Settings:
  Output files: "/projects/NBL/HS1198/30UBRAAXX_4/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/HS1198/30UBRAAXX_4/tophat/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: 00:00:10
bmax according to bmaxDivN setting: 42939503
Using parameters --bmax 32204628 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 32204628 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:08
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:03
  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: 00:00:14
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.45369e+07 (target: 32204627)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 31782898
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 31782899
Getting block 2 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 26898916
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 26898917
Getting block 3 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 22007104
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 22007105
Getting block 4 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 27377083
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 27377084
Getting block 5 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 27348183
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 27348184
Getting block 6 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 14617169
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 14617170
Getting block 7 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 21726655
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 21726656
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 46698037
fchr[G]: 86654961
fchr[T]: 125248171
fchr[$]: 171758014
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 314652930 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_4/tophat/tmp/segment_juncs.1.ebwt
Wrote 21469756 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_4/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 171758014
    bwtLen: 171758015
    sz: 42939504
    bwtSz: 42939504
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5367438
    offsSz: 21469752
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 383389
    numSides: 766778
    numLines: 766778
    ebwtTotLen: 49073792
    ebwtTotSz: 49073792
Total time for call to driver() for forward index: 00:05:22
Reading reference sizes
  Time reading reference sizes: 00:00:03
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:10
bmax according to bmaxDivN setting: 42939503
Using parameters --bmax 32204628 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 32204628 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:07
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:02
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:02
  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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  40%
  50%
  60%
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  100%
  Binary sorting into buckets time: 00:00:14
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.45369e+07 (target: 32204627)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 29337478
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 29337479
Getting block 2 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 16851318
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 16851319
Getting block 3 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 25933299
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 25933300
Getting block 4 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 22097305
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 22097306
Getting block 5 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 29244035
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 29244036
Getting block 6 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 23045847
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 23045848
Getting block 7 of 7
  Reserving size (32204628) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 25248726
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 25248727
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 46698037
fchr[G]: 86654961
fchr[T]: 125248171
fchr[$]: 171758014
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 314652930 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_4/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 21469756 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_4/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 171758014
    bwtLen: 171758015
    sz: 42939504
    bwtSz: 42939504
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 5367438
    offsSz: 21469752
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 383389
    numSides: 766778
    numLines: 766778
    ebwtTotLen: 49073792
    ebwtTotSz: 49073792
Total time for backward call to driver() for mirror index: 00:05:12