Settings:
  Output files: "/projects/NBL/HS1795/700B4AAXX_3/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/HS1795/700B4AAXX_3/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:01:44
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:48
bmax according to bmaxDivN setting: 102065106
Using parameters --bmax 76548830 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76548830 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:28
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:05
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:10
  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: 00:00:47
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: 00:00:38
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: 00:00:42
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.83229e+07 (target: 76548829)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (76548830) 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 67029314
  (Using difference cover)
  Sorting block time: 00:01:27
Returning block of 67029315
Getting block 2 of 7
  Reserving size (76548830) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:16
  Sorting block of length 75056467
  (Using difference cover)
  Sorting block time: 00:01:42
Returning block of 75056468
Getting block 3 of 7
  Reserving size (76548830) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:18
  Sorting block of length 64925963
  (Using difference cover)
  Sorting block time: 00:01:34
Returning block of 64925964
Getting block 4 of 7
  Reserving size (76548830) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:17
  Sorting block of length 39374452
  (Using difference cover)
  Sorting block time: 00:00:55
Returning block of 39374453
Getting block 5 of 7
  Reserving size (76548830) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:21
  Sorting block of length 53275622
  (Using difference cover)
  Sorting block time: 00:01:15
Returning block of 53275623
Getting block 6 of 7
  Reserving size (76548830) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:22
  Sorting block of length 48452092
  (Using difference cover)
  Sorting block time: 00:01:06
Returning block of 48452093
Getting block 7 of 7
  Reserving size (76548830) 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 60146508
  (Using difference cover)
  Sorting block time: 00:01:19
Returning block of 60146509
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101308050
fchr[G]: 202408790
fchr[T]: 303254568
fchr[$]: 408260424
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 741842997 bytes to primary EBWT file: /projects/NBL/HS1795/700B4AAXX_3/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 51032560 bytes to secondary EBWT file: /projects/NBL/HS1795/700B4AAXX_3/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 408260424
    bwtLen: 408260425
    sz: 102065106
    bwtSz: 102065107
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12758139
    offsSz: 51032556
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 911296
    numSides: 1822592
    numLines: 1822592
    ebwtTotLen: 116645888
    ebwtTotSz: 116645888
Total time for call to driver() for forward index: 00:19:13
Reading reference sizes
  Time reading reference sizes: 00:00:09
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:34
bmax according to bmaxDivN setting: 102065106
Using parameters --bmax 76548830 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76548830 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:27
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:05
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:11
  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: 00:00:45
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: 00:00:36
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.83229e+07 (target: 76548829)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (76548830) 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 53564358
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 53564359
Getting block 2 of 7
  Reserving size (76548830) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:16
  Sorting block of length 67466048
  (Using difference cover)
  Sorting block time: 00:01:29
Returning block of 67466049
Getting block 3 of 7
  Reserving size (76548830) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:17
  Sorting block of length 54883964
  (Using difference cover)
  Sorting block time: 00:01:19
Returning block of 54883965
Getting block 4 of 7
  Reserving size (76548830) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:19
  Sorting block of length 66712269
  (Using difference cover)
  Sorting block time: 00:01:33
Returning block of 66712270
Getting block 5 of 7
  Reserving size (76548830) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:19
  Sorting block of length 56564334
  (Using difference cover)
  Sorting block time: 00:01:18
Returning block of 56564335
Getting block 6 of 7
  Reserving size (76548830) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:21
  Sorting block of length 64746951
  (Using difference cover)
  Sorting block time: 00:01:27
Returning block of 64746952
Getting block 7 of 7
  Reserving size (76548830) 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 44322494
  (Using difference cover)
  Sorting block time: 00:00:57
Returning block of 44322495
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101308050
fchr[G]: 202408790
fchr[T]: 303254568
fchr[$]: 408260424
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 741842997 bytes to primary EBWT file: /projects/NBL/HS1795/700B4AAXX_3/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 51032560 bytes to secondary EBWT file: /projects/NBL/HS1795/700B4AAXX_3/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 408260424
    bwtLen: 408260425
    sz: 102065106
    bwtSz: 102065107
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12758139
    offsSz: 51032556
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 911296
    numSides: 1822592
    numLines: 1822592
    ebwtTotLen: 116645888
    ebwtTotSz: 116645888
Total time for backward call to driver() for mirror index: 00:16:22