Settings:
  Output files: "/projects/NBL/HS1198/30UBRAAXX_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/HS1198/30UBRAAXX_3/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:28
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: 44627618
Using parameters --bmax 33470714 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 33470714 --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: 00:00:02
  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: 00:00:15
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: 00:00:11
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.55015e+07 (target: 33470713)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (33470714) 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 12084684
  (Using difference cover)
  Sorting block time: 00:00:11
Returning block of 12084685
Getting block 2 of 7
  Reserving size (33470714) 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 30045575
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 30045576
Getting block 3 of 7
  Reserving size (33470714) 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 18627608
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 18627609
Getting block 4 of 7
  Reserving size (33470714) 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 33434039
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 33434040
Getting block 5 of 7
  Reserving size (33470714) 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 32045927
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 32045928
Getting block 6 of 7
  Reserving size (33470714) 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 25137997
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 25137998
Getting block 7 of 7
  Reserving size (33470714) 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 27134639
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 27134640
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 49548752
fchr[G]: 89888817
fchr[T]: 129265889
fchr[$]: 178510475
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 327135625 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_3/tophat/tmp/segment_juncs.1.ebwt
Wrote 22313816 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_3/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 178510475
    bwtLen: 178510476
    sz: 44627619
    bwtSz: 44627619
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5578453
    offsSz: 22313812
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 398461
    numSides: 796922
    numLines: 796922
    ebwtTotLen: 51003008
    ebwtTotSz: 51003008
Total time for call to driver() for forward index: 00:05:52
Reading reference sizes
  Time reading reference sizes: 00:00:02
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: 44627618
Using parameters --bmax 33470714 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 33470714 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:08
  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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  100%
  Binary sorting into buckets time: 00:00:15
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
  Binary sorting into buckets
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  30%
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  100%
  Binary sorting into buckets time: 00:00:10
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.55015e+07 (target: 33470713)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (33470714) 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 30298436
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 30298437
Getting block 2 of 7
  Reserving size (33470714) 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 23536700
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 23536701
Getting block 3 of 7
  Reserving size (33470714) 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 28207894
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 28207895
Getting block 4 of 7
  Reserving size (33470714) 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 10739101
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 10739102
Getting block 5 of 7
  Reserving size (33470714) 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 31800603
  (Using difference cover)
  Sorting block time: 00:00:41
Returning block of 31800604
Getting block 6 of 7
  Reserving size (33470714) 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 31339557
  (Using difference cover)
  Sorting block time: 00:00:40
Returning block of 31339558
Getting block 7 of 7
  Reserving size (33470714) 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 22588178
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 22588179
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 49548752
fchr[G]: 89888817
fchr[T]: 129265889
fchr[$]: 178510475
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 327135625 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_3/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 22313816 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_3/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 178510475
    bwtLen: 178510476
    sz: 44627619
    bwtSz: 44627619
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5578453
    offsSz: 22313812
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 398461
    numSides: 796922
    numLines: 796922
    ebwtTotLen: 51003008
    ebwtTotSz: 51003008
Total time for backward call to driver() for mirror index: 00:05:36