Settings:
  Output files: "/projects/NBL/HS1797/616GYAAXX_1/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/HS1797/616GYAAXX_1/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:01:02
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:28
bmax according to bmaxDivN setting: 103483754
Using parameters --bmax 77612816 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 77612816 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:26
  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: 00:00:37
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: 00:00:29
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.91336e+07 (target: 77612815)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (77612816) 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 53586280
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 53586281
Getting block 2 of 7
  Reserving size (77612816) 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 74030311
  (Using difference cover)
  Sorting block time: 00:01:34
Returning block of 74030312
Getting block 3 of 7
  Reserving size (77612816) 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 74782781
  (Using difference cover)
  Sorting block time: 00:01:40
Returning block of 74782782
Getting block 4 of 7
  Reserving size (77612816) 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 56946022
  (Using difference cover)
  Sorting block time: 00:01:14
Returning block of 56946023
Getting block 5 of 7
  Reserving size (77612816) 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 25123512
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 25123513
Getting block 6 of 7
  Reserving size (77612816) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:18
  Sorting block of length 53289340
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 53289341
Getting block 7 of 7
  Reserving size (77612816) 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 76176764
  (Using difference cover)
  Sorting block time: 00:01:36
Returning block of 76176765
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 102310247
fchr[G]: 204991306
fchr[T]: 307437552
fchr[$]: 413935016
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 752371808 bytes to primary EBWT file: /projects/NBL/HS1797/616GYAAXX_1/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 51741884 bytes to secondary EBWT file: /projects/NBL/HS1797/616GYAAXX_1/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 413935016
    bwtLen: 413935017
    sz: 103483754
    bwtSz: 103483755
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12935470
    offsSz: 51741880
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 923963
    numSides: 1847926
    numLines: 1847926
    ebwtTotLen: 118267264
    ebwtTotSz: 118267264
Total time for call to driver() for forward index: 00:15:39
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: 00:00:28
bmax according to bmaxDivN setting: 103483754
Using parameters --bmax 77612816 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 77612816 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:27
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:06
  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: 00:00:34
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
  Binary sorting into buckets
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  100%
  Binary sorting into buckets time: 00:00:28
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.17419e+07 (target: 77612815)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (77612816) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:10
  Sorting block of length 12869261
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 12869262
Getting block 2 of 8
  Reserving size (77612816) 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 75775899
  (Using difference cover)
  Sorting block time: 00:01:36
Returning block of 75775900
Getting block 3 of 8
  Reserving size (77612816) 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 74051174
  (Using difference cover)
  Sorting block time: 00:01:39
Returning block of 74051175
Getting block 4 of 8
  Reserving size (77612816) 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 68625818
  (Using difference cover)
  Sorting block time: 00:01:32
Returning block of 68625819
Getting block 5 of 8
  Reserving size (77612816) 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 42681287
  (Using difference cover)
  Sorting block time: 00:00:59
Returning block of 42681288
Getting block 6 of 8
  Reserving size (77612816) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:18
  Sorting block of length 51236201
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 51236202
Getting block 7 of 8
  Reserving size (77612816) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:18
  Sorting block of length 54160853
  (Using difference cover)
  Sorting block time: 00:01:11
Returning block of 54160854
Getting block 8 of 8
  Reserving size (77612816) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:10
  Sorting block of length 34534516
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 34534517
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 102310247
fchr[G]: 204991306
fchr[T]: 307437552
fchr[$]: 413935016
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 752371808 bytes to primary EBWT file: /projects/NBL/HS1797/616GYAAXX_1/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 51741884 bytes to secondary EBWT file: /projects/NBL/HS1797/616GYAAXX_1/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 413935016
    bwtLen: 413935017
    sz: 103483754
    bwtSz: 103483755
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12935470
    offsSz: 51741880
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 923963
    numSides: 1847926
    numLines: 1847926
    ebwtTotLen: 118267264
    ebwtTotSz: 118267264
Total time for backward call to driver() for mirror index: 00:15:03