Settings:
  Output files: "/projects/NBL/HS1194/311L9AAXX_5/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/HS1194/311L9AAXX_5/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: 00:00:10
bmax according to bmaxDivN setting: 37578939
Using parameters --bmax 28184205 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 28184205 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:09
  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: 00:00:03
  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: 00:00:13
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: 00:00:12
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: 00:00:13
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: 00:00:13
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.14737e+07 (target: 28184204)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (28184205) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 23563990
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 23563991
Getting block 2 of 7
  Reserving size (28184205) 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 20768856
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 20768857
Getting block 3 of 7
  Reserving size (28184205) 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 23470093
  (Using difference cover)
  Sorting block time: 00:00:49
Returning block of 23470094
Getting block 4 of 7
  Reserving size (28184205) 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 22073655
  (Using difference cover)
  Sorting block time: 00:00:41
Returning block of 22073656
Getting block 5 of 7
  Reserving size (28184205) 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 26541511
  (Using difference cover)
  Sorting block time: 00:00:52
Returning block of 26541512
Getting block 6 of 7
  Reserving size (28184205) 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 16727075
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 16727076
Getting block 7 of 7
  Reserving size (28184205) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 17170572
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 17170573
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 38463392
fchr[G]: 76411846
fchr[T]: 111397987
fchr[$]: 150315758
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 275842613 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_5/tophat/tmp/segment_juncs.1.ebwt
Wrote 18789476 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_5/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 150315758
    bwtLen: 150315759
    sz: 37578940
    bwtSz: 37578940
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4697368
    offsSz: 18789472
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 335527
    numSides: 671054
    numLines: 671054
    ebwtTotLen: 42947456
    ebwtTotSz: 42947456
Total time for call to driver() for forward index: 00:07:43
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: 00:00:10
bmax according to bmaxDivN setting: 37578939
Using parameters --bmax 28184205 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 28184205 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:10
  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: 00:00:03
  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: 00:00:13
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: 00:00:11
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: 00:00:13
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: 00:00:11
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: 00:00:12
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.14737e+07 (target: 28184204)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (28184205) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 18526542
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 18526543
Getting block 2 of 7
  Reserving size (28184205) 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 19842382
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 19842383
Getting block 3 of 7
  Reserving size (28184205) 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 24017261
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 24017262
Getting block 4 of 7
  Reserving size (28184205) 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 24019555
  (Using difference cover)
  Sorting block time: 00:00:48
Returning block of 24019556
Getting block 5 of 7
  Reserving size (28184205) 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 26387443
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 26387444
Getting block 6 of 7
  Reserving size (28184205) 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 20857974
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 20857975
Getting block 7 of 7
  Reserving size (28184205) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 16664595
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 16664596
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 38463392
fchr[G]: 76411846
fchr[T]: 111397987
fchr[$]: 150315758
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 275842613 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_5/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 18789476 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_5/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 150315758
    bwtLen: 150315759
    sz: 37578940
    bwtSz: 37578940
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4697368
    offsSz: 18789472
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 335527
    numSides: 671054
    numLines: 671054
    ebwtTotLen: 42947456
    ebwtTotSz: 42947456
Total time for backward call to driver() for mirror index: 00:07:35