Settings:
  Output files: "/projects/NBL/HS1194/302P8AAXX_4/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/HS1194/302P8AAXX_4/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:13
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:08
bmax according to bmaxDivN setting: 35916532
Using parameters --bmax 26937399 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 26937399 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:07
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  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: 00:00:13
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: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.79583e+07 (target: 26937398)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (26937399) 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 17583998
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 17583999
Getting block 2 of 8
  Reserving size (26937399) 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 25035101
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 25035102
Getting block 3 of 8
  Reserving size (26937399) 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 16541381
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 16541382
Getting block 4 of 8
  Reserving size (26937399) 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 11097265
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 11097266
Getting block 5 of 8
  Reserving size (26937399) 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 22696787
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 22696788
Getting block 6 of 8
  Reserving size (26937399) 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 23075631
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 23075632
Getting block 7 of 8
  Reserving size (26937399) 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 21731750
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 21731751
Getting block 8 of 8
  Reserving size (26937399) 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 5904210
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 5904211
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 35265428
fchr[G]: 72558350
fchr[T]: 107845664
fchr[$]: 143666130
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 263893450 bytes to primary EBWT file: /projects/NBL/HS1194/302P8AAXX_4/tophat/tmp/segment_juncs.1.ebwt
Wrote 17958272 bytes to secondary EBWT file: /projects/NBL/HS1194/302P8AAXX_4/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 143666130
    bwtLen: 143666131
    sz: 35916533
    bwtSz: 35916533
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4489567
    offsSz: 17958268
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 320684
    numSides: 641368
    numLines: 641368
    ebwtTotLen: 41047552
    ebwtTotSz: 41047552
Total time for call to driver() for forward index: 00:05:15
Reading reference sizes
  Time reading reference sizes: 00:00:02
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:09
bmax according to bmaxDivN setting: 35916532
Using parameters --bmax 26937399 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 26937399 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:08
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:03
  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: 00:00:11
Splitting and merging
  Splitting and merging time: 00:00:00
Split 3, 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
Split 1, merged 2; 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
Split 1, merged 1; 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: 1.79583e+07 (target: 26937398)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (26937399) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:02
  Sorting block of length 9280167
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 9280168
Getting block 2 of 8
  Reserving size (26937399) 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 25985259
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 25985260
Getting block 3 of 8
  Reserving size (26937399) 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 14670406
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 14670407
Getting block 4 of 8
  Reserving size (26937399) 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 15840037
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 15840038
Getting block 5 of 8
  Reserving size (26937399) 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 12189652
  (Using difference cover)
  Sorting block time: 00:00:16
Returning block of 12189653
Getting block 6 of 8
  Reserving size (26937399) 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 18112765
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 18112766
Getting block 7 of 8
  Reserving size (26937399) 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 21827844
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 21827845
Getting block 8 of 8
  Reserving size (26937399) 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 25759993
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 25759994
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 35265428
fchr[G]: 72558350
fchr[T]: 107845664
fchr[$]: 143666130
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 263893450 bytes to primary EBWT file: /projects/NBL/HS1194/302P8AAXX_4/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 17958272 bytes to secondary EBWT file: /projects/NBL/HS1194/302P8AAXX_4/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 143666130
    bwtLen: 143666131
    sz: 35916533
    bwtSz: 35916533
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4489567
    offsSz: 17958268
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 320684
    numSides: 641368
    numLines: 641368
    ebwtTotLen: 41047552
    ebwtTotSz: 41047552
Total time for backward call to driver() for mirror index: 00:05:03