Settings:
  Output files: "aln_tophat_wt/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:
  aln_tophat_wt/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: 297505
Using parameters --bmax 223129 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 223129 --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 3, 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
Split 2, merged 3; 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
Split 1, merged 2; 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: 132224 (target: 223128)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 9
  Reserving size (223129) 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 55696
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 55697
Getting block 2 of 9
  Reserving size (223129) 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 196320
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 196321
Getting block 3 of 9
  Reserving size (223129) 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 204855
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 204856
Getting block 4 of 9
  Reserving size (223129) 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 176541
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 176542
Getting block 5 of 9
  Reserving size (223129) 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 93254
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 93255
Getting block 6 of 9
  Reserving size (223129) 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 150766
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 150767
Getting block 7 of 9
  Reserving size (223129) 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 78054
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 78055
Getting block 8 of 9
  Reserving size (223129) 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 199031
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 199032
Getting block 9 of 9
  Reserving size (223129) 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 35495
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 35496
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 348091
fchr[G]: 595988
fchr[T]: 837542
fchr[$]: 1190020
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 6221041 bytes to primary EBWT file: aln_tophat_wt/tmp/segment_juncs.1.bt2
Wrote 297512 bytes to secondary EBWT file: aln_tophat_wt/tmp/segment_juncs.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 1190020
    bwtLen: 1190021
    sz: 297505
    bwtSz: 297506
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 74377
    offsSz: 297508
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 6199
    numLines: 6199
    ebwtTotLen: 396736
    ebwtTotSz: 396736
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:01
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: 297505
Using parameters --bmax 223129 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 223129 --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
Split 1, merged 0; 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: 148752 (target: 223128)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (223129) 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 209926
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 209927
Getting block 2 of 8
  Reserving size (223129) 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 84589
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 84590
Getting block 3 of 8
  Reserving size (223129) 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 217324
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 217325
Getting block 4 of 8
  Reserving size (223129) 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 170760
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 170761
Getting block 5 of 8
  Reserving size (223129) 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 66496
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 66497
Getting block 6 of 8
  Reserving size (223129) 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 187464
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 187465
Getting block 7 of 8
  Reserving size (223129) 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 222545
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 222546
Getting block 8 of 8
  Reserving size (223129) 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 30909
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 30910
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 348091
fchr[G]: 595988
fchr[T]: 837542
fchr[$]: 1190020
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 6221041 bytes to primary EBWT file: aln_tophat_wt/tmp/segment_juncs.rev.1.bt2
Wrote 297512 bytes to secondary EBWT file: aln_tophat_wt/tmp/segment_juncs.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 1190020
    bwtLen: 1190021
    sz: 297505
    bwtSz: 297506
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 74377
    offsSz: 297508
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 6199
    numLines: 6199
    ebwtTotLen: 396736
    ebwtTotSz: 396736
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:02