Settings:
  Output files: "/projects/NBL/HS1194/311L9AAXX_6/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/HS1194/311L9AAXX_6/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:13
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: 40204963
Using parameters --bmax 30153723 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 30153723 --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: 00:00:14
Splitting and merging
  Splitting and merging time: 00:00:00
Split 3, merged 7; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:10
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 2; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:11
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.01025e+07 (target: 30153722)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (30153723) 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 16847955
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 16847956
Getting block 2 of 8
  Reserving size (30153723) 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 18886437
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 18886438
Getting block 3 of 8
  Reserving size (30153723) 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 22750917
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 22750918
Getting block 4 of 8
  Reserving size (30153723) 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 26679387
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 26679388
Getting block 5 of 8
  Reserving size (30153723) 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 19383958
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 19383959
Getting block 6 of 8
  Reserving size (30153723) 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 21101244
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 21101245
Getting block 7 of 8
  Reserving size (30153723) 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 10672010
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 10672011
Getting block 8 of 8
  Reserving size (30153723) 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 24497940
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 24497941
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 41748700
fchr[G]: 81846994
fchr[T]: 119351908
fchr[$]: 160819855
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 295089244 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_6/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 20102488 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_6/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 160819855
    bwtLen: 160819856
    sz: 40204964
    bwtSz: 40204964
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5025621
    offsSz: 20102484
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 358973
    numSides: 717946
    numLines: 717946
    ebwtTotLen: 45948544
    ebwtTotSz: 45948544
Total time for call to driver() for forward index: 00:05:23
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: 00:00:10
bmax according to bmaxDivN setting: 40204963
Using parameters --bmax 30153723 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 30153723 --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: 00:00:01
  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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  100%
  Binary sorting into buckets time: 00:00:13
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.01025e+07 (target: 30153722)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (30153723) 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 26995985
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 26995986
Getting block 2 of 8
  Reserving size (30153723) 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 23449291
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 23449292
Getting block 3 of 8
  Reserving size (30153723) 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 17940117
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 17940118
Getting block 4 of 8
  Reserving size (30153723) 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 13087092
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 13087093
Getting block 5 of 8
  Reserving size (30153723) 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 26900964
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 26900965
Getting block 6 of 8
  Reserving size (30153723) 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 16288776
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 16288777
Getting block 7 of 8
  Reserving size (30153723) 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 27485712
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 27485713
Getting block 8 of 8
  Reserving size (30153723) 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 8671911
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 8671912
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 41748700
fchr[G]: 81846994
fchr[T]: 119351908
fchr[$]: 160819855
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 295089244 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_6/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 20102488 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_6/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 160819855
    bwtLen: 160819856
    sz: 40204964
    bwtSz: 40204964
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5025621
    offsSz: 20102484
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 358973
    numSides: 717946
    numLines: 717946
    ebwtTotLen: 45948544
    ebwtTotSz: 45948544
Total time for backward call to driver() for mirror index: 00:04:52