Settings:
  Output files: "/projects/NBL/HS1797/616GYAAXX_2/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/HS1797/616GYAAXX_2/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:49
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:28
bmax according to bmaxDivN setting: 103392772
Using parameters --bmax 77544579 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 77544579 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:26
  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: 00:00:38
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.16964e+07 (target: 77544578)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (77544579) 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 64227949
  (Using difference cover)
  Sorting block time: 00:01:20
Returning block of 64227950
Getting block 2 of 8
  Reserving size (77544579) 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 56263332
  (Using difference cover)
  Sorting block time: 00:01:11
Returning block of 56263333
Getting block 3 of 8
  Reserving size (77544579) 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 36787928
  (Using difference cover)
  Sorting block time: 00:00:48
Returning block of 36787929
Getting block 4 of 8
  Reserving size (77544579) 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 57818134
  (Using difference cover)
  Sorting block time: 00:01:15
Returning block of 57818135
Getting block 5 of 8
  Reserving size (77544579) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:16
  Sorting block of length 51187205
  (Using difference cover)
  Sorting block time: 00:01:08
Returning block of 51187206
Getting block 6 of 8
  Reserving size (77544579) 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 39306020
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 39306021
Getting block 7 of 8
  Reserving size (77544579) 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 66438698
  (Using difference cover)
  Sorting block time: 00:01:21
Returning block of 66438699
Getting block 8 of 8
  Reserving size (77544579) 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 41541815
  (Using difference cover)
  Sorting block time: 00:00:48
Returning block of 41541816
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 102078382
fchr[G]: 204940681
fchr[T]: 307538935
fchr[$]: 413571088
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 751964869 bytes to primary EBWT file: /projects/NBL/HS1797/616GYAAXX_2/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 51696392 bytes to secondary EBWT file: /projects/NBL/HS1797/616GYAAXX_2/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 413571088
    bwtLen: 413571089
    sz: 103392772
    bwtSz: 103392773
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12924097
    offsSz: 51696388
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 923150
    numSides: 1846300
    numLines: 1846300
    ebwtTotLen: 118163200
    ebwtTotSz: 118163200
Total time for call to driver() for forward index: 00:15:13
Reading reference sizes
  Time reading reference sizes: 00:00:10
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:28
bmax according to bmaxDivN setting: 103392772
Using parameters --bmax 77544579 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 77544579 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:26
  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: 00:00:36
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: 00:00:34
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.16964e+07 (target: 77544578)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (77544579) 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 15272945
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 15272946
Getting block 2 of 8
  Reserving size (77544579) 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 73057162
  (Using difference cover)
  Sorting block time: 00:01:32
Returning block of 73057163
Getting block 3 of 8
  Reserving size (77544579) 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 51959401
  (Using difference cover)
  Sorting block time: 00:01:06
Returning block of 51959402
Getting block 4 of 8
  Reserving size (77544579) 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 71320757
  (Using difference cover)
  Sorting block time: 00:01:35
Returning block of 71320758
Getting block 5 of 8
  Reserving size (77544579) 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 76411510
  (Using difference cover)
  Sorting block time: 00:01:42
Returning block of 76411511
Getting block 6 of 8
  Reserving size (77544579) 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 39406022
  (Using difference cover)
  Sorting block time: 00:00:48
Returning block of 39406023
Getting block 7 of 8
  Reserving size (77544579) 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 40730951
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 40730952
Getting block 8 of 8
  Reserving size (77544579) 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 45412333
  (Using difference cover)
  Sorting block time: 00:00:55
Returning block of 45412334
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 102078382
fchr[G]: 204940681
fchr[T]: 307538935
fchr[$]: 413571088
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 751964869 bytes to primary EBWT file: /projects/NBL/HS1797/616GYAAXX_2/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 51696392 bytes to secondary EBWT file: /projects/NBL/HS1797/616GYAAXX_2/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 413571088
    bwtLen: 413571089
    sz: 103392772
    bwtSz: 103392773
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12924097
    offsSz: 51696388
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 923150
    numSides: 1846300
    numLines: 1846300
    ebwtTotLen: 118163200
    ebwtTotSz: 118163200
Total time for backward call to driver() for mirror index: 00:15:32