Settings:
  Output files: "/projects/NBL/HS1195/302NNAAXX_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/HS1195/302NNAAXX_5/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:30
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:20
bmax according to bmaxDivN setting: 85507089
Using parameters --bmax 64130317 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 64130317 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:15
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:03
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:06
  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: 00:00:28
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: 00:00:20
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: 00:00:21
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: 00:00:21
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.88612e+07 (target: 64130316)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (64130317) 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 60348703
  (Using difference cover)
  Sorting block time: 00:00:56
Returning block of 60348704
Getting block 2 of 7
  Reserving size (64130317) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:09
  Sorting block of length 60931084
  (Using difference cover)
  Sorting block time: 00:01:05
Returning block of 60931085
Getting block 3 of 7
  Reserving size (64130317) 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 24342567
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 24342568
Getting block 4 of 7
  Reserving size (64130317) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:12
  Sorting block of length 60677078
  (Using difference cover)
  Sorting block time: 00:01:06
Returning block of 60677079
Getting block 5 of 7
  Reserving size (64130317) 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 63369393
  (Using difference cover)
  Sorting block time: 00:01:11
Returning block of 63369394
Getting block 6 of 7
  Reserving size (64130317) 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 63381816
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 63381817
Getting block 7 of 7
  Reserving size (64130317) 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 8977712
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 8977713
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 95798655
fchr[G]: 170464182
fchr[T]: 244869556
fchr[$]: 342028359
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 622740697 bytes to primary EBWT file: /projects/NBL/HS1195/302NNAAXX_5/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 42753552 bytes to secondary EBWT file: /projects/NBL/HS1195/302NNAAXX_5/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 342028359
    bwtLen: 342028360
    sz: 85507090
    bwtSz: 85507090
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 10688387
    offsSz: 42753548
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 763457
    numSides: 1526914
    numLines: 1526914
    ebwtTotLen: 97722496
    ebwtTotSz: 97722496
Total time for call to driver() for forward index: 00:11:06
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: 00:00:20
bmax according to bmaxDivN setting: 85507089
Using parameters --bmax 64130317 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 64130317 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:16
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:04
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:06
  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: 00:00:29
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.88612e+07 (target: 64130316)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (64130317) 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 56172666
  (Using difference cover)
  Sorting block time: 00:00:53
Returning block of 56172667
Getting block 2 of 7
  Reserving size (64130317) 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 62091280
  (Using difference cover)
  Sorting block time: 00:01:09
Returning block of 62091281
Getting block 3 of 7
  Reserving size (64130317) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:12
  Sorting block of length 62686665
  (Using difference cover)
  Sorting block time: 00:01:09
Returning block of 62686666
Getting block 4 of 7
  Reserving size (64130317) 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 35162515
  (Using difference cover)
  Sorting block time: 00:00:40
Returning block of 35162516
Getting block 5 of 7
  Reserving size (64130317) 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 55740432
  (Using difference cover)
  Sorting block time: 00:01:00
Returning block of 55740433
Getting block 6 of 7
  Reserving size (64130317) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:12
  Sorting block of length 28992491
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 28992492
Getting block 7 of 7
  Reserving size (64130317) 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 41182304
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 41182305
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 95798655
fchr[G]: 170464182
fchr[T]: 244869556
fchr[$]: 342028359
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 622740697 bytes to primary EBWT file: /projects/NBL/HS1195/302NNAAXX_5/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 42753552 bytes to secondary EBWT file: /projects/NBL/HS1195/302NNAAXX_5/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 342028359
    bwtLen: 342028360
    sz: 85507090
    bwtSz: 85507090
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 10688387
    offsSz: 42753548
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 763457
    numSides: 1526914
    numLines: 1526914
    ebwtTotLen: 97722496
    ebwtTotSz: 97722496
Total time for backward call to driver() for mirror index: 00:09:42