Settings:
  Output files: "/projects/NBL/HS1198/30UBRAAXX_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/HS1198/30UBRAAXX_3/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:20
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:12
bmax according to bmaxDivN setting: 46831732
Using parameters --bmax 35123799 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 35123799 --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: 00:00:15
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.6761e+07 (target: 35123798)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (35123799) 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 25725942
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 25725943
Getting block 2 of 7
  Reserving size (35123799) 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 17607067
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 17607068
Getting block 3 of 7
  Reserving size (35123799) 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 34155687
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 34155688
Getting block 4 of 7
  Reserving size (35123799) 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 32396349
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 32396350
Getting block 5 of 7
  Reserving size (35123799) 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 30952424
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 30952425
Getting block 6 of 7
  Reserving size (35123799) 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 32146622
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 32146623
Getting block 7 of 7
  Reserving size (35123799) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 14342834
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 14342835
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 51711107
fchr[G]: 94296886
fchr[T]: 135914975
fchr[$]: 187326931
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 343143929 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_3/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 23415872 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_3/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 187326931
    bwtLen: 187326932
    sz: 46831733
    bwtSz: 46831733
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5853967
    offsSz: 23415868
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 418141
    numSides: 836282
    numLines: 836282
    ebwtTotLen: 53522048
    ebwtTotSz: 53522048
Total time for call to driver() for forward index: 00:05:49
Reading reference sizes
  Time reading reference sizes: 00:00:04
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:11
bmax according to bmaxDivN setting: 46831732
Using parameters --bmax 35123799 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 35123799 --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: 00:00:14
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: 00:00:12
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: 2.34159e+07 (target: 35123798)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (35123799) 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 20968611
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 20968612
Getting block 2 of 8
  Reserving size (35123799) 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 14651151
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 14651152
Getting block 3 of 8
  Reserving size (35123799) 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 22827098
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 22827099
Getting block 4 of 8
  Reserving size (35123799) 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 26109859
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 26109860
Getting block 5 of 8
  Reserving size (35123799) 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 11782657
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 11782658
Getting block 6 of 8
  Reserving size (35123799) 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 32025988
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 32025989
Getting block 7 of 8
  Reserving size (35123799) 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 24046219
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 24046220
Getting block 8 of 8
  Reserving size (35123799) 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 34915341
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 34915342
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 51711107
fchr[G]: 94296886
fchr[T]: 135914975
fchr[$]: 187326931
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 343143929 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_3/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 23415872 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_3/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 187326931
    bwtLen: 187326932
    sz: 46831733
    bwtSz: 46831733
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5853967
    offsSz: 23415868
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 418141
    numSides: 836282
    numLines: 836282
    ebwtTotLen: 53522048
    ebwtTotSz: 53522048
Total time for backward call to driver() for mirror index: 00:05:57