Settings:
  Output files: "/projects/NBL/HS1795/700B4AAXX_3/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/HS1795/700B4AAXX_3/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:02:03
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:33
bmax according to bmaxDivN setting: 100547700
Using parameters --bmax 75410775 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 75410775 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:28
  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: 00:00:10
  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: 00:00:47
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.02738e+07 (target: 75410774)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (75410775) 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 64908015
  (Using difference cover)
  Sorting block time: 00:01:23
Returning block of 64908016
Getting block 2 of 8
  Reserving size (75410775) 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 63211749
  (Using difference cover)
  Sorting block time: 00:01:24
Returning block of 63211750
Getting block 3 of 8
  Reserving size (75410775) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:17
  Sorting block of length 59270730
  (Using difference cover)
  Sorting block time: 00:01:27
Returning block of 59270731
Getting block 4 of 8
  Reserving size (75410775) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:19
  Sorting block of length 28654123
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 28654124
Getting block 5 of 8
  Reserving size (75410775) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:18
  Sorting block of length 50207743
  (Using difference cover)
  Sorting block time: 00:01:12
Returning block of 50207744
Getting block 6 of 8
  Reserving size (75410775) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:19
  Sorting block of length 46200287
  (Using difference cover)
  Sorting block time: 00:01:02
Returning block of 46200288
Getting block 7 of 8
  Reserving size (75410775) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:20
  Sorting block of length 67291252
  (Using difference cover)
  Sorting block time: 00:01:31
Returning block of 67291253
Getting block 8 of 8
  Reserving size (75410775) 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 22446894
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 22446895
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 99818168
fchr[G]: 199381873
fchr[T]: 298709814
fchr[$]: 402190800
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 730809496 bytes to primary EBWT file: /projects/NBL/HS1795/700B4AAXX_3/tophat/tmp/segment_juncs.1.ebwt
Wrote 50273856 bytes to secondary EBWT file: /projects/NBL/HS1795/700B4AAXX_3/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 402190800
    bwtLen: 402190801
    sz: 100547700
    bwtSz: 100547701
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12568463
    offsSz: 50273852
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 897748
    numSides: 1795496
    numLines: 1795496
    ebwtTotLen: 114911744
    ebwtTotSz: 114911744
Total time for call to driver() for forward index: 00:18:30
Reading reference sizes
  Time reading reference sizes: 00:00:09
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:33
bmax according to bmaxDivN setting: 100547700
Using parameters --bmax 75410775 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 75410775 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:27
  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: 00:00:12
  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: 00:00:47
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.74558e+07 (target: 75410774)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (75410775) 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 61230654
  (Using difference cover)
  Sorting block time: 00:01:18
Returning block of 61230655
Getting block 2 of 7
  Reserving size (75410775) 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 73990228
  (Using difference cover)
  Sorting block time: 00:01:40
Returning block of 73990229
Getting block 3 of 7
  Reserving size (75410775) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:17
  Sorting block of length 61608420
  (Using difference cover)
  Sorting block time: 00:01:29
Returning block of 61608421
Getting block 4 of 7
  Reserving size (75410775) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:20
  Sorting block of length 67746711
  (Using difference cover)
  Sorting block time: 00:01:36
Returning block of 67746712
Getting block 5 of 7
  Reserving size (75410775) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:19
  Sorting block of length 13372826
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 13372827
Getting block 6 of 7
  Reserving size (75410775) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:21
  Sorting block of length 73354479
  (Using difference cover)
  Sorting block time: 00:01:39
Returning block of 73354480
Getting block 7 of 7
  Reserving size (75410775) 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 50887476
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 50887477
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 99818168
fchr[G]: 199381873
fchr[T]: 298709814
fchr[$]: 402190800
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 730809496 bytes to primary EBWT file: /projects/NBL/HS1795/700B4AAXX_3/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 50273856 bytes to secondary EBWT file: /projects/NBL/HS1795/700B4AAXX_3/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 402190800
    bwtLen: 402190801
    sz: 100547700
    bwtSz: 100547701
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12568463
    offsSz: 50273852
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 897748
    numSides: 1795496
    numLines: 1795496
    ebwtTotLen: 114911744
    ebwtTotSz: 114911744
Total time for backward call to driver() for mirror index: 00:16:19