Settings:
  Output files: "/projects/NBL/HS1799/61074AAXX_4/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_4/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:01:44
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:47
bmax according to bmaxDivN setting: 101920913
Using parameters --bmax 76440685 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76440685 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:27
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:05
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:11
  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: 00:00:44
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: 00:00:39
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.82405e+07 (target: 76440684)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (76440685) 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 57956025
  (Using difference cover)
  Sorting block time: 00:01:12
Returning block of 57956026
Getting block 2 of 7
  Reserving size (76440685) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:17
  Sorting block of length 75173802
  (Using difference cover)
  Sorting block time: 00:01:39
Returning block of 75173803
Getting block 3 of 7
  Reserving size (76440685) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:17
  Sorting block of length 58028207
  (Using difference cover)
  Sorting block time: 00:01:23
Returning block of 58028208
Getting block 4 of 7
  Reserving size (76440685) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:21
  Sorting block of length 69533004
  (Using difference cover)
  Sorting block time: 00:01:34
Returning block of 69533005
Getting block 5 of 7
  Reserving size (76440685) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:21
  Sorting block of length 69702134
  (Using difference cover)
  Sorting block time: 00:01:34
Returning block of 69702135
Getting block 6 of 7
  Reserving size (76440685) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:20
  Sorting block of length 19955602
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 19955603
Getting block 7 of 7
  Reserving size (76440685) 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 57334872
  (Using difference cover)
  Sorting block time: 00:01:14
Returning block of 57334873
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101068390
fchr[G]: 202544992
fchr[T]: 303369056
fchr[$]: 407683652
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 741112304 bytes to primary EBWT file: /projects/NBL/HS1799/61074AAXX_4/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 50960464 bytes to secondary EBWT file: /projects/NBL/HS1799/61074AAXX_4/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 407683652
    bwtLen: 407683653
    sz: 101920913
    bwtSz: 101920914
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12740115
    offsSz: 50960460
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 910009
    numSides: 1820018
    numLines: 1820018
    ebwtTotLen: 116481152
    ebwtTotSz: 116481152
Total time for call to driver() for forward index: 00:18:06
Reading reference sizes
  Time reading reference sizes: 00:00:09
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:47
bmax according to bmaxDivN setting: 101920913
Using parameters --bmax 76440685 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76440685 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:27
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:05
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:11
  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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  100%
  Binary sorting into buckets time: 00:00:48
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
  Binary sorting into buckets
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  30%
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  50%
  60%
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  100%
  Binary sorting into buckets time: 00:00:39
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.82405e+07 (target: 76440684)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (76440685) 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 72038707
  (Using difference cover)
  Sorting block time: 00:01:31
Returning block of 72038708
Getting block 2 of 7
  Reserving size (76440685) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:17
  Sorting block of length 69935659
  (Using difference cover)
  Sorting block time: 00:01:33
Returning block of 69935660
Getting block 3 of 7
  Reserving size (76440685) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:17
  Sorting block of length 34558800
  (Using difference cover)
  Sorting block time: 00:00:47
Returning block of 34558801
Getting block 4 of 7
  Reserving size (76440685) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:20
  Sorting block of length 72530784
  (Using difference cover)
  Sorting block time: 00:01:38
Returning block of 72530785
Getting block 5 of 7
  Reserving size (76440685) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:19
  Sorting block of length 37805897
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 37805898
Getting block 6 of 7
  Reserving size (76440685) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:21
  Sorting block of length 45617201
  (Using difference cover)
  Sorting block time: 00:00:59
Returning block of 45617202
Getting block 7 of 7
  Reserving size (76440685) 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 75196598
  (Using difference cover)
  Sorting block time: 00:01:38
Returning block of 75196599
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101068390
fchr[G]: 202544992
fchr[T]: 303369056
fchr[$]: 407683652
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 741112304 bytes to primary EBWT file: /projects/NBL/HS1799/61074AAXX_4/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 50960464 bytes to secondary EBWT file: /projects/NBL/HS1799/61074AAXX_4/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 407683652
    bwtLen: 407683653
    sz: 101920913
    bwtSz: 101920914
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12740115
    offsSz: 50960460
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 910009
    numSides: 1820018
    numLines: 1820018
    ebwtTotLen: 116481152
    ebwtTotSz: 116481152
Total time for backward call to driver() for mirror index: 00:16:24