Settings:
  Output files: "/projects/NBL/HS1198/30UBRAAXX_5/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/HS1198/30UBRAAXX_5/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:19
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: 40428927
Using parameters --bmax 30321696 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 30321696 --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: 00:00:03
  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: 00:00:14
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.31022e+07 (target: 30321695)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (30321696) 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 13506287
  (Using difference cover)
  Sorting block time: 00:00:16
Returning block of 13506288
Getting block 2 of 7
  Reserving size (30321696) 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 20292644
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 20292645
Getting block 3 of 7
  Reserving size (30321696) 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 22399846
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 22399847
Getting block 4 of 7
  Reserving size (30321696) 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 29607998
  (Using difference cover)
  Sorting block time: 00:00:49
Returning block of 29607999
Getting block 5 of 7
  Reserving size (30321696) 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 29677891
  (Using difference cover)
  Sorting block time: 00:00:48
Returning block of 29677892
Getting block 6 of 7
  Reserving size (30321696) 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 20125741
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 20125742
Getting block 7 of 7
  Reserving size (30321696) 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 26105295
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 26105296
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 44200630
fchr[G]: 81677616
fchr[T]: 117840071
fchr[$]: 161715708
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 296559127 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_5/tophat/tmp/segment_juncs.1.ebwt
Wrote 20214468 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_5/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 161715708
    bwtLen: 161715709
    sz: 40428927
    bwtSz: 40428928
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5053616
    offsSz: 20214464
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 360973
    numSides: 721946
    numLines: 721946
    ebwtTotLen: 46204544
    ebwtTotSz: 46204544
Total time for call to driver() for forward index: 00:06:37
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: 00:00:10
bmax according to bmaxDivN setting: 40428927
Using parameters --bmax 30321696 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 30321696 --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: 00:00:03
  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: 00:00:15
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 6; iterating...
  Binary sorting into buckets
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  100%
  Binary sorting into buckets time: 00:00:15
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.02145e+07 (target: 30321695)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (30321696) 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 9477407
  (Using difference cover)
  Sorting block time: 00:00:11
Returning block of 9477408
Getting block 2 of 8
  Reserving size (30321696) 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 29329087
  (Using difference cover)
  Sorting block time: 00:00:45
Returning block of 29329088
Getting block 3 of 8
  Reserving size (30321696) 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 18194841
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 18194842
Getting block 4 of 8
  Reserving size (30321696) 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 22318850
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 22318851
Getting block 5 of 8
  Reserving size (30321696) 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 16744133
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 16744134
Getting block 6 of 8
  Reserving size (30321696) 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 28672878
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 28672879
Getting block 7 of 8
  Reserving size (30321696) 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 21798850
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 21798851
Getting block 8 of 8
  Reserving size (30321696) 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 15179655
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 15179656
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 44200630
fchr[G]: 81677616
fchr[T]: 117840071
fchr[$]: 161715708
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 296559127 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_5/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 20214468 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_5/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 161715708
    bwtLen: 161715709
    sz: 40428927
    bwtSz: 40428928
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5053616
    offsSz: 20214464
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 360973
    numSides: 721946
    numLines: 721946
    ebwtTotLen: 46204544
    ebwtTotSz: 46204544
Total time for backward call to driver() for mirror index: 00:06:36