Settings:
  Output files: "/projects/NBL/HS1195/30TTYAAXX_7/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/HS1195/30TTYAAXX_7/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:30
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:20
bmax according to bmaxDivN setting: 87192918
Using parameters --bmax 65394689 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 65394689 --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: 00:00:26
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: 00:00:20
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.98245e+07 (target: 65394688)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (65394689) 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 59385769
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 59385770
Getting block 2 of 7
  Reserving size (65394689) 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 63039459
  (Using difference cover)
  Sorting block time: 00:01:17
Returning block of 63039460
Getting block 3 of 7
  Reserving size (65394689) 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 65249239
  (Using difference cover)
  Sorting block time: 00:01:26
Returning block of 65249240
Getting block 4 of 7
  Reserving size (65394689) 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 42843666
  (Using difference cover)
  Sorting block time: 00:00:55
Returning block of 42843667
Getting block 5 of 7
  Reserving size (65394689) 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 39907973
  (Using difference cover)
  Sorting block time: 00:00:50
Returning block of 39907974
Getting block 6 of 7
  Reserving size (65394689) 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 42762517
  (Using difference cover)
  Sorting block time: 00:00:56
Returning block of 42762518
Getting block 7 of 7
  Reserving size (65394689) 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 35583043
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 35583044
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 99376678
fchr[G]: 174131689
fchr[T]: 247508140
fchr[$]: 348771672
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 634639263 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_7/tophat/tmp/segment_juncs.1.ebwt
Wrote 43596464 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_7/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 348771672
    bwtLen: 348771673
    sz: 87192918
    bwtSz: 87192919
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 10899115
    offsSz: 43596460
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 778509
    numSides: 1557018
    numLines: 1557018
    ebwtTotLen: 99649152
    ebwtTotSz: 99649152
Total time for call to driver() for forward index: 00:11:20
Reading reference sizes
  Time reading reference sizes: 00:00:05
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:20
bmax according to bmaxDivN setting: 87192918
Using parameters --bmax 65394689 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 65394689 --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: 00:00:04
  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: 00:00:28
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.35965e+07 (target: 65394688)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (65394689) 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 55521897
  (Using difference cover)
  Sorting block time: 00:00:58
Returning block of 55521898
Getting block 2 of 8
  Reserving size (65394689) 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 22879181
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 22879182
Getting block 3 of 8
  Reserving size (65394689) 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 53626339
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 53626340
Getting block 4 of 8
  Reserving size (65394689) 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 46188254
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 46188255
Getting block 5 of 8
  Reserving size (65394689) 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 51911594
  (Using difference cover)
  Sorting block time: 00:01:09
Returning block of 51911595
Getting block 6 of 8
  Reserving size (65394689) 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 30795712
  (Using difference cover)
  Sorting block time: 00:00:40
Returning block of 30795713
Getting block 7 of 8
  Reserving size (65394689) 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 62877296
  (Using difference cover)
  Sorting block time: 00:01:20
Returning block of 62877297
Getting block 8 of 8
  Reserving size (65394689) 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 24971392
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 24971393
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 99376678
fchr[G]: 174131689
fchr[T]: 247508140
fchr[$]: 348771672
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 634639263 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_7/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 43596464 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_7/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 348771672
    bwtLen: 348771673
    sz: 87192918
    bwtSz: 87192919
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 10899115
    offsSz: 43596460
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 778509
    numSides: 1557018
    numLines: 1557018
    ebwtTotLen: 99649152
    ebwtTotSz: 99649152
Total time for backward call to driver() for mirror index: 00:10:59