Settings:
  Output files: "/projects/NBL/HS1799/61074AAXX_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/HS1799/61074AAXX_3/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:21
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:24
bmax according to bmaxDivN setting: 101743504
Using parameters --bmax 76307628 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76307628 --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: 00:00:07
  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: 00:00:31
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: 00:00:24
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: 00:00:26
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: 00:00:25
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.81391e+07 (target: 76307627)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (76307628) 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 51238379
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 51238380
Getting block 2 of 7
  Reserving size (76307628) 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 74618704
  (Using difference cover)
  Sorting block time: 00:01:01
Returning block of 74618705
Getting block 3 of 7
  Reserving size (76307628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:13
  Sorting block of length 63414578
  (Using difference cover)
  Sorting block time: 00:00:55
Returning block of 63414579
Getting block 4 of 7
  Reserving size (76307628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:13
  Sorting block of length 36013605
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 36013606
Getting block 5 of 7
  Reserving size (76307628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:14
  Sorting block of length 55616088
  (Using difference cover)
  Sorting block time: 00:00:49
Returning block of 55616089
Getting block 6 of 7
  Reserving size (76307628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:15
  Sorting block of length 74911943
  (Using difference cover)
  Sorting block time: 00:01:02
Returning block of 74911944
Getting block 7 of 7
  Reserving size (76307628) 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 51160715
  (Using difference cover)
  Sorting block time: 00:00:40
Returning block of 51160716
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 100750033
fchr[G]: 202077280
fchr[T]: 302821339
fchr[$]: 406974018
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 739636457 bytes to primary EBWT file: /projects/NBL/HS1799/61074AAXX_3/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 50871760 bytes to secondary EBWT file: /projects/NBL/HS1799/61074AAXX_3/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 406974018
    bwtLen: 406974019
    sz: 101743505
    bwtSz: 101743505
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12717939
    offsSz: 50871756
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 908425
    numSides: 1816850
    numLines: 1816850
    ebwtTotLen: 116278400
    ebwtTotSz: 116278400
Total time for call to driver() for forward index: 00:11:01
Reading reference sizes
  Time reading reference sizes: 00:00:07
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:24
bmax according to bmaxDivN setting: 101743504
Using parameters --bmax 76307628 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76307628 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:16
  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: 00:00:07
  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: 00:00:33
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: 00:00:25
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.08718e+07 (target: 76307627)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (76307628) 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 54779586
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 54779587
Getting block 2 of 8
  Reserving size (76307628) 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 44318525
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 44318526
Getting block 3 of 8
  Reserving size (76307628) 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 60369466
  (Using difference cover)
  Sorting block time: 00:00:52
Returning block of 60369467
Getting block 4 of 8
  Reserving size (76307628) 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 17628332
  (Using difference cover)
  Sorting block time: 00:00:16
Returning block of 17628333
Getting block 5 of 8
  Reserving size (76307628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:14
  Sorting block of length 72295098
  (Using difference cover)
  Sorting block time: 00:01:02
Returning block of 72295099
Getting block 6 of 8
  Reserving size (76307628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:15
  Sorting block of length 64871779
  (Using difference cover)
  Sorting block time: 00:00:54
Returning block of 64871780
Getting block 7 of 8
  Reserving size (76307628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:13
  Sorting block of length 41032128
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 41032129
Getting block 8 of 8
  Reserving size (76307628) 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 51679097
  (Using difference cover)
  Sorting block time: 00:00:40
Returning block of 51679098
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 100750033
fchr[G]: 202077280
fchr[T]: 302821339
fchr[$]: 406974018
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 739636457 bytes to primary EBWT file: /projects/NBL/HS1799/61074AAXX_3/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 50871760 bytes to secondary EBWT file: /projects/NBL/HS1799/61074AAXX_3/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 406974018
    bwtLen: 406974019
    sz: 101743505
    bwtSz: 101743505
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12717939
    offsSz: 50871756
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 908425
    numSides: 1816850
    numLines: 1816850
    ebwtTotLen: 116278400
    ebwtTotSz: 116278400
Total time for backward call to driver() for mirror index: 00:10:03