Settings:
  Output files: "/projects/NBL/HS1799/61074AAXX_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/HS1799/61074AAXX_3/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:02:30
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:27
bmax according to bmaxDivN setting: 100243863
Using parameters --bmax 75182898 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 75182898 --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: 00:00:43
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: 00:00:35
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.72822e+07 (target: 75182897)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (75182898) 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 52745148
  (Using difference cover)
  Sorting block time: 00:01:03
Returning block of 52745149
Getting block 2 of 7
  Reserving size (75182898) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:36
  Sorting block of length 73423287
  (Using difference cover)
  Sorting block time: 00:01:35
Returning block of 73423288
Getting block 3 of 7
  Reserving size (75182898) 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 58094777
  (Using difference cover)
  Sorting block time: 00:01:20
Returning block of 58094778
Getting block 4 of 7
  Reserving size (75182898) 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 57686481
  (Using difference cover)
  Sorting block time: 00:01:15
Returning block of 57686482
Getting block 5 of 7
  Reserving size (75182898) 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 62145804
  (Using difference cover)
  Sorting block time: 00:01:22
Returning block of 62145805
Getting block 6 of 7
  Reserving size (75182898) 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 50361681
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 50361682
Getting block 7 of 7
  Reserving size (75182898) 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 46518270
  (Using difference cover)
  Sorting block time: 00:00:58
Returning block of 46518271
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 99278481
fchr[G]: 199085326
fchr[T]: 298328690
fchr[$]: 400975454
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 728732542 bytes to primary EBWT file: /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/segment_juncs.1.ebwt
Wrote 50121936 bytes to secondary EBWT file: /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 400975454
    bwtLen: 400975455
    sz: 100243864
    bwtSz: 100243864
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12530483
    offsSz: 50121932
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 895035
    numSides: 1790070
    numLines: 1790070
    ebwtTotLen: 114564480
    ebwtTotSz: 114564480
Total time for call to driver() for forward index: 00:18:27
Reading reference sizes
  Time reading reference sizes: 00:00:08
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:27
bmax according to bmaxDivN setting: 100243863
Using parameters --bmax 75182898 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 75182898 --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: 00:00:12
  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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  Binary sorting into buckets time: 00:00:33
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
  Binary sorting into buckets
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  100%
  Binary sorting into buckets time: 00:00:32
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:33
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:37
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:34
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.72822e+07 (target: 75182897)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (75182898) 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 66022089
  (Using difference cover)
  Sorting block time: 00:01:22
Returning block of 66022090
Getting block 2 of 7
  Reserving size (75182898) 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 55340663
  (Using difference cover)
  Sorting block time: 00:01:09
Returning block of 55340664
Getting block 3 of 7
  Reserving size (75182898) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:14
  Sorting block of length 62370044
  (Using difference cover)
  Sorting block time: 00:01:25
Returning block of 62370045
Getting block 4 of 7
  Reserving size (75182898) 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 42051848
  (Using difference cover)
  Sorting block time: 00:00:53
Returning block of 42051849
Getting block 5 of 7
  Reserving size (75182898) 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 74557840
  (Using difference cover)
  Sorting block time: 00:01:39
Returning block of 74557841
Getting block 6 of 7
  Reserving size (75182898) 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 69508355
  (Using difference cover)
  Sorting block time: 00:01:30
Returning block of 69508356
Getting block 7 of 7
  Reserving size (75182898) 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 31124609
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 31124610
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 99278481
fchr[G]: 199085326
fchr[T]: 298328690
fchr[$]: 400975454
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 728732542 bytes to primary EBWT file: /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 50121936 bytes to secondary EBWT file: /projects/NBL/HS1799/61074AAXX_3/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 400975454
    bwtLen: 400975455
    sz: 100243864
    bwtSz: 100243864
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12530483
    offsSz: 50121932
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 895035
    numSides: 1790070
    numLines: 1790070
    ebwtTotLen: 114564480
    ebwtTotSz: 114564480
Total time for backward call to driver() for mirror index: 00:17:16