Settings:
  Output files: "/projects/NBL/HS1195/30TTYAAXX_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/HS1195/30TTYAAXX_3/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:01:43
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:23
bmax according to bmaxDivN setting: 90163503
Using parameters --bmax 67622628 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 67622628 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:26
  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: 00:00:09
  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: 00:00:30
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: 00:00:30
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.1522e+07 (target: 67622627)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (67622628) 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 61297410
  (Using difference cover)
  Sorting block time: 00:01:30
Returning block of 61297411
Getting block 2 of 7
  Reserving size (67622628) 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 59265767
  (Using difference cover)
  Sorting block time: 00:01:45
Returning block of 59265768
Getting block 3 of 7
  Reserving size (67622628) 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 62557635
  (Using difference cover)
  Sorting block time: 00:01:58
Returning block of 62557636
Getting block 4 of 7
  Reserving size (67622628) 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 50966275
  (Using difference cover)
  Sorting block time: 00:01:38
Returning block of 50966276
Getting block 5 of 7
  Reserving size (67622628) 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 31437665
  (Using difference cover)
  Sorting block time: 00:00:59
Returning block of 31437666
Getting block 6 of 7
  Reserving size (67622628) 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 41719198
  (Using difference cover)
  Sorting block time: 00:01:15
Returning block of 41719199
Getting block 7 of 7
  Reserving size (67622628) 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 53410058
  (Using difference cover)
  Sorting block time: 00:01:20
Returning block of 53410059
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101532678
fchr[G]: 180328820
fchr[T]: 258306364
fchr[$]: 360654014
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 655755022 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_3/tophat/tmp/segment_juncs.1.ebwt
Wrote 45081756 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_3/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 360654014
    bwtLen: 360654015
    sz: 90163504
    bwtSz: 90163504
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11270438
    offsSz: 45081752
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 805032
    numSides: 1610064
    numLines: 1610064
    ebwtTotLen: 103044096
    ebwtTotSz: 103044096
Total time for call to driver() for forward index: 00:19:20
Reading reference sizes
  Time reading reference sizes: 00:00:50
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:01:18
bmax according to bmaxDivN setting: 90163503
Using parameters --bmax 67622628 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 67622628 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:26
  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: 00:00:09
  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: 00:00:31
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: 00:00:29
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: 00:00:32
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.00727e+07 (target: 67622627)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 9
  Reserving size (67622628) 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 52511088
  (Using difference cover)
  Sorting block time: 00:01:22
Returning block of 52511089
Getting block 2 of 9
  Reserving size (67622628) 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 35439283
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 35439284
Getting block 3 of 9
  Reserving size (67622628) 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 37867759
  (Using difference cover)
  Sorting block time: 00:01:08
Returning block of 37867760
Getting block 4 of 9
  Reserving size (67622628) 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 31669402
  (Using difference cover)
  Sorting block time: 00:01:05
Returning block of 31669403
Getting block 5 of 9
  Reserving size (67622628) 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 54725325
  (Using difference cover)
  Sorting block time: 00:01:42
Returning block of 54725326
Getting block 6 of 9
  Reserving size (67622628) 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 12957126
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 12957127
Getting block 7 of 9
  Reserving size (67622628) 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 66904143
  (Using difference cover)
  Sorting block time: 00:01:58
Returning block of 66904144
Getting block 8 of 9
  Reserving size (67622628) 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 42845897
  (Using difference cover)
  Sorting block time: 00:01:14
Returning block of 42845898
Getting block 9 of 9
  Reserving size (67622628) 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 25733983
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 25733984
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101532678
fchr[G]: 180328820
fchr[T]: 258306364
fchr[$]: 360654014
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 655755022 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_3/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 45081756 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_3/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 360654014
    bwtLen: 360654015
    sz: 90163504
    bwtSz: 90163504
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11270438
    offsSz: 45081752
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 805032
    numSides: 1610064
    numLines: 1610064
    ebwtTotLen: 103044096
    ebwtTotSz: 103044096
Total time for backward call to driver() for mirror index: 00:19:00