Settings:
  Output files: "/projects/NBL/HS1197/302NNAAXX_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/HS1197/302NNAAXX_7/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:32
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:18
bmax according to bmaxDivN setting: 70915397
Using parameters --bmax 53186548 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 53186548 --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: 00:00:08
  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: 00:00:26
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: 00:00:21
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.05231e+07 (target: 53186547)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (53186548) 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 52663043
  (Using difference cover)
  Sorting block time: 00:01:22
Returning block of 52663044
Getting block 2 of 7
  Reserving size (53186548) 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 22237338
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 22237339
Getting block 3 of 7
  Reserving size (53186548) 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 52230180
  (Using difference cover)
  Sorting block time: 00:01:34
Returning block of 52230181
Getting block 4 of 7
  Reserving size (53186548) 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 38028368
  (Using difference cover)
  Sorting block time: 00:01:06
Returning block of 38028369
Getting block 5 of 7
  Reserving size (53186548) 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 32152860
  (Using difference cover)
  Sorting block time: 00:00:57
Returning block of 32152861
Getting block 6 of 7
  Reserving size (53186548) 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 51569393
  (Using difference cover)
  Sorting block time: 00:01:34
Returning block of 51569394
Getting block 7 of 7
  Reserving size (53186548) 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 34780403
  (Using difference cover)
  Sorting block time: 00:00:54
Returning block of 34780404
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 76493030
fchr[G]: 141695708
fchr[T]: 206995613
fchr[$]: 283661591
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 517474549 bytes to primary EBWT file: /projects/NBL/HS1197/302NNAAXX_7/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 35457704 bytes to secondary EBWT file: /projects/NBL/HS1197/302NNAAXX_7/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 283661591
    bwtLen: 283661592
    sz: 70915398
    bwtSz: 70915398
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 8864425
    offsSz: 35457700
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 633174
    numSides: 1266348
    numLines: 1266348
    ebwtTotLen: 81046272
    ebwtTotSz: 81046272
Total time for call to driver() for forward index: 00:12:39
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: 00:00:18
bmax according to bmaxDivN setting: 70915397
Using parameters --bmax 53186548 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 53186548 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:21
  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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  100%
  Binary sorting into buckets time: 00:00:26
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 6; iterating...
  Binary sorting into buckets
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  30%
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  50%
  60%
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  100%
  Binary sorting into buckets time: 00:00:26
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.05231e+07 (target: 53186547)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (53186548) 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 41334995
  (Using difference cover)
  Sorting block time: 00:01:03
Returning block of 41334996
Getting block 2 of 7
  Reserving size (53186548) 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 40899807
  (Using difference cover)
  Sorting block time: 00:01:11
Returning block of 40899808
Getting block 3 of 7
  Reserving size (53186548) 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 44928634
  (Using difference cover)
  Sorting block time: 00:01:21
Returning block of 44928635
Getting block 4 of 7
  Reserving size (53186548) 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 49287037
  (Using difference cover)
  Sorting block time: 00:01:30
Returning block of 49287038
Getting block 5 of 7
  Reserving size (53186548) 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 36959818
  (Using difference cover)
  Sorting block time: 00:01:05
Returning block of 36959819
Getting block 6 of 7
  Reserving size (53186548) 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 50622341
  (Using difference cover)
  Sorting block time: 00:01:32
Returning block of 50622342
Getting block 7 of 7
  Reserving size (53186548) 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 19628953
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 19628954
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 76493030
fchr[G]: 141695708
fchr[T]: 206995613
fchr[$]: 283661591
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 517474549 bytes to primary EBWT file: /projects/NBL/HS1197/302NNAAXX_7/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 35457704 bytes to secondary EBWT file: /projects/NBL/HS1197/302NNAAXX_7/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 283661591
    bwtLen: 283661592
    sz: 70915398
    bwtSz: 70915398
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 8864425
    offsSz: 35457700
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 633174
    numSides: 1266348
    numLines: 1266348
    ebwtTotLen: 81046272
    ebwtTotSz: 81046272
Total time for backward call to driver() for mirror index: 00:12:27