Settings:
  Output files: "/projects/NBL/HS1194/311L9AAXX_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/HS1194/311L9AAXX_4/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:27
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:09
bmax according to bmaxDivN setting: 37892967
Using parameters --bmax 28419726 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 28419726 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:07
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:02
  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: 00:00:11
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: 00:00:09
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: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.16531e+07 (target: 28419725)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (28419726) 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 25961408
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 25961409
Getting block 2 of 7
  Reserving size (28419726) 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 28207341
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 28207342
Getting block 3 of 7
  Reserving size (28419726) 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 17119485
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 17119486
Getting block 4 of 7
  Reserving size (28419726) 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 20341544
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 20341545
Getting block 5 of 7
  Reserving size (28419726) 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 12758252
  (Using difference cover)
  Sorting block time: 00:00:16
Returning block of 12758253
Getting block 6 of 7
  Reserving size (28419726) 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 24115867
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 24115868
Getting block 7 of 7
  Reserving size (28419726) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 23067965
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 23067966
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 38902421
fchr[G]: 76409717
fchr[T]: 112258646
fchr[$]: 151571868
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 277958956 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_4/tophat/tmp/segment_juncs.1.ebwt
Wrote 18946488 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_4/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 151571868
    bwtLen: 151571869
    sz: 37892967
    bwtSz: 37892968
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4736621
    offsSz: 18946484
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 338331
    numSides: 676662
    numLines: 676662
    ebwtTotLen: 43306368
    ebwtTotSz: 43306368
Total time for call to driver() for forward index: 00:05:31
Reading reference sizes
  Time reading reference sizes: 00:00:02
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:08
bmax according to bmaxDivN setting: 37892967
Using parameters --bmax 28419726 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 28419726 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:06
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  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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  100%
  Binary sorting into buckets time: 00:00:12
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.16531e+07 (target: 28419725)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (28419726) 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 24519198
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 24519199
Getting block 2 of 7
  Reserving size (28419726) 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 28203390
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 28203391
Getting block 3 of 7
  Reserving size (28419726) 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 14091450
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 14091451
Getting block 4 of 7
  Reserving size (28419726) 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 28149298
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 28149299
Getting block 5 of 7
  Reserving size (28419726) 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 26581538
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 26581539
Getting block 6 of 7
  Reserving size (28419726) 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 16323250
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 16323251
Getting block 7 of 7
  Reserving size (28419726) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 13703738
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 13703739
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 38902421
fchr[G]: 76409717
fchr[T]: 112258646
fchr[$]: 151571868
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 277958956 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_4/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 18946488 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_4/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 151571868
    bwtLen: 151571869
    sz: 37892967
    bwtSz: 37892968
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4736621
    offsSz: 18946484
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 338331
    numSides: 676662
    numLines: 676662
    ebwtTotLen: 43306368
    ebwtTotSz: 43306368
Total time for backward call to driver() for mirror index: 00:04:44