Settings:
  Output files: "/projects/NBL/HS1195/30TTYAAXX_6/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/HS1195/30TTYAAXX_6/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:58
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:20
bmax according to bmaxDivN setting: 89667817
Using parameters --bmax 67250863 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 67250863 --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: 00:00:03
  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
Avg bucket size: 5.12388e+07 (target: 67250862)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (67250863) 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 57231834
  (Using difference cover)
  Sorting block time: 00:00:53
Returning block of 57231835
Getting block 2 of 7
  Reserving size (67250863) 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 66761806
  (Using difference cover)
  Sorting block time: 00:01:16
Returning block of 66761807
Getting block 3 of 7
  Reserving size (67250863) 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 55904836
  (Using difference cover)
  Sorting block time: 00:01:09
Returning block of 55904837
Getting block 4 of 7
  Reserving size (67250863) 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 42565610
  (Using difference cover)
  Sorting block time: 00:00:53
Returning block of 42565611
Getting block 5 of 7
  Reserving size (67250863) 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 25929757
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 25929758
Getting block 6 of 7
  Reserving size (67250863) 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 61366775
  (Using difference cover)
  Sorting block time: 00:01:11
Returning block of 61366776
Getting block 7 of 7
  Reserving size (67250863) 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 48910646
  (Using difference cover)
  Sorting block time: 00:00:49
Returning block of 48910647
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 102545261
fchr[G]: 179048831
fchr[T]: 254642227
fchr[$]: 358671270
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 652762234 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_6/tophat/tmp/segment_juncs.1.ebwt
Wrote 44833916 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_6/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 358671270
    bwtLen: 358671271
    sz: 89667818
    bwtSz: 89667818
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11208478
    offsSz: 44833912
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 800606
    numSides: 1601212
    numLines: 1601212
    ebwtTotLen: 102477568
    ebwtTotSz: 102477568
Total time for call to driver() for forward index: 00:11:44
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: 00:00:20
bmax according to bmaxDivN setting: 89667817
Using parameters --bmax 67250863 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 67250863 --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: 00:00:03
  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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  100%
  Binary sorting into buckets time: 00:00:30
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.12388e+07 (target: 67250862)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (67250863) 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 58821062
  (Using difference cover)
  Sorting block time: 00:00:54
Returning block of 58821063
Getting block 2 of 7
  Reserving size (67250863) 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 49538953
  (Using difference cover)
  Sorting block time: 00:00:57
Returning block of 49538954
Getting block 3 of 7
  Reserving size (67250863) 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 64361278
  (Using difference cover)
  Sorting block time: 00:01:20
Returning block of 64361279
Getting block 4 of 7
  Reserving size (67250863) 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 40752565
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 40752566
Getting block 5 of 7
  Reserving size (67250863) 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 64145321
  (Using difference cover)
  Sorting block time: 00:01:17
Returning block of 64145322
Getting block 6 of 7
  Reserving size (67250863) 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 63501911
  (Using difference cover)
  Sorting block time: 00:01:29
Returning block of 63501912
Getting block 7 of 7
  Reserving size (67250863) 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 17550174
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 17550175
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 102545261
fchr[G]: 179048831
fchr[T]: 254642227
fchr[$]: 358671270
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 652762234 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_6/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 44833916 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_6/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 358671270
    bwtLen: 358671271
    sz: 89667818
    bwtSz: 89667818
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11208478
    offsSz: 44833912
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 800606
    numSides: 1601212
    numLines: 1601212
    ebwtTotLen: 102477568
    ebwtTotSz: 102477568
Total time for backward call to driver() for mirror index: 00:11:12