Settings:
  Output files: "/projects/NBL/HS1196/3153YAAXX_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/HS1196/3153YAAXX_7/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:15
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:10
bmax according to bmaxDivN setting: 41689687
Using parameters --bmax 31267266 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 31267266 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:08
  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: 00:00:03
  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: 00:00:15
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.08448e+07 (target: 31267265)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (31267266) 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 27842012
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 27842013
Getting block 2 of 8
  Reserving size (31267266) 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 16682691
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 16682692
Getting block 3 of 8
  Reserving size (31267266) 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 15342792
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 15342793
Getting block 4 of 8
  Reserving size (31267266) 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 26933450
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 26933451
Getting block 5 of 8
  Reserving size (31267266) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 22805975
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 22805976
Getting block 6 of 8
  Reserving size (31267266) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 18763452
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 18763453
Getting block 7 of 8
  Reserving size (31267266) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 25485407
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 25485408
Getting block 8 of 8
  Reserving size (31267266) 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 12902962
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 12902963
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 42332134
fchr[G]: 83568700
fchr[T]: 124142456
fchr[$]: 166758748
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 305441223 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_7/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 20844848 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_7/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 166758748
    bwtLen: 166758749
    sz: 41689687
    bwtSz: 41689688
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5211211
    offsSz: 20844844
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 372230
    numSides: 744460
    numLines: 744460
    ebwtTotLen: 47645440
    ebwtTotSz: 47645440
Total time for call to driver() for forward index: 00:05:14
Reading reference sizes
  Time reading reference sizes: 00:00:03
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:10
bmax according to bmaxDivN setting: 41689687
Using parameters --bmax 31267266 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 31267266 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:07
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:02
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:03
  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: 00:00:13
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: 00:00:10
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.38227e+07 (target: 31267265)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (31267266) 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 14079340
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 14079341
Getting block 2 of 7
  Reserving size (31267266) 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 28252792
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 28252793
Getting block 3 of 7
  Reserving size (31267266) 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 24237628
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 24237629
Getting block 4 of 7
  Reserving size (31267266) 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 25687757
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 25687758
Getting block 5 of 7
  Reserving size (31267266) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 29613478
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 29613479
Getting block 6 of 7
  Reserving size (31267266) 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 30330557
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 30330558
Getting block 7 of 7
  Reserving size (31267266) 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 14557190
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 14557191
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 42332134
fchr[G]: 83568700
fchr[T]: 124142456
fchr[$]: 166758748
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 305441223 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_7/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 20844848 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_7/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 166758748
    bwtLen: 166758749
    sz: 41689687
    bwtSz: 41689688
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5211211
    offsSz: 20844844
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 372230
    numSides: 744460
    numLines: 744460
    ebwtTotLen: 47645440
    ebwtTotSz: 47645440
Total time for backward call to driver() for mirror index: 00:05:02