Settings:
  Output files: "/projects/NBL/HS1195/30TTYAAXX_5/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_5/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:42
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:21
bmax according to bmaxDivN setting: 90558741
Using parameters --bmax 67919056 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 67919056 --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: 00:00:06
  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 7; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:21
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: 00:00:24
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: 00:00:23
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.52794e+07 (target: 67919055)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (67919056) 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 35194725
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 35194726
Getting block 2 of 8
  Reserving size (67919056) 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 37268433
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 37268434
Getting block 3 of 8
  Reserving size (67919056) 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 66326604
  (Using difference cover)
  Sorting block time: 00:01:22
Returning block of 66326605
Getting block 4 of 8
  Reserving size (67919056) 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 53146256
  (Using difference cover)
  Sorting block time: 00:01:12
Returning block of 53146257
Getting block 5 of 8
  Reserving size (67919056) 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 53132387
  (Using difference cover)
  Sorting block time: 00:01:10
Returning block of 53132388
Getting block 6 of 8
  Reserving size (67919056) 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 28810441
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 28810442
Getting block 7 of 8
  Reserving size (67919056) 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 49936128
  (Using difference cover)
  Sorting block time: 00:01:06
Returning block of 49936129
Getting block 8 of 8
  Reserving size (67919056) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 38419984
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 38419985
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 102183698
fchr[G]: 181039867
fchr[T]: 258291357
fchr[$]: 362234965
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 658753611 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_5/tophat/tmp/segment_juncs.1.ebwt
Wrote 45279376 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_5/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 362234965
    bwtLen: 362234966
    sz: 90558742
    bwtSz: 90558742
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11319843
    offsSz: 45279372
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 808561
    numSides: 1617122
    numLines: 1617122
    ebwtTotLen: 103495808
    ebwtTotSz: 103495808
Total time for call to driver() for forward index: 00:13:14
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: 00:00:21
bmax according to bmaxDivN setting: 90558741
Using parameters --bmax 67919056 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 67919056 --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: 00:00:05
  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: 00:00:27
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: 00:00:22
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: 00:00:23
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.17478e+07 (target: 67919055)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (67919056) 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 64070805
  (Using difference cover)
  Sorting block time: 00:01:12
Returning block of 64070806
Getting block 2 of 7
  Reserving size (67919056) 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 23336458
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 23336459
Getting block 3 of 7
  Reserving size (67919056) 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 59050444
  (Using difference cover)
  Sorting block time: 00:01:21
Returning block of 59050445
Getting block 4 of 7
  Reserving size (67919056) 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 46591946
  (Using difference cover)
  Sorting block time: 00:01:03
Returning block of 46591947
Getting block 5 of 7
  Reserving size (67919056) 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 60701712
  (Using difference cover)
  Sorting block time: 00:01:23
Returning block of 60701713
Getting block 6 of 7
  Reserving size (67919056) 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 48543313
  (Using difference cover)
  Sorting block time: 00:00:56
Returning block of 48543314
Getting block 7 of 7
  Reserving size (67919056) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 59940281
  (Using difference cover)
  Sorting block time: 00:01:06
Returning block of 59940282
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 102183698
fchr[G]: 181039867
fchr[T]: 258291357
fchr[$]: 362234965
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 658753611 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_5/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 45279376 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_5/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 362234965
    bwtLen: 362234966
    sz: 90558742
    bwtSz: 90558742
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11319843
    offsSz: 45279372
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 808561
    numSides: 1617122
    numLines: 1617122
    ebwtTotLen: 103495808
    ebwtTotSz: 103495808
Total time for backward call to driver() for mirror index: 00:12:28