Settings:
  Output files: "/projects/NBL/HS1197/311NGAAXX_2/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/HS1197/311NGAAXX_2/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:17
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:17
bmax according to bmaxDivN setting: 57026395
Using parameters --bmax 42769797 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 42769797 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:11
  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: 00:00:04
  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: 00:00:19
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.25865e+07 (target: 42769796)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (42769797) 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 20966516
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 20966517
Getting block 2 of 7
  Reserving size (42769797) 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 39387597
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 39387598
Getting block 3 of 7
  Reserving size (42769797) 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 6374297
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 6374298
Getting block 4 of 7
  Reserving size (42769797) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 36988278
  (Using difference cover)
  Sorting block time: 00:00:46
Returning block of 36988279
Getting block 5 of 7
  Reserving size (42769797) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 40985921
  (Using difference cover)
  Sorting block time: 00:00:46
Returning block of 40985922
Getting block 6 of 7
  Reserving size (42769797) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 40706223
  (Using difference cover)
  Sorting block time: 00:00:48
Returning block of 40706224
Getting block 7 of 7
  Reserving size (42769797) 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 42696743
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 42696744
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 60184406
fchr[G]: 114800330
fchr[T]: 168336557
fchr[$]: 228105581
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 417255466 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_2/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 28513204 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_2/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 228105581
    bwtLen: 228105582
    sz: 57026396
    bwtSz: 57026396
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 7128300
    offsSz: 28513200
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 509165
    numSides: 1018330
    numLines: 1018330
    ebwtTotLen: 65173120
    ebwtTotSz: 65173120
Total time for call to driver() for forward index: 00:06:41
Reading reference sizes
  Time reading reference sizes: 00:00:04
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:13
bmax according to bmaxDivN setting: 57026395
Using parameters --bmax 42769797 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 42769797 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:09
  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: 00:00:19
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: 00:00:15
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.25865e+07 (target: 42769796)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (42769797) 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 24587478
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 24587479
Getting block 2 of 7
  Reserving size (42769797) 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 31429987
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 31429988
Getting block 3 of 7
  Reserving size (42769797) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 38901945
  (Using difference cover)
  Sorting block time: 00:00:47
Returning block of 38901946
Getting block 4 of 7
  Reserving size (42769797) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 25172222
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 25172223
Getting block 5 of 7
  Reserving size (42769797) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 28899697
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 28899698
Getting block 6 of 7
  Reserving size (42769797) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:08
  Sorting block of length 39584803
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 39584804
Getting block 7 of 7
  Reserving size (42769797) 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 39529443
  (Using difference cover)
  Sorting block time: 00:00:41
Returning block of 39529444
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 60184406
fchr[G]: 114800330
fchr[T]: 168336557
fchr[$]: 228105581
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 417255466 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_2/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 28513204 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_2/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 228105581
    bwtLen: 228105582
    sz: 57026396
    bwtSz: 57026396
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 7128300
    offsSz: 28513200
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 509165
    numSides: 1018330
    numLines: 1018330
    ebwtTotLen: 65173120
    ebwtTotSz: 65173120
Total time for backward call to driver() for mirror index: 00:06:37