Settings:
  Output files: "/projects/NBL/HS1801/61074AAXX_7/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/HS1801/61074AAXX_7/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:01:58
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:25
bmax according to bmaxDivN setting: 101614635
Using parameters --bmax 76210977 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76210977 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:19
  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: 00:00:07
  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: 00:00:35
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: 00:00:24
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.80655e+07 (target: 76210976)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (76210977) 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 35951630
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 35951631
Getting block 2 of 7
  Reserving size (76210977) 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 68834699
  (Using difference cover)
  Sorting block time: 00:01:03
Returning block of 68834700
Getting block 3 of 7
  Reserving size (76210977) 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 57194734
  (Using difference cover)
  Sorting block time: 00:00:54
Returning block of 57194735
Getting block 4 of 7
  Reserving size (76210977) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:12
  Sorting block of length 27024827
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 27024828
Getting block 5 of 7
  Reserving size (76210977) 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 73625134
  (Using difference cover)
  Sorting block time: 00:01:09
Returning block of 73625135
Getting block 6 of 7
  Reserving size (76210977) 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 73211768
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 73211769
Getting block 7 of 7
  Reserving size (76210977) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:09
  Sorting block of length 70615742
  (Using difference cover)
  Sorting block time: 00:01:01
Returning block of 70615743
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101310651
fchr[G]: 201921743
fchr[T]: 302077211
fchr[$]: 406458540
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 737958531 bytes to primary EBWT file: /projects/NBL/HS1801/61074AAXX_7/tophat/tmp/segment_juncs.1.ebwt
Wrote 50807324 bytes to secondary EBWT file: /projects/NBL/HS1801/61074AAXX_7/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 406458540
    bwtLen: 406458541
    sz: 101614635
    bwtSz: 101614636
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12701830
    offsSz: 50807320
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 907274
    numSides: 1814548
    numLines: 1814548
    ebwtTotLen: 116131072
    ebwtTotSz: 116131072
Total time for call to driver() for forward index: 00:13:05
Reading reference sizes
  Time reading reference sizes: 00:00:06
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:25
bmax according to bmaxDivN setting: 101614635
Using parameters --bmax 76210977 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76210977 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:18
  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: 00:00:08
  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: 00:00:32
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: 00:00:23
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: 00:00:24
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: 00:00:26
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.08073e+07 (target: 76210976)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (76210977) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:09
  Sorting block of length 70256131
  (Using difference cover)
  Sorting block time: 00:01:02
Returning block of 70256132
Getting block 2 of 8
  Reserving size (76210977) 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 53049778
  (Using difference cover)
  Sorting block time: 00:00:47
Returning block of 53049779
Getting block 3 of 8
  Reserving size (76210977) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:12
  Sorting block of length 59832185
  (Using difference cover)
  Sorting block time: 00:00:57
Returning block of 59832186
Getting block 4 of 8
  Reserving size (76210977) 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 64111583
  (Using difference cover)
  Sorting block time: 00:01:01
Returning block of 64111584
Getting block 5 of 8
  Reserving size (76210977) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:14
  Sorting block of length 50638466
  (Using difference cover)
  Sorting block time: 00:00:48
Returning block of 50638467
Getting block 6 of 8
  Reserving size (76210977) 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 28860489
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 28860490
Getting block 7 of 8
  Reserving size (76210977) 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 56253122
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 56253123
Getting block 8 of 8
  Reserving size (76210977) 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 23456779
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 23456780
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101310651
fchr[G]: 201921743
fchr[T]: 302077211
fchr[$]: 406458540
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 737958531 bytes to primary EBWT file: /projects/NBL/HS1801/61074AAXX_7/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 50807324 bytes to secondary EBWT file: /projects/NBL/HS1801/61074AAXX_7/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 406458540
    bwtLen: 406458541
    sz: 101614635
    bwtSz: 101614636
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12701830
    offsSz: 50807320
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 907274
    numSides: 1814548
    numLines: 1814548
    ebwtTotLen: 116131072
    ebwtTotSz: 116131072
Total time for backward call to driver() for mirror index: 00:12:11