Settings:
  Output files: "/projects/NBL/HS1198/30UBRAAXX_6/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/HS1198/30UBRAAXX_6/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:10
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:27
bmax according to bmaxDivN setting: 40567296
Using parameters --bmax 30425472 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 30425472 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:06
  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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  Binary sorting into buckets time: 00:00:16
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: 00:00:10
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.02836e+07 (target: 30425471)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (30425472) 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 20323691
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 20323692
Getting block 2 of 8
  Reserving size (30425472) 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 29394373
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 29394374
Getting block 3 of 8
  Reserving size (30425472) 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 21889450
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 21889451
Getting block 4 of 8
  Reserving size (30425472) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:21
  Sorting block of length 17903657
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 17903658
Getting block 5 of 8
  Reserving size (30425472) 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 12731142
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 12731143
Getting block 6 of 8
  Reserving size (30425472) 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 27998273
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 27998274
Getting block 7 of 8
  Reserving size (30425472) 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 9580513
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 9580514
Getting block 8 of 8
  Reserving size (30425472) 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 22448078
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 22448079
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 43856634
fchr[G]: 81731753
fchr[T]: 118553395
fchr[$]: 162269184
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 297618772 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_6/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 20283656 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_6/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 162269184
    bwtLen: 162269185
    sz: 40567296
    bwtSz: 40567297
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5070913
    offsSz: 20283652
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 362209
    numSides: 724418
    numLines: 724418
    ebwtTotLen: 46362752
    ebwtTotSz: 46362752
Total time for call to driver() for forward index: 00:06:13
Reading reference sizes
  Time reading reference sizes: 00:00:04
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:10
bmax according to bmaxDivN setting: 40567296
Using parameters --bmax 30425472 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 30425472 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:06
  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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  Binary sorting into buckets time: 00:00:18
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: 00:00:14
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: 00:00:14
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.02836e+07 (target: 30425471)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (30425472) 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 19134184
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 19134185
Getting block 2 of 8
  Reserving size (30425472) 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 11498391
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 11498392
Getting block 3 of 8
  Reserving size (30425472) 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 25584243
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 25584244
Getting block 4 of 8
  Reserving size (30425472) 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 21142759
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 21142760
Getting block 5 of 8
  Reserving size (30425472) 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 19082602
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 19082603
Getting block 6 of 8
  Reserving size (30425472) 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 30390868
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 30390869
Getting block 7 of 8
  Reserving size (30425472) 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 5577138
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 5577139
Getting block 8 of 8
  Reserving size (30425472) 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 29858992
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 29858993
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 43856634
fchr[G]: 81731753
fchr[T]: 118553395
fchr[$]: 162269184
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 297618772 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_6/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 20283656 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_6/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 162269184
    bwtLen: 162269185
    sz: 40567296
    bwtSz: 40567297
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5070913
    offsSz: 20283652
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 362209
    numSides: 724418
    numLines: 724418
    ebwtTotLen: 46362752
    ebwtTotSz: 46362752
Total time for backward call to driver() for mirror index: 00:05:29