Settings:
  Output files: "/projects/NBL/HS1197/311NGAAXX_7/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/HS1197/311NGAAXX_7/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:19
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:14
bmax according to bmaxDivN setting: 57757021
Using parameters --bmax 43317766 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 43317766 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:10
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:03
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:04
  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: 00:00:19
Splitting and merging
  Splitting and merging time: 00:00:00
Split 3, merged 5; iterating...
  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 1, merged 3; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:15
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.88785e+07 (target: 43317765)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (43317766) 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 9091348
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 9091349
Getting block 2 of 8
  Reserving size (43317766) 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 43198572
  (Using difference cover)
  Sorting block time: 00:00:53
Returning block of 43198573
Getting block 3 of 8
  Reserving size (43317766) 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 41997400
  (Using difference cover)
  Sorting block time: 00:00:55
Returning block of 41997401
Getting block 4 of 8
  Reserving size (43317766) 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 33758698
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 33758699
Getting block 5 of 8
  Reserving size (43317766) 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 39804124
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 39804125
Getting block 6 of 8
  Reserving size (43317766) 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 4081194
  (Using difference cover)
  Sorting block time: 00:00:05
Returning block of 4081195
Getting block 7 of 8
  Reserving size (43317766) 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 41514124
  (Using difference cover)
  Sorting block time: 00:00:52
Returning block of 41514125
Getting block 8 of 8
  Reserving size (43317766) 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 17582620
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 17582621
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 60813055
fchr[G]: 116013815
fchr[T]: 170198885
fchr[$]: 231028087
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 422364011 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_7/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 28878516 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_7/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 231028087
    bwtLen: 231028088
    sz: 57757022
    bwtSz: 57757022
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 7219628
    offsSz: 28878512
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 515688
    numSides: 1031376
    numLines: 1031376
    ebwtTotLen: 66008064
    ebwtTotSz: 66008064
Total time for call to driver() for forward index: 00:07:52
Reading reference sizes
  Time reading reference sizes: 00:00:03
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:13
bmax according to bmaxDivN setting: 57757021
Using parameters --bmax 43317766 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 43317766 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:11
  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: 00:00:04
  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
Avg bucket size: 3.3004e+07 (target: 43317765)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (43317766) 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 43258464
  (Using difference cover)
  Sorting block time: 00:00:49
Returning block of 43258465
Getting block 2 of 7
  Reserving size (43317766) 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 24331225
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 24331226
Getting block 3 of 7
  Reserving size (43317766) 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 33221537
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 33221538
Getting block 4 of 7
  Reserving size (43317766) 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 33966305
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 33966306
Getting block 5 of 7
  Reserving size (43317766) 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 16848412
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 16848413
Getting block 6 of 7
  Reserving size (43317766) 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 39964207
  (Using difference cover)
  Sorting block time: 00:00:49
Returning block of 39964208
Getting block 7 of 7
  Reserving size (43317766) 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 39437931
  (Using difference cover)
  Sorting block time: 00:00:45
Returning block of 39437932
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 60813055
fchr[G]: 116013815
fchr[T]: 170198885
fchr[$]: 231028087
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 422364011 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_7/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 28878516 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_7/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 231028087
    bwtLen: 231028088
    sz: 57757022
    bwtSz: 57757022
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 7219628
    offsSz: 28878512
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 515688
    numSides: 1031376
    numLines: 1031376
    ebwtTotLen: 66008064
    ebwtTotSz: 66008064
Total time for backward call to driver() for mirror index: 00:06:58