Settings:
  Output files: "/projects/NBL/HS1195/302NNAAXX_5/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/HS1195/302NNAAXX_5/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:01:03
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: 83326526
Using parameters --bmax 62494895 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 62494895 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:22
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:05
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:09
  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
Avg bucket size: 4.76152e+07 (target: 62494894)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (62494895) 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 35861106
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 35861107
Getting block 2 of 7
  Reserving size (62494895) 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 35364026
  (Using difference cover)
  Sorting block time: 00:00:57
Returning block of 35364027
Getting block 3 of 7
  Reserving size (62494895) 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 52382082
  (Using difference cover)
  Sorting block time: 00:01:22
Returning block of 52382083
Getting block 4 of 7
  Reserving size (62494895) 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 51840892
  (Using difference cover)
  Sorting block time: 00:01:27
Returning block of 51840893
Getting block 5 of 7
  Reserving size (62494895) 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 50946857
  (Using difference cover)
  Sorting block time: 00:01:27
Returning block of 50946858
Getting block 6 of 7
  Reserving size (62494895) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:15
  Sorting block of length 59687168
  (Using difference cover)
  Sorting block time: 00:01:36
Returning block of 59687169
Getting block 7 of 7
  Reserving size (62494895) 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 47223970
  (Using difference cover)
  Sorting block time: 00:01:05
Returning block of 47223971
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 93657388
fchr[G]: 166104608
fchr[T]: 238295278
fchr[$]: 333306107
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 606901262 bytes to primary EBWT file: /projects/NBL/HS1195/302NNAAXX_5/tophat/tmp/segment_juncs.1.ebwt
Wrote 41663268 bytes to secondary EBWT file: /projects/NBL/HS1195/302NNAAXX_5/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 333306107
    bwtLen: 333306108
    sz: 83326527
    bwtSz: 83326527
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 10415816
    offsSz: 41663264
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 743987
    numSides: 1487974
    numLines: 1487974
    ebwtTotLen: 95230336
    ebwtTotSz: 95230336
Total time for call to driver() for forward index: 00:14:13
Reading reference sizes
  Time reading reference sizes: 00:00:07
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: 83326526
Using parameters --bmax 62494895 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 62494895 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:20
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:05
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:08
  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 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: 00:00:25
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.76152e+07 (target: 62494894)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (62494895) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:08
  Sorting block of length 59040456
  (Using difference cover)
  Sorting block time: 00:01:19
Returning block of 59040457
Getting block 2 of 7
  Reserving size (62494895) 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 60526269
  (Using difference cover)
  Sorting block time: 00:01:34
Returning block of 60526270
Getting block 3 of 7
  Reserving size (62494895) 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 44542677
  (Using difference cover)
  Sorting block time: 00:01:10
Returning block of 44542678
Getting block 4 of 7
  Reserving size (62494895) 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 27415508
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 27415509
Getting block 5 of 7
  Reserving size (62494895) 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 51442202
  (Using difference cover)
  Sorting block time: 00:01:21
Returning block of 51442203
Getting block 6 of 7
  Reserving size (62494895) 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 48755026
  (Using difference cover)
  Sorting block time: 00:01:15
Returning block of 48755027
Getting block 7 of 7
  Reserving size (62494895) 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 41583963
  (Using difference cover)
  Sorting block time: 00:00:53
Returning block of 41583964
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 93657388
fchr[G]: 166104608
fchr[T]: 238295278
fchr[$]: 333306107
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 606901262 bytes to primary EBWT file: /projects/NBL/HS1195/302NNAAXX_5/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 41663268 bytes to secondary EBWT file: /projects/NBL/HS1195/302NNAAXX_5/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 333306107
    bwtLen: 333306108
    sz: 83326527
    bwtSz: 83326527
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 10415816
    offsSz: 41663264
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 743987
    numSides: 1487974
    numLines: 1487974
    ebwtTotLen: 95230336
    ebwtTotSz: 95230336
Total time for backward call to driver() for mirror index: 00:13:35