Settings:
  Output files: "/projects/NBL/HS1799/61074AAXX_4/tophat/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/HS1799/61074AAXX_4/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:49
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:27
bmax according to bmaxDivN setting: 100415332
Using parameters --bmax 75311499 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 75311499 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:26
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:06
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:10
  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: 00:00:35
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:28
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.73802e+07 (target: 75311498)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:10
  Sorting block of length 37612298
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 37612299
Getting block 2 of 7
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:13
  Sorting block of length 70578493
  (Using difference cover)
  Sorting block time: 00:01:32
Returning block of 70578494
Getting block 3 of 7
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:15
  Sorting block of length 74885243
  (Using difference cover)
  Sorting block time: 00:01:44
Returning block of 74885244
Getting block 4 of 7
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:16
  Sorting block of length 50308648
  (Using difference cover)
  Sorting block time: 00:01:06
Returning block of 50308649
Getting block 5 of 7
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:17
  Sorting block of length 46764267
  (Using difference cover)
  Sorting block time: 00:01:00
Returning block of 46764268
Getting block 6 of 7
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:17
  Sorting block of length 60981427
  (Using difference cover)
  Sorting block time: 00:01:13
Returning block of 60981428
Getting block 7 of 7
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:10
  Sorting block of length 60530946
  (Using difference cover)
  Sorting block time: 00:01:10
Returning block of 60530947
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 99591131
fchr[G]: 199541390
fchr[T]: 298860501
fchr[$]: 401661328
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 730166727 bytes to primary EBWT file: /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/segment_juncs.1.ebwt
Wrote 50207672 bytes to secondary EBWT file: /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 401661328
    bwtLen: 401661329
    sz: 100415332
    bwtSz: 100415333
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12551917
    offsSz: 50207668
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 896566
    numSides: 1793132
    numLines: 1793132
    ebwtTotLen: 114760448
    ebwtTotSz: 114760448
Total time for call to driver() for forward index: 00:15:05
Reading reference sizes
  Time reading reference sizes: 00:00:09
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:28
bmax according to bmaxDivN setting: 100415332
Using parameters --bmax 75311499 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 75311499 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:22
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:05
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:11
  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: 00:00:33
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: 00:00:32
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: 00:00:32
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.02077e+07 (target: 75311498)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:11
  Sorting block of length 54431972
  (Using difference cover)
  Sorting block time: 00:01:00
Returning block of 54431973
Getting block 2 of 8
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:13
  Sorting block of length 75261279
  (Using difference cover)
  Sorting block time: 00:01:28
Returning block of 75261280
Getting block 3 of 8
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:14
  Sorting block of length 44245519
  (Using difference cover)
  Sorting block time: 00:00:57
Returning block of 44245520
Getting block 4 of 8
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:15
  Sorting block of length 59646745
  (Using difference cover)
  Sorting block time: 00:01:12
Returning block of 59646746
Getting block 5 of 8
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:17
  Sorting block of length 72455151
  (Using difference cover)
  Sorting block time: 00:01:29
Returning block of 72455152
Getting block 6 of 8
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:15
  Sorting block of length 6794448
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 6794449
Getting block 7 of 8
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:18
  Sorting block of length 69655202
  (Using difference cover)
  Sorting block time: 00:01:23
Returning block of 69655203
Getting block 8 of 8
  Reserving size (75311499) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:10
  Sorting block of length 19171005
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 19171006
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 99591131
fchr[G]: 199541390
fchr[T]: 298860501
fchr[$]: 401661328
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 730166727 bytes to primary EBWT file: /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 50207672 bytes to secondary EBWT file: /projects/NBL/HS1799/61074AAXX_4/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 401661328
    bwtLen: 401661329
    sz: 100415332
    bwtSz: 100415333
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12551917
    offsSz: 50207668
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 896566
    numSides: 1793132
    numLines: 1793132
    ebwtTotLen: 114760448
    ebwtTotSz: 114760448
Total time for backward call to driver() for mirror index: 00:14:35