Settings:
  Output files: "/projects/NBL/HS1803/616GYAAXX_4/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/HS1803/616GYAAXX_4/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:49
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:25
bmax according to bmaxDivN setting: 102941124
Using parameters --bmax 77205843 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 77205843 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:20
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:04
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:09
  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 7; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:26
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.88235e+07 (target: 77205842)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (77205843) 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 76203184
  (Using difference cover)
  Sorting block time: 00:01:11
Returning block of 76203185
Getting block 2 of 7
  Reserving size (77205843) 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 65380764
  (Using difference cover)
  Sorting block time: 00:01:02
Returning block of 65380765
Getting block 3 of 7
  Reserving size (77205843) 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 75614804
  (Using difference cover)
  Sorting block time: 00:01:18
Returning block of 75614805
Getting block 4 of 7
  Reserving size (77205843) 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 47520460
  (Using difference cover)
  Sorting block time: 00:00:49
Returning block of 47520461
Getting block 5 of 7
  Reserving size (77205843) 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 69433392
  (Using difference cover)
  Sorting block time: 00:01:13
Returning block of 69433393
Getting block 6 of 7
  Reserving size (77205843) 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 16679150
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 16679151
Getting block 7 of 7
  Reserving size (77205843) 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 60932736
  (Using difference cover)
  Sorting block time: 00:00:58
Returning block of 60932737
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 104718969
fchr[G]: 204602628
fchr[T]: 303661769
fchr[$]: 411764496
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 748206660 bytes to primary EBWT file: /projects/NBL/HS1803/616GYAAXX_4/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 51470568 bytes to secondary EBWT file: /projects/NBL/HS1803/616GYAAXX_4/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 411764496
    bwtLen: 411764497
    sz: 102941124
    bwtSz: 102941125
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12867641
    offsSz: 51470564
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 919118
    numSides: 1838236
    numLines: 1838236
    ebwtTotLen: 117647104
    ebwtTotSz: 117647104
Total time for call to driver() for forward index: 00:12:19
Reading reference sizes
  Time reading reference sizes: 00:00:06
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:25
bmax according to bmaxDivN setting: 102941124
Using parameters --bmax 77205843 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 77205843 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:19
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:04
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:08
  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: 00:00:35
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: 00:00:27
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.14706e+07 (target: 77205842)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (77205843) 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 44332509
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 44332510
Getting block 2 of 8
  Reserving size (77205843) 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 68864533
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 68864534
Getting block 3 of 8
  Reserving size (77205843) 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 35185071
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 35185072
Getting block 4 of 8
  Reserving size (77205843) 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 56387493
  (Using difference cover)
  Sorting block time: 00:00:55
Returning block of 56387494
Getting block 5 of 8
  Reserving size (77205843) 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 75285123
  (Using difference cover)
  Sorting block time: 00:01:16
Returning block of 75285124
Getting block 6 of 8
  Reserving size (77205843) 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 53388632
  (Using difference cover)
  Sorting block time: 00:00:49
Returning block of 53388633
Getting block 7 of 8
  Reserving size (77205843) 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 62357372
  (Using difference cover)
  Sorting block time: 00:00:59
Returning block of 62357373
Getting block 8 of 8
  Reserving size (77205843) 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 15963756
  (Using difference cover)
  Sorting block time: 00:00:13
Returning block of 15963757
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 104718969
fchr[G]: 204602628
fchr[T]: 303661769
fchr[$]: 411764496
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 748206660 bytes to primary EBWT file: /projects/NBL/HS1803/616GYAAXX_4/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 51470568 bytes to secondary EBWT file: /projects/NBL/HS1803/616GYAAXX_4/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 411764496
    bwtLen: 411764497
    sz: 102941124
    bwtSz: 102941125
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12867641
    offsSz: 51470564
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 919118
    numSides: 1838236
    numLines: 1838236
    ebwtTotLen: 117647104
    ebwtTotSz: 117647104
Total time for backward call to driver() for mirror index: 00:11:24