Settings:
  Output files: "/projects/NBL/HS1195/30TTYAAXX_7/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/HS1195/30TTYAAXX_7/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:30
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:22
bmax according to bmaxDivN setting: 89393468
Using parameters --bmax 67045101 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 67045101 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:18
  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
Split 1, merged 6; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:23
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.1082e+07 (target: 67045100)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (67045101) 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 35528646
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 35528647
Getting block 2 of 7
  Reserving size (67045101) 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 63203914
  (Using difference cover)
  Sorting block time: 00:01:14
Returning block of 63203915
Getting block 3 of 7
  Reserving size (67045101) 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 57950682
  (Using difference cover)
  Sorting block time: 00:01:12
Returning block of 57950683
Getting block 4 of 7
  Reserving size (67045101) 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 59877816
  (Using difference cover)
  Sorting block time: 00:01:12
Returning block of 59877817
Getting block 5 of 7
  Reserving size (67045101) 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 55056568
  (Using difference cover)
  Sorting block time: 00:01:10
Returning block of 55056569
Getting block 6 of 7
  Reserving size (67045101) 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 61082894
  (Using difference cover)
  Sorting block time: 00:01:16
Returning block of 61082895
Getting block 7 of 7
  Reserving size (67045101) 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 24873346
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 24873347
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101536410
fchr[G]: 178532651
fchr[T]: 254145819
fchr[$]: 357573872
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 650623373 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_7/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 44696740 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_7/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 357573872
    bwtLen: 357573873
    sz: 89393468
    bwtSz: 89393469
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11174184
    offsSz: 44696736
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 798156
    numSides: 1596312
    numLines: 1596312
    ebwtTotLen: 102163968
    ebwtTotSz: 102163968
Total time for call to driver() for forward index: 00:11:27
Reading reference sizes
  Time reading reference sizes: 00:00:06
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:22
bmax according to bmaxDivN setting: 89393468
Using parameters --bmax 67045101 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 67045101 --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: 00:00:30
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:24
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: 00:00:24
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.1082e+07 (target: 67045100)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (67045101) 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 39476851
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 39476852
Getting block 2 of 7
  Reserving size (67045101) 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 36800290
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 36800291
Getting block 3 of 7
  Reserving size (67045101) 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 65690707
  (Using difference cover)
  Sorting block time: 00:01:21
Returning block of 65690708
Getting block 4 of 7
  Reserving size (67045101) 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 64088048
  (Using difference cover)
  Sorting block time: 00:01:21
Returning block of 64088049
Getting block 5 of 7
  Reserving size (67045101) 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 57508668
  (Using difference cover)
  Sorting block time: 00:01:16
Returning block of 57508669
Getting block 6 of 7
  Reserving size (67045101) 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 37650929
  (Using difference cover)
  Sorting block time: 00:00:48
Returning block of 37650930
Getting block 7 of 7
  Reserving size (67045101) 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 56358373
  (Using difference cover)
  Sorting block time: 00:00:59
Returning block of 56358374
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101536410
fchr[G]: 178532651
fchr[T]: 254145819
fchr[$]: 357573872
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 650623373 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_7/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 44696740 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_7/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 357573872
    bwtLen: 357573873
    sz: 89393468
    bwtSz: 89393469
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11174184
    offsSz: 44696736
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 798156
    numSides: 1596312
    numLines: 1596312
    ebwtTotLen: 102163968
    ebwtTotSz: 102163968
Total time for backward call to driver() for mirror index: 00:11:35