Settings:
  Output files: "/projects/NBL/HS1795/700FNAAXX_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/HS1795/700FNAAXX_8/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:01:21
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:23
bmax according to bmaxDivN setting: 97676156
Using parameters --bmax 73257117 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 73257117 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:14
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:04
  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: 00:00:33
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 5; iterating...
  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 1; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:26
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.88381e+07 (target: 73257116)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (73257117) 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 28501061
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 28501062
Getting block 2 of 8
  Reserving size (73257117) 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 63311334
  (Using difference cover)
  Sorting block time: 00:00:52
Returning block of 63311335
Getting block 3 of 8
  Reserving size (73257117) 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 71303537
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 71303538
Getting block 4 of 8
  Reserving size (73257117) 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 15243396
  (Using difference cover)
  Sorting block time: 00:00:13
Returning block of 15243397
Getting block 5 of 8
  Reserving size (73257117) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:16
  Sorting block of length 63526903
  (Using difference cover)
  Sorting block time: 00:01:05
Returning block of 63526904
Getting block 6 of 8
  Reserving size (73257117) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:17
  Sorting block of length 52843432
  (Using difference cover)
  Sorting block time: 00:00:54
Returning block of 52843433
Getting block 7 of 8
  Reserving size (73257117) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:14
  Sorting block of length 40130267
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 40130268
Getting block 8 of 8
  Reserving size (73257117) 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 55844689
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 55844690
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 97098078
fchr[G]: 193595532
fchr[T]: 290238054
fchr[$]: 390704626
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 710205246 bytes to primary EBWT file: /projects/NBL/HS1795/700FNAAXX_8/tophat/tmp/segment_juncs.1.ebwt
Wrote 48838084 bytes to secondary EBWT file: /projects/NBL/HS1795/700FNAAXX_8/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 390704626
    bwtLen: 390704627
    sz: 97676157
    bwtSz: 97676157
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12209520
    offsSz: 48838080
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 872109
    numSides: 1744218
    numLines: 1744218
    ebwtTotLen: 111629952
    ebwtTotSz: 111629952
Total time for call to driver() for forward index: 00:14:19
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: 00:00:24
bmax according to bmaxDivN setting: 97676156
Using parameters --bmax 73257117 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 73257117 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:14
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:04
  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: 00:00:43
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 5; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:36
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: 00:00:36
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.88381e+07 (target: 73257116)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (73257117) 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 26619520
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 26619521
Getting block 2 of 8
  Reserving size (73257117) 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 66227112
  (Using difference cover)
  Sorting block time: 00:00:53
Returning block of 66227113
Getting block 3 of 8
  Reserving size (73257117) 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 59628691
  (Using difference cover)
  Sorting block time: 00:00:49
Returning block of 59628692
Getting block 4 of 8
  Reserving size (73257117) 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 68248100
  (Using difference cover)
  Sorting block time: 00:00:56
Returning block of 68248101
Getting block 5 of 8
  Reserving size (73257117) 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 27495796
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 27495797
Getting block 6 of 8
  Reserving size (73257117) 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 56081671
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 56081672
Getting block 7 of 8
  Reserving size (73257117) 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 60981846
  (Using difference cover)
  Sorting block time: 00:00:48
Returning block of 60981847
Getting block 8 of 8
  Reserving size (73257117) 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 25421883
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 25421884
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 97098078
fchr[G]: 193595532
fchr[T]: 290238054
fchr[$]: 390704626
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 710205246 bytes to primary EBWT file: /projects/NBL/HS1795/700FNAAXX_8/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 48838084 bytes to secondary EBWT file: /projects/NBL/HS1795/700FNAAXX_8/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 390704626
    bwtLen: 390704627
    sz: 97676157
    bwtSz: 97676157
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12209520
    offsSz: 48838080
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 872109
    numSides: 1744218
    numLines: 1744218
    ebwtTotLen: 111629952
    ebwtTotSz: 111629952
Total time for backward call to driver() for mirror index: 00:12:36