Settings:
  Output files: "/projects/NBL/HS1197/311NGAAXX_7/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_7/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:16
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: 55803916
Using parameters --bmax 41852937 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 41852937 --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: 00:00:16
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 7; 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: 2.7902e+07 (target: 41852936)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (41852937) 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 26573779
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 26573780
Getting block 2 of 8
  Reserving size (41852937) 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 33033303
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 33033304
Getting block 3 of 8
  Reserving size (41852937) 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 35657563
  (Using difference cover)
  Sorting block time: 00:00:49
Returning block of 35657564
Getting block 4 of 8
  Reserving size (41852937) 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 38762115
  (Using difference cover)
  Sorting block time: 00:00:46
Returning block of 38762116
Getting block 5 of 8
  Reserving size (41852937) 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 22403027
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 22403028
Getting block 6 of 8
  Reserving size (41852937) 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 24560642
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 24560643
Getting block 7 of 8
  Reserving size (41852937) 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 26623191
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 26623192
Getting block 8 of 8
  Reserving size (41852937) 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 15602040
  (Using difference cover)
  Sorting block time: 00:00:13
Returning block of 15602041
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 58907986
fchr[G]: 112108651
fchr[T]: 164298298
fchr[$]: 223215667
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 408179166 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_7/tophat/tmp/segment_juncs.1.ebwt
Wrote 27901964 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_7/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 223215667
    bwtLen: 223215668
    sz: 55803917
    bwtSz: 55803917
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 6975490
    offsSz: 27901960
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 498250
    numSides: 996500
    numLines: 996500
    ebwtTotLen: 63776000
    ebwtTotSz: 63776000
Total time for call to driver() for forward index: 00:07:13
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: 55803916
Using parameters --bmax 41852937 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 41852937 --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: 00:00:03
  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 2, merged 7; 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
Avg bucket size: 3.1888e+07 (target: 41852936)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (41852937) 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 21816215
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 21816216
Getting block 2 of 7
  Reserving size (41852937) 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 40033807
  (Using difference cover)
  Sorting block time: 00:00:49
Returning block of 40033808
Getting block 3 of 7
  Reserving size (41852937) 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 38317418
  (Using difference cover)
  Sorting block time: 00:00:52
Returning block of 38317419
Getting block 4 of 7
  Reserving size (41852937) 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 27912013
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 27912014
Getting block 5 of 7
  Reserving size (41852937) 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 32829668
  (Using difference cover)
  Sorting block time: 00:00:41
Returning block of 32829669
Getting block 6 of 7
  Reserving size (41852937) 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 25643720
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 25643721
Getting block 7 of 7
  Reserving size (41852937) 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 36662820
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 36662821
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 58907986
fchr[G]: 112108651
fchr[T]: 164298298
fchr[$]: 223215667
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 408179166 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_7/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 27901964 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_7/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 223215667
    bwtLen: 223215668
    sz: 55803917
    bwtSz: 55803917
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 6975490
    offsSz: 27901960
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 498250
    numSides: 996500
    numLines: 996500
    ebwtTotLen: 63776000
    ebwtTotSz: 63776000
Total time for backward call to driver() for mirror index: 00:06:59