Settings:
  Output files: "/projects/NBL/HS1196/302NNAAXX_6/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/HS1196/302NNAAXX_6/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:20
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:13
bmax according to bmaxDivN setting: 56332307
Using parameters --bmax 42249231 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 42249231 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:10
  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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  Binary sorting into buckets time: 00:00:18
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 6; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:15
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.21899e+07 (target: 42249230)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (42249231) 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 29056001
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 29056002
Getting block 2 of 7
  Reserving size (42249231) 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 39803940
  (Using difference cover)
  Sorting block time: 00:00:46
Returning block of 39803941
Getting block 3 of 7
  Reserving size (42249231) 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 17702381
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 17702382
Getting block 4 of 7
  Reserving size (42249231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:08
  Sorting block of length 29525650
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 29525651
Getting block 5 of 7
  Reserving size (42249231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:08
  Sorting block of length 40522505
  (Using difference cover)
  Sorting block time: 00:00:50
Returning block of 40522506
Getting block 6 of 7
  Reserving size (42249231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:08
  Sorting block of length 29537243
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 29537244
Getting block 7 of 7
  Reserving size (42249231) 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 39181503
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 39181504
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 59744198
fchr[G]: 113172513
fchr[T]: 165831591
fchr[$]: 225329229
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 411405570 bytes to primary EBWT file: /projects/NBL/HS1196/302NNAAXX_6/tophat/tmp/segment_juncs.1.ebwt
Wrote 28166160 bytes to secondary EBWT file: /projects/NBL/HS1196/302NNAAXX_6/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 225329229
    bwtLen: 225329230
    sz: 56332308
    bwtSz: 56332308
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 7041539
    offsSz: 28166156
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 502968
    numSides: 1005936
    numLines: 1005936
    ebwtTotLen: 64379904
    ebwtTotSz: 64379904
Total time for call to driver() for forward index: 00:07:11
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: 00:00:14
bmax according to bmaxDivN setting: 56332307
Using parameters --bmax 42249231 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 42249231 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:11
  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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  Binary sorting into buckets time: 00:00:19
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
  Binary sorting into buckets
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  100%
  Binary sorting into buckets time: 00:00:13
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.21899e+07 (target: 42249230)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (42249231) 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 38252332
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 38252333
Getting block 2 of 7
  Reserving size (42249231) 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 36828058
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 36828059
Getting block 3 of 7
  Reserving size (42249231) 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 31538840
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 31538841
Getting block 4 of 7
  Reserving size (42249231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:08
  Sorting block of length 38899738
  (Using difference cover)
  Sorting block time: 00:00:48
Returning block of 38899739
Getting block 5 of 7
  Reserving size (42249231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:08
  Sorting block of length 23412339
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 23412340
Getting block 6 of 7
  Reserving size (42249231) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:08
  Sorting block of length 21657249
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 21657250
Getting block 7 of 7
  Reserving size (42249231) 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 34740667
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 34740668
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 59744198
fchr[G]: 113172513
fchr[T]: 165831591
fchr[$]: 225329229
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 411405570 bytes to primary EBWT file: /projects/NBL/HS1196/302NNAAXX_6/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 28166160 bytes to secondary EBWT file: /projects/NBL/HS1196/302NNAAXX_6/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 225329229
    bwtLen: 225329230
    sz: 56332308
    bwtSz: 56332308
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 7041539
    offsSz: 28166156
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 502968
    numSides: 1005936
    numLines: 1005936
    ebwtTotLen: 64379904
    ebwtTotSz: 64379904
Total time for backward call to driver() for mirror index: 00:06:47