Settings:
  Output files: "/projects/NBL/HS1797/616GYAAXX_3/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_3/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:17
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: 103379981
Using parameters --bmax 77534986 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 77534986 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:17
  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: 00:00:07
  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: 00:00:33
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: 00:00:25
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; 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: 5.90743e+07 (target: 77534985)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (77534986) 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 63316810
  (Using difference cover)
  Sorting block time: 00:00:52
Returning block of 63316811
Getting block 2 of 7
  Reserving size (77534986) 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 51175797
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 51175798
Getting block 3 of 7
  Reserving size (77534986) 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 48710648
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 48710649
Getting block 4 of 7
  Reserving size (77534986) 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 49207040
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 49207041
Getting block 5 of 7
  Reserving size (77534986) 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 72274011
  (Using difference cover)
  Sorting block time: 00:01:05
Returning block of 72274012
Getting block 6 of 7
  Reserving size (77534986) 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 52506538
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 52506539
Getting block 7 of 7
  Reserving size (77534986) 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 76329076
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 76329077
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 102140668
fchr[G]: 204963943
fchr[T]: 307463375
fchr[$]: 413519926
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 751703348 bytes to primary EBWT file: /projects/NBL/HS1797/616GYAAXX_3/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 51689996 bytes to secondary EBWT file: /projects/NBL/HS1797/616GYAAXX_3/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 413519926
    bwtLen: 413519927
    sz: 103379982
    bwtSz: 103379982
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12922498
    offsSz: 51689992
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 923036
    numSides: 1846072
    numLines: 1846072
    ebwtTotLen: 118148608
    ebwtTotSz: 118148608
Total time for call to driver() for forward index: 00:10:49
Reading reference sizes
  Time reading reference sizes: 00:00:07
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:24
bmax according to bmaxDivN setting: 103379981
Using parameters --bmax 77534986 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 77534986 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:17
  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: 00:00:07
  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: 00:00:31
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: 00:00:27
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: 00:00:26
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: 00:00:26
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:28
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.169e+07 (target: 77534985)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (77534986) 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 62438405
  (Using difference cover)
  Sorting block time: 00:00:50
Returning block of 62438406
Getting block 2 of 8
  Reserving size (77534986) 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 24691376
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 24691377
Getting block 3 of 8
  Reserving size (77534986) 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 58425591
  (Using difference cover)
  Sorting block time: 00:00:49
Returning block of 58425592
Getting block 4 of 8
  Reserving size (77534986) 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 70762569
  (Using difference cover)
  Sorting block time: 00:01:02
Returning block of 70762570
Getting block 5 of 8
  Reserving size (77534986) 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 21391817
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 21391818
Getting block 6 of 8
  Reserving size (77534986) 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 77203662
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 77203663
Getting block 7 of 8
  Reserving size (77534986) 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 58298363
  (Using difference cover)
  Sorting block time: 00:00:50
Returning block of 58298364
Getting block 8 of 8
  Reserving size (77534986) 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 40308136
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 40308137
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 102140668
fchr[G]: 204963943
fchr[T]: 307463375
fchr[$]: 413519926
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 751703348 bytes to primary EBWT file: /projects/NBL/HS1797/616GYAAXX_3/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 51689996 bytes to secondary EBWT file: /projects/NBL/HS1797/616GYAAXX_3/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 413519926
    bwtLen: 413519927
    sz: 103379982
    bwtSz: 103379982
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12922498
    offsSz: 51689992
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 923036
    numSides: 1846072
    numLines: 1846072
    ebwtTotLen: 118148608
    ebwtTotSz: 118148608
Total time for backward call to driver() for mirror index: 00:11:38