Settings:
  Output files: "/projects/NBL/HS1196/3153YAAXX_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/HS1196/3153YAAXX_6/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:13
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:09
bmax according to bmaxDivN setting: 36858240
Using parameters --bmax 27643680 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 27643680 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:06
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:02
  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: 00:00:12
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: 00:00:10
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.10619e+07 (target: 27643679)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 23259630
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 23259631
Getting block 2 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 23624059
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 23624060
Getting block 3 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 21791861
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 21791862
Getting block 4 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 24734021
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 24734022
Getting block 5 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 14283068
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 14283069
Getting block 6 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 19635613
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 19635614
Getting block 7 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 20104702
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 20104703
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 37603577
fchr[G]: 74248247
fchr[T]: 110102061
fchr[$]: 147432960
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 270531919 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_6/tophat/tmp/segment_juncs.1.ebwt
Wrote 18429128 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_6/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 147432960
    bwtLen: 147432961
    sz: 36858240
    bwtSz: 36858241
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4607281
    offsSz: 18429124
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 329092
    numSides: 658184
    numLines: 658184
    ebwtTotLen: 42123776
    ebwtTotSz: 42123776
Total time for call to driver() for forward index: 00:04:22
Reading reference sizes
  Time reading reference sizes: 00:00:02
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:09
bmax according to bmaxDivN setting: 36858240
Using parameters --bmax 27643680 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 27643680 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:06
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:02
  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: 00:00:12
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.10619e+07 (target: 27643679)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 22489275
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 22489276
Getting block 2 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 27531440
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 27531441
Getting block 3 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 17895858
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 17895859
Getting block 4 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 21867787
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 21867788
Getting block 5 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 23038106
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 23038107
Getting block 6 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 25232613
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 25232614
Getting block 7 of 7
  Reserving size (27643680) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 9377875
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 9377876
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 37603577
fchr[G]: 74248247
fchr[T]: 110102061
fchr[$]: 147432960
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 270531919 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_6/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 18429128 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_6/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 147432960
    bwtLen: 147432961
    sz: 36858240
    bwtSz: 36858241
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4607281
    offsSz: 18429124
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 329092
    numSides: 658184
    numLines: 658184
    ebwtTotLen: 42123776
    ebwtTotSz: 42123776
Total time for backward call to driver() for mirror index: 00:04:01