Settings:
  Output files: "/projects/NBL/HS1797/616GYAAXX_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/HS1797/616GYAAXX_3/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:01:14
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:27
bmax according to bmaxDivN setting: 101861475
Using parameters --bmax 76396107 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76396107 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:25
  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: 00:00:34
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: 00:00:32
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: 00:00:35
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.09307e+07 (target: 76396106)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (76396107) 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 74320808
  (Using difference cover)
  Sorting block time: 00:01:29
Returning block of 74320809
Getting block 2 of 8
  Reserving size (76396107) 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 42158642
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 42158643
Getting block 3 of 8
  Reserving size (76396107) 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 75379413
  (Using difference cover)
  Sorting block time: 00:01:40
Returning block of 75379414
Getting block 4 of 8
  Reserving size (76396107) 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 9453733
  (Using difference cover)
  Sorting block time: 00:00:13
Returning block of 9453734
Getting block 5 of 8
  Reserving size (76396107) 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 68815166
  (Using difference cover)
  Sorting block time: 00:01:36
Returning block of 68815167
Getting block 6 of 8
  Reserving size (76396107) 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 43672154
  (Using difference cover)
  Sorting block time: 00:00:58
Returning block of 43672155
Getting block 7 of 8
  Reserving size (76396107) 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 57238083
  (Using difference cover)
  Sorting block time: 00:01:15
Returning block of 57238084
Getting block 8 of 8
  Reserving size (76396107) 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 36407896
  (Using difference cover)
  Sorting block time: 00:00:45
Returning block of 36407897
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 100656619
fchr[G]: 201936539
fchr[T]: 302918569
fchr[$]: 407445902
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 740664287 bytes to primary EBWT file: /projects/NBL/HS1797/616GYAAXX_3/tophat/tmp/segment_juncs.1.ebwt
Wrote 50930744 bytes to secondary EBWT file: /projects/NBL/HS1797/616GYAAXX_3/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 407445902
    bwtLen: 407445903
    sz: 101861476
    bwtSz: 101861476
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12732685
    offsSz: 50930740
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 909478
    numSides: 1818956
    numLines: 1818956
    ebwtTotLen: 116413184
    ebwtTotSz: 116413184
Total time for call to driver() for forward index: 00:16:48
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: 00:00:28
bmax according to bmaxDivN setting: 101861475
Using parameters --bmax 76396107 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76396107 --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: 00:00:06
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:12
  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: 00:00:34
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 8; iterating...
  Binary sorting into buckets
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  100%
  Binary sorting into buckets time: 00:00:27
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: 00:00:30
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.82066e+07 (target: 76396106)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (76396107) 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 67039067
  (Using difference cover)
  Sorting block time: 00:01:26
Returning block of 67039068
Getting block 2 of 7
  Reserving size (76396107) 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 58376304
  (Using difference cover)
  Sorting block time: 00:01:16
Returning block of 58376305
Getting block 3 of 7
  Reserving size (76396107) 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 71186916
  (Using difference cover)
  Sorting block time: 00:01:40
Returning block of 71186917
Getting block 4 of 7
  Reserving size (76396107) 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 38530263
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 38530264
Getting block 5 of 7
  Reserving size (76396107) 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 75136158
  (Using difference cover)
  Sorting block time: 00:01:42
Returning block of 75136159
Getting block 6 of 7
  Reserving size (76396107) 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 45850498
  (Using difference cover)
  Sorting block time: 00:01:00
Returning block of 45850499
Getting block 7 of 7
  Reserving size (76396107) 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 51326690
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 51326691
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 100656619
fchr[G]: 201936539
fchr[T]: 302918569
fchr[$]: 407445902
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 740664287 bytes to primary EBWT file: /projects/NBL/HS1797/616GYAAXX_3/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 50930744 bytes to secondary EBWT file: /projects/NBL/HS1797/616GYAAXX_3/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 407445902
    bwtLen: 407445903
    sz: 101861476
    bwtSz: 101861476
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12732685
    offsSz: 50930740
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 909478
    numSides: 1818956
    numLines: 1818956
    ebwtTotLen: 116413184
    ebwtTotSz: 116413184
Total time for backward call to driver() for mirror index: 00:15:44