Settings:
  Output files: "/projects/NBL/HS1797/616GYAAXX_2/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/HS1797/616GYAAXX_2/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:51
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: 101874959
Using parameters --bmax 76406220 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76406220 --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: 00:00:07
  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: 00:00:34
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: 00:00:26
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.82143e+07 (target: 76406219)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (76406220) 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 60091710
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 60091711
Getting block 2 of 7
  Reserving size (76406220) 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 75051461
  (Using difference cover)
  Sorting block time: 00:01:06
Returning block of 75051462
Getting block 3 of 7
  Reserving size (76406220) 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 67498918
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 67498919
Getting block 4 of 7
  Reserving size (76406220) 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 62690729
  (Using difference cover)
  Sorting block time: 00:00:58
Returning block of 62690730
Getting block 5 of 7
  Reserving size (76406220) 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 48508784
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 48508785
Getting block 6 of 7
  Reserving size (76406220) 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 38665253
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 38665254
Getting block 7 of 7
  Reserving size (76406220) 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 54992975
  (Using difference cover)
  Sorting block time: 00:00:47
Returning block of 54992976
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 100593027
fchr[G]: 201913454
fchr[T]: 302996240
fchr[$]: 407499836
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 740930876 bytes to primary EBWT file: /projects/NBL/HS1797/616GYAAXX_2/tophat/tmp/segment_juncs.1.ebwt
Wrote 50937484 bytes to secondary EBWT file: /projects/NBL/HS1797/616GYAAXX_2/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 407499836
    bwtLen: 407499837
    sz: 101874959
    bwtSz: 101874960
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12734370
    offsSz: 50937480
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 909598
    numSides: 1819196
    numLines: 1819196
    ebwtTotLen: 116428544
    ebwtTotSz: 116428544
Total time for call to driver() for forward index: 00:11:55
Reading reference sizes
  Time reading reference sizes: 00:00:05
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: 101874959
Using parameters --bmax 76406220 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76406220 --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: 00:00:08
  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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  100%
  Binary sorting into buckets time: 00:00:33
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.09375e+07 (target: 76406219)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (76406220) 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 69967952
  (Using difference cover)
  Sorting block time: 00:01:01
Returning block of 69967953
Getting block 2 of 8
  Reserving size (76406220) 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 60172828
  (Using difference cover)
  Sorting block time: 00:00:54
Returning block of 60172829
Getting block 3 of 8
  Reserving size (76406220) 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 53577505
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 53577506
Getting block 4 of 8
  Reserving size (76406220) 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 59785518
  (Using difference cover)
  Sorting block time: 00:00:56
Returning block of 59785519
Getting block 5 of 8
  Reserving size (76406220) 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 42395771
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 42395772
Getting block 6 of 8
  Reserving size (76406220) 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 34570295
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 34570296
Getting block 7 of 8
  Reserving size (76406220) 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 73688774
  (Using difference cover)
  Sorting block time: 00:01:08
Returning block of 73688775
Getting block 8 of 8
  Reserving size (76406220) 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 13341186
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 13341187
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 100593027
fchr[G]: 201913454
fchr[T]: 302996240
fchr[$]: 407499836
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 740930876 bytes to primary EBWT file: /projects/NBL/HS1797/616GYAAXX_2/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 50937484 bytes to secondary EBWT file: /projects/NBL/HS1797/616GYAAXX_2/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 407499836
    bwtLen: 407499837
    sz: 101874959
    bwtSz: 101874960
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12734370
    offsSz: 50937480
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 909598
    numSides: 1819196
    numLines: 1819196
    ebwtTotLen: 116428544
    ebwtTotSz: 116428544
Total time for backward call to driver() for mirror index: 00:11:19