Settings:
  Output files: "/projects/NBL/HS1196/3153YAAXX_6/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/HS1196/3153YAAXX_6/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:14
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: 38813061
Using parameters --bmax 29109796 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 29109796 --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: 00:00:01
  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: 00:00:13
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.58754e+07 (target: 29109795)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 6
  Reserving size (29109796) 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 28618882
  (Using difference cover)
  Sorting block time: 00:00:40
Returning block of 28618883
Getting block 2 of 6
  Reserving size (29109796) 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 23019919
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 23019920
Getting block 3 of 6
  Reserving size (29109796) 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 25192647
  (Using difference cover)
  Sorting block time: 00:00:40
Returning block of 25192648
Getting block 4 of 6
  Reserving size (29109796) 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 23269745
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 23269746
Getting block 5 of 6
  Reserving size (29109796) 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 28347342
  (Using difference cover)
  Sorting block time: 00:00:41
Returning block of 28347343
Getting block 6 of 6
  Reserving size (29109796) 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 26803704
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 26803705
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 39530054
fchr[G]: 78155613
fchr[T]: 115989148
fchr[$]: 155252244
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 284733838 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_6/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 19406536 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_6/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 155252244
    bwtLen: 155252245
    sz: 38813061
    bwtSz: 38813062
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4851633
    offsSz: 19406532
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 346546
    numSides: 693092
    numLines: 693092
    ebwtTotLen: 44357888
    ebwtTotSz: 44357888
Total time for call to driver() for forward index: 00:05:44
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: 00:00:10
bmax according to bmaxDivN setting: 38813061
Using parameters --bmax 29109796 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 29109796 --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: 00:00:01
  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: 00:00:14
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: 00:00:12
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.94065e+07 (target: 29109795)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (29109796) 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 27585672
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 27585673
Getting block 2 of 8
  Reserving size (29109796) 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 12698818
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 12698819
Getting block 3 of 8
  Reserving size (29109796) 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 18649223
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 18649224
Getting block 4 of 8
  Reserving size (29109796) 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 11813590
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 11813591
Getting block 5 of 8
  Reserving size (29109796) 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 23389922
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 23389923
Getting block 6 of 8
  Reserving size (29109796) 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 7707695
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 7707696
Getting block 7 of 8
  Reserving size (29109796) 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 26327172
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 26327173
Getting block 8 of 8
  Reserving size (29109796) 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 27080145
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 27080146
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 39530054
fchr[G]: 78155613
fchr[T]: 115989148
fchr[$]: 155252244
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 284733838 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_6/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 19406536 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_6/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 155252244
    bwtLen: 155252245
    sz: 38813061
    bwtSz: 38813062
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4851633
    offsSz: 19406532
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 346546
    numSides: 693092
    numLines: 693092
    ebwtTotLen: 44357888
    ebwtTotSz: 44357888
Total time for backward call to driver() for mirror index: 00:05:56