Settings:
  Output files: "/projects/NBL/HS1197/311NGAAXX_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/HS1197/311NGAAXX_5/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:29
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: 53767356
Using parameters --bmax 40325517 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 40325517 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:09
  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: 00:00:18
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: 00:00:13
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: 00:00:14
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.68837e+07 (target: 40325516)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (40325517) 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 28299621
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 28299622
Getting block 2 of 8
  Reserving size (40325517) 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 20226840
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 20226841
Getting block 3 of 8
  Reserving size (40325517) 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 34988708
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 34988709
Getting block 4 of 8
  Reserving size (40325517) 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 15670274
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 15670275
Getting block 5 of 8
  Reserving size (40325517) 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 24770622
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 24770623
Getting block 6 of 8
  Reserving size (40325517) 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 30599375
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 30599376
Getting block 7 of 8
  Reserving size (40325517) 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 35689698
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 35689699
Getting block 8 of 8
  Reserving size (40325517) 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 24824281
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 24824282
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 56504298
fchr[G]: 108083559
fchr[T]: 158511894
fchr[$]: 215069426
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 393565487 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_5/tophat/tmp/segment_juncs.1.ebwt
Wrote 26883684 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_5/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 215069426
    bwtLen: 215069427
    sz: 53767357
    bwtSz: 53767357
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 6720920
    offsSz: 26883680
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 480066
    numSides: 960132
    numLines: 960132
    ebwtTotLen: 61448448
    ebwtTotSz: 61448448
Total time for call to driver() for forward index: 00:07:14
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: 00:00:13
bmax according to bmaxDivN setting: 53767356
Using parameters --bmax 40325517 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 40325517 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:09
  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: 00:00:18
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; 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: 2.68837e+07 (target: 40325516)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (40325517) 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 10926828
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 10926829
Getting block 2 of 8
  Reserving size (40325517) 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 32967895
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 32967896
Getting block 3 of 8
  Reserving size (40325517) 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 27102563
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 27102564
Getting block 4 of 8
  Reserving size (40325517) 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 37086269
  (Using difference cover)
  Sorting block time: 00:00:47
Returning block of 37086270
Getting block 5 of 8
  Reserving size (40325517) 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 24295233
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 24295234
Getting block 6 of 8
  Reserving size (40325517) 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 35493825
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 35493826
Getting block 7 of 8
  Reserving size (40325517) 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 21548739
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 21548740
Getting block 8 of 8
  Reserving size (40325517) 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 25648067
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 25648068
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 56504298
fchr[G]: 108083559
fchr[T]: 158511894
fchr[$]: 215069426
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 393565487 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_5/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 26883684 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_5/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 215069426
    bwtLen: 215069427
    sz: 53767357
    bwtSz: 53767357
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 6720920
    offsSz: 26883680
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 480066
    numSides: 960132
    numLines: 960132
    ebwtTotLen: 61448448
    ebwtTotSz: 61448448
Total time for backward call to driver() for mirror index: 00:06:34