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 12527
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 12528
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 47190
fchr[G]: 70983
fchr[T]: 94893
fchr[$]: 141240
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4409265 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.1.ebwt
Wrote 17660 bytes to secondary EBWT file: ./tophat_out/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 141240
    bwtLen: 141241
    sz: 35310
    bwtSz: 35311
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4414
    offsSz: 17656
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 316
    numSides: 632
    numLines: 632
    ebwtTotLen: 40448
    ebwtTotSz: 40448
    reverse: 0
Total time for call to driver() for forward index: 00:00:00
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: 00:00:00
bmax according to bmaxDivN setting: 35310
Using parameters --bmax 26483 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 26483 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  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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  100%
  Binary sorting into buckets time: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 5; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 15692.4 (target: 26482)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 9
  Reserving size (26483) 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 18499
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 18500
Getting block 2 of 9
  Reserving size (26483) 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 13129
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 13130
Getting block 3 of 9
  Reserving size (26483) 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 15540
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 15541
Getting block 4 of 9
  Reserving size (26483) 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 12984
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 12985
Getting block 5 of 9
  Reserving size (26483) 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 21951
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 21952
Getting block 6 of 9
  Reserving size (26483) 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 17684
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 17685
Getting block 7 of 9
  Reserving size (26483) 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 10754
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 10755
Getting block 8 of 9
  Reserving size (26483) 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 23369
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 23370
Getting block 9 of 9
  Reserving size (26483) 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 7322
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 7323
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 47190
fchr[G]: 70983
fchr[T]: 94893
fchr[$]: 141240
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4409265 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.rev.1.ebwt
Wrote 17660 bytes to secondary EBWT file: ./tophat_out/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 141240
    bwtLen: 141241
    sz: 35310
    bwtSz: 35311
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4414
    offsSz: 17656
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 316
    numSides: 632
    numLines: 632
    ebwtTotLen: 40448
    ebwtTotSz: 40448
    reverse: 0
Total time for backward call to driver() for mirror index: 00:00:00