Settings:
  Output files: "/projects/NBL/HS1198/30UBRAAXX_5/tophat_wj/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:
  /projects/NBL/HS1198/30UBRAAXX_5/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:15
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:10
bmax according to bmaxDivN setting: 42577194
Using parameters --bmax 31932896 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 31932896 --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: 00:00:01
  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: 00:00:14
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: 00:00:11
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.43298e+07 (target: 31932895)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (31932896) 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 22476111
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 22476112
Getting block 2 of 7
  Reserving size (31932896) 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 22038881
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 22038882
Getting block 3 of 7
  Reserving size (31932896) 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 31805014
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 31805015
Getting block 4 of 7
  Reserving size (31932896) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 24523806
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 24523807
Getting block 5 of 7
  Reserving size (31932896) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 28835283
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 28835284
Getting block 6 of 7
  Reserving size (31932896) 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 27106219
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 27106220
Getting block 7 of 7
  Reserving size (31932896) 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 13523456
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 13523457
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 46306630
fchr[G]: 85974010
fchr[T]: 124321528
fchr[$]: 170308776
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 312162115 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_5/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 21288604 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_5/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 170308776
    bwtLen: 170308777
    sz: 42577194
    bwtSz: 42577195
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5322150
    offsSz: 21288600
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 380154
    numSides: 760308
    numLines: 760308
    ebwtTotLen: 48659712
    ebwtTotSz: 48659712
Total time for call to driver() for forward index: 00:05:22
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: 00:00:10
bmax according to bmaxDivN setting: 42577194
Using parameters --bmax 31932896 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 31932896 --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: 00:00:02
  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
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  Binary sorting into buckets time: 00:00:13
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 0; iterating...
  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 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: 2.43298e+07 (target: 31932895)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (31932896) 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 27891280
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 27891281
Getting block 2 of 7
  Reserving size (31932896) 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 26595391
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 26595392
Getting block 3 of 7
  Reserving size (31932896) 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 19844145
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 19844146
Getting block 4 of 7
  Reserving size (31932896) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 26927418
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 26927419
Getting block 5 of 7
  Reserving size (31932896) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 24344722
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 24344723
Getting block 6 of 7
  Reserving size (31932896) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 14391663
  (Using difference cover)
  Sorting block time: 00:00:16
Returning block of 14391664
Getting block 7 of 7
  Reserving size (31932896) 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 30314151
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 30314152
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 46306630
fchr[G]: 85974010
fchr[T]: 124321528
fchr[$]: 170308776
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 312162115 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_5/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 21288604 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_5/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 170308776
    bwtLen: 170308777
    sz: 42577194
    bwtSz: 42577195
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5322150
    offsSz: 21288600
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 380154
    numSides: 760308
    numLines: 760308
    ebwtTotLen: 48659712
    ebwtTotSz: 48659712
Total time for backward call to driver() for mirror index: 00:05:29