Settings:
  Output files: "/projects/NBL/HS1196/3153YAAXX_8/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/HS1196/3153YAAXX_8/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:11
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:09
bmax according to bmaxDivN setting: 37073968
Using parameters --bmax 27805476 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 27805476 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:08
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  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: 00:00:12
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: 00:00:10
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: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.8537e+07 (target: 27805475)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (27805476) 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 21224102
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 21224103
Getting block 2 of 8
  Reserving size (27805476) 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 19037717
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 19037718
Getting block 3 of 8
  Reserving size (27805476) 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 22761804
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 22761805
Getting block 4 of 8
  Reserving size (27805476) 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 6947101
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 6947102
Getting block 5 of 8
  Reserving size (27805476) 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 21162794
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 21162795
Getting block 6 of 8
  Reserving size (27805476) 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 10683322
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 10683323
Getting block 7 of 8
  Reserving size (27805476) 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 23351460
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 23351461
Getting block 8 of 8
  Reserving size (27805476) 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 23127567
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 23127568
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 37922065
fchr[G]: 74596659
fchr[T]: 110375009
fchr[$]: 148295874
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 272180742 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_8/tophat/tmp/segment_juncs.1.ebwt
Wrote 18536992 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_8/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 148295874
    bwtLen: 148295875
    sz: 37073969
    bwtSz: 37073969
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4634247
    offsSz: 18536988
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 331018
    numSides: 662036
    numLines: 662036
    ebwtTotLen: 42370304
    ebwtTotSz: 42370304
Total time for call to driver() for forward index: 00:05:08
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: 00:00:09
bmax according to bmaxDivN setting: 37073968
Using parameters --bmax 27805476 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 27805476 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:08
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  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: 00:00:12
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
  Binary sorting into buckets
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  100%
  Binary sorting into buckets time: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.8537e+07 (target: 27805475)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (27805476) 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 14907150
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 14907151
Getting block 2 of 8
  Reserving size (27805476) 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 15721306
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 15721307
Getting block 3 of 8
  Reserving size (27805476) 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 20937136
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 20937137
Getting block 4 of 8
  Reserving size (27805476) 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 19795786
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 19795787
Getting block 5 of 8
  Reserving size (27805476) 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 24460171
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 24460172
Getting block 6 of 8
  Reserving size (27805476) 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 19732552
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 19732553
Getting block 7 of 8
  Reserving size (27805476) 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 11523991
  (Using difference cover)
  Sorting block time: 00:00:13
Returning block of 11523992
Getting block 8 of 8
  Reserving size (27805476) 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 21217775
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 21217776
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 37922065
fchr[G]: 74596659
fchr[T]: 110375009
fchr[$]: 148295874
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 272180742 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_8/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 18536992 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_8/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 148295874
    bwtLen: 148295875
    sz: 37073969
    bwtSz: 37073969
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4634247
    offsSz: 18536988
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 331018
    numSides: 662036
    numLines: 662036
    ebwtTotLen: 42370304
    ebwtTotSz: 42370304
Total time for backward call to driver() for mirror index: 00:04:45