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: 00:00:04
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: 60090296
Using parameters --bmax 45067722 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 45067722 --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: 00:00:02
  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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  Binary sorting into buckets time: 00:00:11
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 8; iterating...
  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 1; iterating...
  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
Avg bucket size: 3.43373e+07 (target: 45067721)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (45067722) 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 42325511
  (Using difference cover)
  Sorting block time: 00:00:16
Returning block of 42325512
Getting block 2 of 7
  Reserving size (45067722) 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 36974060
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 36974061
Getting block 3 of 7
  Reserving size (45067722) 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 32069156
  (Using difference cover)
  Sorting block time: 00:00:16
Returning block of 32069157
Getting block 4 of 7
  Reserving size (45067722) 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 14052690
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 14052691
Getting block 5 of 7
  Reserving size (45067722) 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 39834078
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 39834079
Getting block 6 of 7
  Reserving size (45067722) 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 34860115
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 34860116
Getting block 7 of 7
  Reserving size (45067722) 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 40245570
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 40245571
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 80933951
fchr[G]: 121254365
fchr[T]: 161576578
fchr[$]: 240361186
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 405183063 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.1.bt2
Wrote 60090304 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: 240361186
    bwtLen: 240361187
    sz: 60090297
    bwtSz: 60090297
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 15022575
    offsSz: 60090300
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1251882
    numLines: 1251882
    ebwtTotLen: 80120448
    ebwtTotSz: 80120448
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:03:59
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
  Time to reverse reference sequence: 00:00:01
bmax according to bmaxDivN setting: 60090296
Using parameters --bmax 45067722 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 45067722 --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: 00:00:02
  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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  50%
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  90%
  100%
  Binary sorting into buckets time: 00:00:12
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
  Binary sorting into buckets
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  30%
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  50%
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  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:10
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.43373e+07 (target: 45067721)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (45067722) 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 27562381
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 27562382
Getting block 2 of 7
  Reserving size (45067722) 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 37001892
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 37001893
Getting block 3 of 7
  Reserving size (45067722) 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 20649957
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 20649958
Getting block 4 of 7
  Reserving size (45067722) 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 42174152
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 42174153
Getting block 5 of 7
  Reserving size (45067722) 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 28761233
  (Using difference cover)
  Sorting block time: 00:00:16
Returning block of 28761234
Getting block 6 of 7
  Reserving size (45067722) 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 44538041
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 44538042
Getting block 7 of 7
  Reserving size (45067722) 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 39673524
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 39673525
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 80933951
fchr[G]: 121254365
fchr[T]: 161576578
fchr[$]: 240361186
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 405183063 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.rev.1.bt2
Wrote 60090304 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: 240361186
    bwtLen: 240361187
    sz: 60090297
    bwtSz: 60090297
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 15022575
    offsSz: 60090300
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1251882
    numLines: 1251882
    ebwtTotLen: 80120448
    ebwtTotSz: 80120448
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:03:52