Settings:
  Output files: "/projects/NBL/HS1803/616GYAAXX_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/HS1803/616GYAAXX_6/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:16
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: 104435824
Using parameters --bmax 78326868 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 78326868 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:16
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:03
  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: 00:00:33
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: 00:00:25
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
Avg bucket size: 5.96776e+07 (target: 78326867)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (78326868) 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 70427779
  (Using difference cover)
  Sorting block time: 00:00:59
Returning block of 70427780
Getting block 2 of 7
  Reserving size (78326868) 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 45281330
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 45281331
Getting block 3 of 7
  Reserving size (78326868) 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 66114125
  (Using difference cover)
  Sorting block time: 00:01:02
Returning block of 66114126
Getting block 4 of 7
  Reserving size (78326868) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:13
  Sorting block of length 69607514
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 69607515
Getting block 5 of 7
  Reserving size (78326868) 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 59844248
  (Using difference cover)
  Sorting block time: 00:00:55
Returning block of 59844249
Getting block 6 of 7
  Reserving size (78326868) 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 28909600
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 28909601
Getting block 7 of 7
  Reserving size (78326868) 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 77558697
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 77558698
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 107308270
fchr[G]: 207445430
fchr[T]: 306868732
fchr[$]: 417743299
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 758410979 bytes to primary EBWT file: /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 52217920 bytes to secondary EBWT file: /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 417743299
    bwtLen: 417743300
    sz: 104435825
    bwtSz: 104435825
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 13054479
    offsSz: 52217916
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 932463
    numSides: 1864926
    numLines: 1864926
    ebwtTotLen: 119355264
    ebwtTotSz: 119355264
Total time for call to driver() for forward index: 00:10:58
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: 104435824
Using parameters --bmax 78326868 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 78326868 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:15
  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: 00:00:06
  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: 00:00:34
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.96776e+07 (target: 78326867)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (78326868) 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 66152335
  (Using difference cover)
  Sorting block time: 00:00:55
Returning block of 66152336
Getting block 2 of 7
  Reserving size (78326868) 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 52370974
  (Using difference cover)
  Sorting block time: 00:00:45
Returning block of 52370975
Getting block 3 of 7
  Reserving size (78326868) 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 59014549
  (Using difference cover)
  Sorting block time: 00:00:56
Returning block of 59014550
Getting block 4 of 7
  Reserving size (78326868) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:13
  Sorting block of length 57198211
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 57198212
Getting block 5 of 7
  Reserving size (78326868) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:13
  Sorting block of length 48228382
  (Using difference cover)
  Sorting block time: 00:00:47
Returning block of 48228383
Getting block 6 of 7
  Reserving size (78326868) 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 69262240
  (Using difference cover)
  Sorting block time: 00:01:01
Returning block of 69262241
Getting block 7 of 7
  Reserving size (78326868) 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 65516602
  (Using difference cover)
  Sorting block time: 00:00:56
Returning block of 65516603
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 107308270
fchr[G]: 207445430
fchr[T]: 306868732
fchr[$]: 417743299
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 758410979 bytes to primary EBWT file: /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 52217920 bytes to secondary EBWT file: /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 417743299
    bwtLen: 417743300
    sz: 104435825
    bwtSz: 104435825
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 13054479
    offsSz: 52217916
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 932463
    numSides: 1864926
    numLines: 1864926
    ebwtTotLen: 119355264
    ebwtTotSz: 119355264
Total time for backward call to driver() for mirror index: 00:10:00