Settings:
  Output files: "/projects/NBL/HS1803/616GYAAXX_6/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/HS1803/616GYAAXX_6/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:01:49
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: 102758159
Using parameters --bmax 77068620 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 77068620 --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: 00:00:32
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: 00:00:23
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: 00:00:24
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: 00:00:25
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.87189e+07 (target: 77068619)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (77068620) 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 68200201
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 68200202
Getting block 2 of 7
  Reserving size (77068620) 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 76975837
  (Using difference cover)
  Sorting block time: 00:01:12
Returning block of 76975838
Getting block 3 of 7
  Reserving size (77068620) 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 9217754
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 9217755
Getting block 4 of 7
  Reserving size (77068620) 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 74990910
  (Using difference cover)
  Sorting block time: 00:01:14
Returning block of 74990911
Getting block 5 of 7
  Reserving size (77068620) 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 64029505
  (Using difference cover)
  Sorting block time: 00:01:06
Returning block of 64029506
Getting block 6 of 7
  Reserving size (77068620) 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 66932067
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 66932068
Getting block 7 of 7
  Reserving size (77068620) 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 50686359
  (Using difference cover)
  Sorting block time: 00:00:46
Returning block of 50686360
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 105671678
fchr[G]: 204098171
fchr[T]: 301835897
fchr[$]: 411032639
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 746216569 bytes to primary EBWT file: /projects/NBL/HS1803/616GYAAXX_6/tophat/tmp/segment_juncs.1.ebwt
Wrote 51379084 bytes to secondary EBWT file: /projects/NBL/HS1803/616GYAAXX_6/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 411032639
    bwtLen: 411032640
    sz: 102758160
    bwtSz: 102758160
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12844770
    offsSz: 51379080
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 917484
    numSides: 1834968
    numLines: 1834968
    ebwtTotLen: 117437952
    ebwtTotSz: 117437952
Total time for call to driver() for forward index: 00:14:21
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: 102758159
Using parameters --bmax 77068620 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 77068620 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:18
  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: 00:00:08
  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: 00:00:32
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 5; 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: 5.13791e+07 (target: 77068619)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (77068620) 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 48579045
  (Using difference cover)
  Sorting block time: 00:00:45
Returning block of 48579046
Getting block 2 of 8
  Reserving size (77068620) 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 41358181
  (Using difference cover)
  Sorting block time: 00:00:40
Returning block of 41358182
Getting block 3 of 8
  Reserving size (77068620) 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 72829637
  (Using difference cover)
  Sorting block time: 00:01:12
Returning block of 72829638
Getting block 4 of 8
  Reserving size (77068620) 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 30576942
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 30576943
Getting block 5 of 8
  Reserving size (77068620) 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 69691728
  (Using difference cover)
  Sorting block time: 00:01:14
Returning block of 69691729
Getting block 6 of 8
  Reserving size (77068620) 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 69190175
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 69190176
Getting block 7 of 8
  Reserving size (77068620) 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 22090943
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 22090944
Getting block 8 of 8
  Reserving size (77068620) 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 56715981
  (Using difference cover)
  Sorting block time: 00:00:52
Returning block of 56715982
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 105671678
fchr[G]: 204098171
fchr[T]: 301835897
fchr[$]: 411032639
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 746216569 bytes to primary EBWT file: /projects/NBL/HS1803/616GYAAXX_6/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 51379084 bytes to secondary EBWT file: /projects/NBL/HS1803/616GYAAXX_6/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 411032639
    bwtLen: 411032640
    sz: 102758160
    bwtSz: 102758160
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12844770
    offsSz: 51379080
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 917484
    numSides: 1834968
    numLines: 1834968
    ebwtTotLen: 117437952
    ebwtTotSz: 117437952
Total time for backward call to driver() for mirror index: 00:12:21