Settings:
  Output files: "/projects/NBL/HS1195/30TTYAAXX_6/tophat_wj/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_6/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:29
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: 91831066
Using parameters --bmax 68873300 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 68873300 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:16
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:03
  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
Avg bucket size: 5.24749e+07 (target: 68873299)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (68873300) 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 65965474
  (Using difference cover)
  Sorting block time: 00:01:03
Returning block of 65965475
Getting block 2 of 7
  Reserving size (68873300) 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 46234370
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 46234371
Getting block 3 of 7
  Reserving size (68873300) 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 59567715
  (Using difference cover)
  Sorting block time: 00:01:16
Returning block of 59567716
Getting block 4 of 7
  Reserving size (68873300) 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 64767627
  (Using difference cover)
  Sorting block time: 00:01:20
Returning block of 64767628
Getting block 5 of 7
  Reserving size (68873300) 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 15323491
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 15323492
Getting block 6 of 7
  Reserving size (68873300) 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 67022625
  (Using difference cover)
  Sorting block time: 00:01:18
Returning block of 67022626
Getting block 7 of 7
  Reserving size (68873300) 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 48442958
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 48442959
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 104664503
fchr[G]: 183373826
fchr[T]: 261168420
fchr[$]: 367324266
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 668475192 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_6/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 45915540 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_6/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 367324266
    bwtLen: 367324267
    sz: 91831067
    bwtSz: 91831067
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11478884
    offsSz: 45915536
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 819921
    numSides: 1639842
    numLines: 1639842
    ebwtTotLen: 104949888
    ebwtTotSz: 104949888
Total time for call to driver() for forward index: 00:11:00
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: 91831066
Using parameters --bmax 68873300 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 68873300 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:15
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:03
  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: 00:00:28
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 6; 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 2; 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
Split 1, merged 1; 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
Avg bucket size: 4.59155e+07 (target: 68873299)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (68873300) 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 43201425
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 43201426
Getting block 2 of 8
  Reserving size (68873300) 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 61463076
  (Using difference cover)
  Sorting block time: 00:01:09
Returning block of 61463077
Getting block 3 of 8
  Reserving size (68873300) 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 15942265
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 15942266
Getting block 4 of 8
  Reserving size (68873300) 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 64371962
  (Using difference cover)
  Sorting block time: 00:01:18
Returning block of 64371963
Getting block 5 of 8
  Reserving size (68873300) 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 20537866
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 20537867
Getting block 6 of 8
  Reserving size (68873300) 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 65764254
  (Using difference cover)
  Sorting block time: 00:01:22
Returning block of 65764255
Getting block 7 of 8
  Reserving size (68873300) 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 62931568
  (Using difference cover)
  Sorting block time: 00:01:14
Returning block of 62931569
Getting block 8 of 8
  Reserving size (68873300) 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 33111843
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 33111844
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 104664503
fchr[G]: 183373826
fchr[T]: 261168420
fchr[$]: 367324266
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 668475192 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_6/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 45915540 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_6/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 367324266
    bwtLen: 367324267
    sz: 91831067
    bwtSz: 91831067
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11478884
    offsSz: 45915536
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 819921
    numSides: 1639842
    numLines: 1639842
    ebwtTotLen: 104949888
    ebwtTotSz: 104949888
Total time for backward call to driver() for mirror index: 00:11:49