Settings:
  Output files: "./tophat_out/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:
  ./tophat_out/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: 00:00:07
bmax according to bmaxDivN setting: 79921574
Using parameters --bmax 59941181 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 59941181 --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: 00:00:04
  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: 00:00:14
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: 00:00:13
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.56695e+07 (target: 59941180)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (59941181) 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 59630548
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 59630549
Getting block 2 of 7
  Reserving size (59941181) 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 45401208
  (Using difference cover)
  Sorting block time: 00:00:16
Returning block of 45401209
Getting block 3 of 7
  Reserving size (59941181) 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 42450879
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 42450880
Getting block 4 of 7
  Reserving size (59941181) 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 50362040
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 50362041
Getting block 5 of 7
  Reserving size (59941181) 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 59186365
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 59186366
Getting block 6 of 7
  Reserving size (59941181) 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 55446233
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 55446234
Getting block 7 of 7
  Reserving size (59941181) 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 7209019
  (Using difference cover)
  Sorting block time: 00:00:03
Returning block of 7209020
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 110470973
fchr[G]: 159651118
fchr[T]: 208758370
fchr[$]: 319686298
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 442809084 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.1.bt2
Wrote 79921580 bytes to secondary EBWT file: ./tophat_out/tmp/segment_juncs.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 319686298
    bwtLen: 319686299
    sz: 79921575
    bwtSz: 79921575
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 19980394
    offsSz: 79921576
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1665033
    numLines: 1665033
    ebwtTotLen: 106562112
    ebwtTotSz: 106562112
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:04:02
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: 00:00:07
  Time to reverse reference sequence: 00:00:01
bmax according to bmaxDivN setting: 79921574
Using parameters --bmax 59941181 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 59941181 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:08
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:02
  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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  100%
  Binary sorting into buckets time: 00:00:15
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.99608e+07 (target: 59941180)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (59941181) 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 16595193
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 16595194
Getting block 2 of 8
  Reserving size (59941181) 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 49132311
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 49132312
Getting block 3 of 8
  Reserving size (59941181) 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 34011553
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 34011554
Getting block 4 of 8
  Reserving size (59941181) 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 56541682
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 56541683
Getting block 5 of 8
  Reserving size (59941181) 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 25947937
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 25947938
Getting block 6 of 8
  Reserving size (59941181) 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 37487858
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 37487859
Getting block 7 of 8
  Reserving size (59941181) 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 45370928
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 45370929
Getting block 8 of 8
  Reserving size (59941181) 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 54598829
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 54598830
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 110470973
fchr[G]: 159651118
fchr[T]: 208758370
fchr[$]: 319686298
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 442809084 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.rev.1.bt2
Wrote 79921580 bytes to secondary EBWT file: ./tophat_out/tmp/segment_juncs.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 319686298
    bwtLen: 319686299
    sz: 79921575
    bwtSz: 79921575
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 19980394
    offsSz: 79921576
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1665033
    numLines: 1665033
    ebwtTotLen: 106562112
    ebwtTotSz: 106562112
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:04:12