Settings:
  Output files: "/projects/NBL/HS1194/311L9AAXX_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/HS1194/311L9AAXX_3/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:25
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:09
bmax according to bmaxDivN setting: 37599790
Using parameters --bmax 28199843 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 28199843 --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: 00:00:12
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.87999e+07 (target: 28199842)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (28199843) 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 12800767
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 12800768
Getting block 2 of 8
  Reserving size (28199843) 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 24511271
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 24511272
Getting block 3 of 8
  Reserving size (28199843) 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 26393097
  (Using difference cover)
  Sorting block time: 00:00:40
Returning block of 26393098
Getting block 4 of 8
  Reserving size (28199843) 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 10120168
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 10120169
Getting block 5 of 8
  Reserving size (28199843) 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 22866764
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 22866765
Getting block 6 of 8
  Reserving size (28199843) 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 22263130
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 22263131
Getting block 7 of 8
  Reserving size (28199843) 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 18645480
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 18645481
Getting block 8 of 8
  Reserving size (28199843) 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 12798478
  (Using difference cover)
  Sorting block time: 00:00:13
Returning block of 12798479
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 39081950
fchr[G]: 76314826
fchr[T]: 111159037
fchr[$]: 150399162
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 275947622 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_3/tophat/tmp/segment_juncs.1.ebwt
Wrote 18799900 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_3/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 150399162
    bwtLen: 150399163
    sz: 37599791
    bwtSz: 37599791
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4699974
    offsSz: 18799896
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 335713
    numSides: 671426
    numLines: 671426
    ebwtTotLen: 42971264
    ebwtTotSz: 42971264
Total time for call to driver() for forward index: 00:05:43
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: 00:00:08
bmax according to bmaxDivN setting: 37599790
Using parameters --bmax 28199843 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 28199843 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:06
  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: 00:00:02
  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: 00:00:12
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: 00:00:09
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: 00:00:09
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: 00:00:09
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: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.14856e+07 (target: 28199842)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (28199843) 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 27054589
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 27054590
Getting block 2 of 7
  Reserving size (28199843) 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 27337728
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 27337729
Getting block 3 of 7
  Reserving size (28199843) 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 12447337
  (Using difference cover)
  Sorting block time: 00:00:16
Returning block of 12447338
Getting block 4 of 7
  Reserving size (28199843) 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 23059756
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 23059757
Getting block 5 of 7
  Reserving size (28199843) 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 25323678
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 25323679
Getting block 6 of 7
  Reserving size (28199843) 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 25209719
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 25209720
Getting block 7 of 7
  Reserving size (28199843) 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 9966349
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 9966350
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 39081950
fchr[G]: 76314826
fchr[T]: 111159037
fchr[$]: 150399162
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 275947622 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_3/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 18799900 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_3/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 150399162
    bwtLen: 150399163
    sz: 37599791
    bwtSz: 37599791
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4699974
    offsSz: 18799896
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 335713
    numSides: 671426
    numLines: 671426
    ebwtTotLen: 42971264
    ebwtTotSz: 42971264
Total time for backward call to driver() for mirror index: 00:05:22