Settings:
  Output files: "/projects/NBL/HS1197/302NNAAXX_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/HS1197/302NNAAXX_7/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: 00:00:15
bmax according to bmaxDivN setting: 68770628
Using parameters --bmax 51577971 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 51577971 --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: 00:00:03
  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: 00:00:23
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.92975e+07 (target: 51577970)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (51577971) 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 50616953
  (Using difference cover)
  Sorting block time: 00:00:48
Returning block of 50616954
Getting block 2 of 7
  Reserving size (51577971) 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 38146444
  (Using difference cover)
  Sorting block time: 00:00:41
Returning block of 38146445
Getting block 3 of 7
  Reserving size (51577971) 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 30371821
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 30371822
Getting block 4 of 7
  Reserving size (51577971) 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 42882736
  (Using difference cover)
  Sorting block time: 00:00:48
Returning block of 42882737
Getting block 5 of 7
  Reserving size (51577971) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:09
  Sorting block of length 46939451
  (Using difference cover)
  Sorting block time: 00:00:55
Returning block of 46939452
Getting block 6 of 7
  Reserving size (51577971) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:09
  Sorting block of length 33246127
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 33246128
Getting block 7 of 7
  Reserving size (51577971) 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 32878977
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 32878978
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 74401668
fchr[G]: 137407526
fchr[T]: 200514843
fchr[$]: 275082515
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 501899784 bytes to primary EBWT file: /projects/NBL/HS1197/302NNAAXX_7/tophat/tmp/segment_juncs.1.ebwt
Wrote 34385320 bytes to secondary EBWT file: /projects/NBL/HS1197/302NNAAXX_7/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 275082515
    bwtLen: 275082516
    sz: 68770629
    bwtSz: 68770629
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 8596329
    offsSz: 34385316
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 614024
    numSides: 1228048
    numLines: 1228048
    ebwtTotLen: 78595072
    ebwtTotSz: 78595072
Total time for call to driver() for forward index: 00:08:06
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: 00:00:17
bmax according to bmaxDivN setting: 68770628
Using parameters --bmax 51577971 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 51577971 --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: 00:00:05
  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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  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:23
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.92975e+07 (target: 51577970)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (51577971) 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 47355446
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 47355447
Getting block 2 of 7
  Reserving size (51577971) 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 33061938
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 33061939
Getting block 3 of 7
  Reserving size (51577971) 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 36285470
  (Using difference cover)
  Sorting block time: 00:00:41
Returning block of 36285471
Getting block 4 of 7
  Reserving size (51577971) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:09
  Sorting block of length 51495451
  (Using difference cover)
  Sorting block time: 00:00:59
Returning block of 51495452
Getting block 5 of 7
  Reserving size (51577971) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:09
  Sorting block of length 19275859
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 19275860
Getting block 6 of 7
  Reserving size (51577971) 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 50268665
  (Using difference cover)
  Sorting block time: 00:00:56
Returning block of 50268666
Getting block 7 of 7
  Reserving size (51577971) 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 37339680
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 37339681
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 74401668
fchr[G]: 137407526
fchr[T]: 200514843
fchr[$]: 275082515
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 501899784 bytes to primary EBWT file: /projects/NBL/HS1197/302NNAAXX_7/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 34385320 bytes to secondary EBWT file: /projects/NBL/HS1197/302NNAAXX_7/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 275082515
    bwtLen: 275082516
    sz: 68770629
    bwtSz: 68770629
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 8596329
    offsSz: 34385316
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 614024
    numSides: 1228048
    numLines: 1228048
    ebwtTotLen: 78595072
    ebwtTotSz: 78595072
Total time for backward call to driver() for mirror index: 00:07:39