Settings:
  Output files: "/projects/NBL/HS1795/700B4AAXX_4/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/HS1795/700B4AAXX_4/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:01:42
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:34
bmax according to bmaxDivN setting: 101867497
Using parameters --bmax 76400623 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76400623 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:26
  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: 00:00:48
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: 00:00:38
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.09337e+07 (target: 76400622)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (76400623) 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 11071148
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 11071149
Getting block 2 of 8
  Reserving size (76400623) 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 68770313
  (Using difference cover)
  Sorting block time: 00:01:27
Returning block of 68770314
Getting block 3 of 8
  Reserving size (76400623) 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 60601055
  (Using difference cover)
  Sorting block time: 00:01:16
Returning block of 60601056
Getting block 4 of 8
  Reserving size (76400623) 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 67908694
  (Using difference cover)
  Sorting block time: 00:01:32
Returning block of 67908695
Getting block 5 of 8
  Reserving size (76400623) 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 20179243
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 20179244
Getting block 6 of 8
  Reserving size (76400623) 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 61001844
  (Using difference cover)
  Sorting block time: 00:01:23
Returning block of 61001845
Getting block 7 of 8
  Reserving size (76400623) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:22
  Sorting block of length 72329410
  (Using difference cover)
  Sorting block time: 00:01:33
Returning block of 72329411
Getting block 8 of 8
  Reserving size (76400623) 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 45608274
  (Using difference cover)
  Sorting block time: 00:00:55
Returning block of 45608275
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101145720
fchr[G]: 202144413
fchr[T]: 302720741
fchr[$]: 407469988
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 740597229 bytes to primary EBWT file: /projects/NBL/HS1795/700B4AAXX_4/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 50933756 bytes to secondary EBWT file: /projects/NBL/HS1795/700B4AAXX_4/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 407469988
    bwtLen: 407469989
    sz: 101867497
    bwtSz: 101867498
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12733438
    offsSz: 50933752
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 909532
    numSides: 1819064
    numLines: 1819064
    ebwtTotLen: 116420096
    ebwtTotSz: 116420096
Total time for call to driver() for forward index: 00:17:43
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: 101867497
Using parameters --bmax 76400623 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76400623 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:26
  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: 00:00:11
  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: 00:00:46
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 5; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:45
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.52744e+07 (target: 76400622)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 9
  Reserving size (76400623) 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 41662565
  (Using difference cover)
  Sorting block time: 00:00:50
Returning block of 41662566
Getting block 2 of 9
  Reserving size (76400623) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:15
  Sorting block of length 41027568
  (Using difference cover)
  Sorting block time: 00:00:52
Returning block of 41027569
Getting block 3 of 9
  Reserving size (76400623) 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 57366946
  (Using difference cover)
  Sorting block time: 00:01:14
Returning block of 57366947
Getting block 4 of 9
  Reserving size (76400623) 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 52955238
  (Using difference cover)
  Sorting block time: 00:01:12
Returning block of 52955239
Getting block 5 of 9
  Reserving size (76400623) 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 41105034
  (Using difference cover)
  Sorting block time: 00:00:53
Returning block of 41105035
Getting block 6 of 9
  Reserving size (76400623) 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 52570168
  (Using difference cover)
  Sorting block time: 00:01:10
Returning block of 52570169
Getting block 7 of 9
  Reserving size (76400623) 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 40092377
  (Using difference cover)
  Sorting block time: 00:00:50
Returning block of 40092378
Getting block 8 of 9
  Reserving size (76400623) 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 64826440
  (Using difference cover)
  Sorting block time: 00:01:23
Returning block of 64826441
Getting block 9 of 9
  Reserving size (76400623) 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 15863644
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 15863645
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101145720
fchr[G]: 202144413
fchr[T]: 302720741
fchr[$]: 407469988
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 740597229 bytes to primary EBWT file: /projects/NBL/HS1795/700B4AAXX_4/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 50933756 bytes to secondary EBWT file: /projects/NBL/HS1795/700B4AAXX_4/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 407469988
    bwtLen: 407469989
    sz: 101867497
    bwtSz: 101867498
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12733438
    offsSz: 50933752
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 909532
    numSides: 1819064
    numLines: 1819064
    ebwtTotLen: 116420096
    ebwtTotSz: 116420096
Total time for backward call to driver() for mirror index: 00:16:32