Settings:
  Output files: "/projects/NBL/HS1195/30TTYAAXX_5/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/HS1195/30TTYAAXX_5/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:01:28
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:31
bmax according to bmaxDivN setting: 92712398
Using parameters --bmax 69534299 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 69534299 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:29
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:06
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:09
  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: 00:00:44
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: 00:00:40
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.63562e+07 (target: 69534298)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (69534299) 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 33045530
  (Using difference cover)
  Sorting block time: 00:00:45
Returning block of 33045531
Getting block 2 of 8
  Reserving size (69534299) 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 42538693
  (Using difference cover)
  Sorting block time: 00:01:21
Returning block of 42538694
Getting block 3 of 8
  Reserving size (69534299) 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 38175566
  (Using difference cover)
  Sorting block time: 00:01:08
Returning block of 38175567
Getting block 4 of 8
  Reserving size (69534299) 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 57879081
  (Using difference cover)
  Sorting block time: 00:02:06
Returning block of 57879082
Getting block 5 of 8
  Reserving size (69534299) 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 42874260
  (Using difference cover)
  Sorting block time: 00:01:24
Returning block of 42874261
Getting block 6 of 8
  Reserving size (69534299) 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 53045863
  (Using difference cover)
  Sorting block time: 00:01:52
Returning block of 53045864
Getting block 7 of 8
  Reserving size (69534299) 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 52080451
  (Using difference cover)
  Sorting block time: 00:01:42
Returning block of 52080452
Getting block 8 of 8
  Reserving size (69534299) 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 51210142
  (Using difference cover)
  Sorting block time: 00:01:25
Returning block of 51210143
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 104292390
fchr[G]: 185345319
fchr[T]: 264789347
fchr[$]: 370849593
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 674397163 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_5/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 46356204 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_5/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 370849593
    bwtLen: 370849594
    sz: 92712399
    bwtSz: 92712399
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11589050
    offsSz: 46356200
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 827790
    numSides: 1655580
    numLines: 1655580
    ebwtTotLen: 105957120
    ebwtTotSz: 105957120
Total time for call to driver() for forward index: 00:20:15
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: 00:00:30
bmax according to bmaxDivN setting: 92712398
Using parameters --bmax 69534299 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 69534299 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:25
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:04
  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: 00:00:42
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.29785e+07 (target: 69534298)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (69534299) 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 51153975
  (Using difference cover)
  Sorting block time: 00:01:10
Returning block of 51153976
Getting block 2 of 7
  Reserving size (69534299) 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 38615943
  (Using difference cover)
  Sorting block time: 00:01:08
Returning block of 38615944
Getting block 3 of 7
  Reserving size (69534299) 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 54806520
  (Using difference cover)
  Sorting block time: 00:01:40
Returning block of 54806521
Getting block 4 of 7
  Reserving size (69534299) 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 54558348
  (Using difference cover)
  Sorting block time: 00:01:37
Returning block of 54558349
Getting block 5 of 7
  Reserving size (69534299) 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 64052013
  (Using difference cover)
  Sorting block time: 00:02:05
Returning block of 64052014
Getting block 6 of 7
  Reserving size (69534299) 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 68853081
  (Using difference cover)
  Sorting block time: 00:02:10
Returning block of 68853082
Getting block 7 of 7
  Reserving size (69534299) 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 38809707
  (Using difference cover)
  Sorting block time: 00:00:58
Returning block of 38809708
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 104292390
fchr[G]: 185345319
fchr[T]: 264789347
fchr[$]: 370849593
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 674397163 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_5/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 46356204 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_5/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 370849593
    bwtLen: 370849594
    sz: 92712399
    bwtSz: 92712399
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11589050
    offsSz: 46356200
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 827790
    numSides: 1655580
    numLines: 1655580
    ebwtTotLen: 105957120
    ebwtTotSz: 105957120
Total time for backward call to driver() for mirror index: 00:16:44