Settings:
  Output files: "/projects/NBL/HS1195/30TTYAAXX_2/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_2/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:34
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:26
bmax according to bmaxDivN setting: 94080212
Using parameters --bmax 70560159 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 70560159 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:28
  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: 00:00:10
  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: 00:00:32
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: 00:00:30
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.70401e+07 (target: 70560158)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (70560159) 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 69078266
  (Using difference cover)
  Sorting block time: 00:01:47
Returning block of 69078267
Getting block 2 of 8
  Reserving size (70560159) 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 39293120
  (Using difference cover)
  Sorting block time: 00:01:08
Returning block of 39293121
Getting block 3 of 8
  Reserving size (70560159) 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 40356676
  (Using difference cover)
  Sorting block time: 00:01:17
Returning block of 40356677
Getting block 4 of 8
  Reserving size (70560159) 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 62814879
  (Using difference cover)
  Sorting block time: 00:02:01
Returning block of 62814880
Getting block 5 of 8
  Reserving size (70560159) 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 17652072
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 17652073
Getting block 6 of 8
  Reserving size (70560159) 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 59791504
  (Using difference cover)
  Sorting block time: 00:01:53
Returning block of 59791505
Getting block 7 of 8
  Reserving size (70560159) 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 66994100
  (Using difference cover)
  Sorting block time: 00:02:05
Returning block of 66994101
Getting block 8 of 8
  Reserving size (70560159) 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 20340225
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 20340226
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 106842956
fchr[G]: 187470771
fchr[T]: 267808539
fchr[$]: 376320849
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 684242123 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_2/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 47040112 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_2/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 376320849
    bwtLen: 376320850
    sz: 94080213
    bwtSz: 94080213
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11760027
    offsSz: 47040108
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 840002
    numSides: 1680004
    numLines: 1680004
    ebwtTotLen: 107520256
    ebwtTotSz: 107520256
Total time for call to driver() for forward index: 00:17:56
Reading reference sizes
  Time reading reference sizes: 00:00:09
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:26
bmax according to bmaxDivN setting: 94080212
Using parameters --bmax 70560159 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 70560159 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:28
  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: 00:00:11
  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: 00:00:32
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 6; 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 2; iterating...
  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 1; iterating...
  Binary sorting into buckets
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  100%
  Binary sorting into buckets time: 00:00:33
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.70401e+07 (target: 70560158)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (70560159) 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 29869970
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 29869971
Getting block 2 of 8
  Reserving size (70560159) 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 64180834
  (Using difference cover)
  Sorting block time: 00:01:55
Returning block of 64180835
Getting block 3 of 8
  Reserving size (70560159) 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 42107015
  (Using difference cover)
  Sorting block time: 00:01:16
Returning block of 42107016
Getting block 4 of 8
  Reserving size (70560159) 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 35698412
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 35698413
Getting block 5 of 8
  Reserving size (70560159) 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 38535376
  (Using difference cover)
  Sorting block time: 00:01:12
Returning block of 38535377
Getting block 6 of 8
  Reserving size (70560159) 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 67529406
  (Using difference cover)
  Sorting block time: 00:02:11
Returning block of 67529407
Getting block 7 of 8
  Reserving size (70560159) 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 63640281
  (Using difference cover)
  Sorting block time: 00:01:58
Returning block of 63640282
Getting block 8 of 8
  Reserving size (70560159) 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 34759548
  (Using difference cover)
  Sorting block time: 00:00:45
Returning block of 34759549
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 106842956
fchr[G]: 187470771
fchr[T]: 267808539
fchr[$]: 376320849
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 684242123 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_2/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 47040112 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_2/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 376320849
    bwtLen: 376320850
    sz: 94080213
    bwtSz: 94080213
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11760027
    offsSz: 47040108
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 840002
    numSides: 1680004
    numLines: 1680004
    ebwtTotLen: 107520256
    ebwtTotSz: 107520256
Total time for backward call to driver() for mirror index: 00:18:00