Settings:
  Output files: "/projects/NBL/HS1195/30TTYAAXX_3/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/HS1195/30TTYAAXX_3/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:28
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:23
bmax according to bmaxDivN setting: 92285733
Using parameters --bmax 69214300 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 69214300 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:17
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:04
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:06
  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: 00:00:28
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 8; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:21
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.27347e+07 (target: 69214299)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (69214300) 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 65955980
  (Using difference cover)
  Sorting block time: 00:01:09
Returning block of 65955981
Getting block 2 of 7
  Reserving size (69214300) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:10
  Sorting block of length 67079678
  (Using difference cover)
  Sorting block time: 00:01:24
Returning block of 67079679
Getting block 3 of 7
  Reserving size (69214300) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:11
  Sorting block of length 61426651
  (Using difference cover)
  Sorting block time: 00:01:22
Returning block of 61426652
Getting block 4 of 7
  Reserving size (69214300) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:11
  Sorting block of length 25438813
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 25438814
Getting block 5 of 7
  Reserving size (69214300) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:12
  Sorting block of length 51886561
  (Using difference cover)
  Sorting block time: 00:01:09
Returning block of 51886562
Getting block 6 of 7
  Reserving size (69214300) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:11
  Sorting block of length 28368732
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 28368733
Getting block 7 of 7
  Reserving size (69214300) 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 68986513
  (Using difference cover)
  Sorting block time: 00:01:10
Returning block of 68986514
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 103607191
fchr[G]: 184571352
fchr[T]: 264713327
fchr[$]: 369142934
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 671169523 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_3/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 46142872 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_3/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 369142934
    bwtLen: 369142935
    sz: 92285734
    bwtSz: 92285734
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11535717
    offsSz: 46142868
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 823980
    numSides: 1647960
    numLines: 1647960
    ebwtTotLen: 105469440
    ebwtTotSz: 105469440
Total time for call to driver() for forward index: 00:11:58
Reading reference sizes
  Time reading reference sizes: 00:00:05
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:23
bmax according to bmaxDivN setting: 92285733
Using parameters --bmax 69214300 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 69214300 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:15
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:04
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:06
  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: 00:00:27
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: 00:00:23
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: 00:00:22
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.27347e+07 (target: 69214299)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (69214300) 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 49905282
  (Using difference cover)
  Sorting block time: 00:00:46
Returning block of 49905283
Getting block 2 of 7
  Reserving size (69214300) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:10
  Sorting block of length 63366453
  (Using difference cover)
  Sorting block time: 00:01:16
Returning block of 63366454
Getting block 3 of 7
  Reserving size (69214300) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:10
  Sorting block of length 44316966
  (Using difference cover)
  Sorting block time: 00:00:57
Returning block of 44316967
Getting block 4 of 7
  Reserving size (69214300) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:12
  Sorting block of length 53032542
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 53032543
Getting block 5 of 7
  Reserving size (69214300) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:12
  Sorting block of length 67107042
  (Using difference cover)
  Sorting block time: 00:01:25
Returning block of 67107043
Getting block 6 of 7
  Reserving size (69214300) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:11
  Sorting block of length 34715846
  (Using difference cover)
  Sorting block time: 00:00:40
Returning block of 34715847
Getting block 7 of 7
  Reserving size (69214300) 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 56698797
  (Using difference cover)
  Sorting block time: 00:01:02
Returning block of 56698798
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 103607191
fchr[G]: 184571352
fchr[T]: 264713327
fchr[$]: 369142934
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 671169523 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_3/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 46142872 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_3/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 369142934
    bwtLen: 369142935
    sz: 92285734
    bwtSz: 92285734
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11535717
    offsSz: 46142868
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 823980
    numSides: 1647960
    numLines: 1647960
    ebwtTotLen: 105469440
    ebwtTotSz: 105469440
Total time for backward call to driver() for mirror index: 00:11:38