Settings:
  Output files: "/projects/NBL/HS1194/311L9AAXX_7/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_7/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: 00:00:09
bmax according to bmaxDivN setting: 40864165
Using parameters --bmax 30648124 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 30648124 --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: 00:00:02
  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: 00:00:10
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.04321e+07 (target: 30648123)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (30648124) 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 29234810
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 29234811
Getting block 2 of 8
  Reserving size (30648124) 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 18863748
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 18863749
Getting block 3 of 8
  Reserving size (30648124) 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 15473399
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 15473400
Getting block 4 of 8
  Reserving size (30648124) 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 21252886
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 21252887
Getting block 5 of 8
  Reserving size (30648124) 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 27367159
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 27367160
Getting block 6 of 8
  Reserving size (30648124) 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 20517797
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 20517798
Getting block 7 of 8
  Reserving size (30648124) 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 26620881
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 26620882
Getting block 8 of 8
  Reserving size (30648124) 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 4125973
  (Using difference cover)
  Sorting block time: 00:00:03
Returning block of 4125974
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 42284678
fchr[G]: 83349937
fchr[T]: 121184791
fchr[$]: 163456660
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 299296827 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_7/tophat/tmp/segment_juncs.1.ebwt
Wrote 20432088 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_7/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 163456660
    bwtLen: 163456661
    sz: 40864165
    bwtSz: 40864166
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5108021
    offsSz: 20432084
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 364859
    numSides: 729718
    numLines: 729718
    ebwtTotLen: 46701952
    ebwtTotSz: 46701952
Total time for call to driver() for forward index: 00:07:22
Reading reference sizes
  Time reading reference sizes: 00:00:02
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: 40864165
Using parameters --bmax 30648124 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 30648124 --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: 00:00:02
  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: 00:00:14
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.3351e+07 (target: 30648123)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (30648124) 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 27627148
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 27627149
Getting block 2 of 7
  Reserving size (30648124) 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 21301015
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 21301016
Getting block 3 of 7
  Reserving size (30648124) 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 26104463
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 26104464
Getting block 4 of 7
  Reserving size (30648124) 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 21879876
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 21879877
Getting block 5 of 7
  Reserving size (30648124) 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 24323041
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 24323042
Getting block 6 of 7
  Reserving size (30648124) 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 15992396
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 15992397
Getting block 7 of 7
  Reserving size (30648124) 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 26228715
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 26228716
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 42284678
fchr[G]: 83349937
fchr[T]: 121184791
fchr[$]: 163456660
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 299296827 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_7/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 20432088 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_7/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 163456660
    bwtLen: 163456661
    sz: 40864165
    bwtSz: 40864166
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5108021
    offsSz: 20432084
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 364859
    numSides: 729718
    numLines: 729718
    ebwtTotLen: 46701952
    ebwtTotSz: 46701952
Total time for backward call to driver() for mirror index: 00:06:19