Settings:
  Output files: "/projects/NBL/HS1197/311NGAAXX_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/HS1197/311NGAAXX_6/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:14
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:18
bmax according to bmaxDivN setting: 57309023
Using parameters --bmax 42981768 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 42981768 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:14
  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: 00:00:05
  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: 00:00:26
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.2748e+07 (target: 42981767)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (42981768) 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 40110028
  (Using difference cover)
  Sorting block time: 00:01:06
Returning block of 40110029
Getting block 2 of 7
  Reserving size (42981768) 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 38288883
  (Using difference cover)
  Sorting block time: 00:01:09
Returning block of 38288884
Getting block 3 of 7
  Reserving size (42981768) 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 37853797
  (Using difference cover)
  Sorting block time: 00:01:10
Returning block of 37853798
Getting block 4 of 7
  Reserving size (42981768) 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 32918319
  (Using difference cover)
  Sorting block time: 00:01:02
Returning block of 32918320
Getting block 5 of 7
  Reserving size (42981768) 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 14548350
  (Using difference cover)
  Sorting block time: 00:00:27
Returning block of 14548351
Getting block 6 of 7
  Reserving size (42981768) 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 38369774
  (Using difference cover)
  Sorting block time: 00:01:09
Returning block of 38369775
Getting block 7 of 7
  Reserving size (42981768) 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 27146938
  (Using difference cover)
  Sorting block time: 00:00:41
Returning block of 27146939
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 60493943
fchr[G]: 114711953
fchr[T]: 169103075
fchr[$]: 229236095
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 418856698 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_6/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 28654516 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_6/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 229236095
    bwtLen: 229236096
    sz: 57309024
    bwtSz: 57309024
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 7163628
    offsSz: 28654512
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 511688
    numSides: 1023376
    numLines: 1023376
    ebwtTotLen: 65496064
    ebwtTotSz: 65496064
Total time for call to driver() for forward index: 00:10:02
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: 00:00:20
bmax according to bmaxDivN setting: 57309023
Using parameters --bmax 42981768 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 42981768 --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: 00:00:02
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:05
  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: 00:00:25
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: 00:00:20
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, 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: 00:00:24
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.2748e+07 (target: 42981767)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (42981768) 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 35533957
  (Using difference cover)
  Sorting block time: 00:00:57
Returning block of 35533958
Getting block 2 of 7
  Reserving size (42981768) 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 33978768
  (Using difference cover)
  Sorting block time: 00:01:01
Returning block of 33978769
Getting block 3 of 7
  Reserving size (42981768) 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 35113944
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 35113945
Getting block 4 of 7
  Reserving size (42981768) 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 19729889
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 19729890
Getting block 5 of 7
  Reserving size (42981768) 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 40360411
  (Using difference cover)
  Sorting block time: 00:01:19
Returning block of 40360412
Getting block 6 of 7
  Reserving size (42981768) 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 31845076
  (Using difference cover)
  Sorting block time: 00:00:54
Returning block of 31845077
Getting block 7 of 7
  Reserving size (42981768) 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 32674044
  (Using difference cover)
  Sorting block time: 00:00:52
Returning block of 32674045
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 60493943
fchr[G]: 114711953
fchr[T]: 169103075
fchr[$]: 229236095
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 418856698 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_6/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 28654516 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_6/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 229236095
    bwtLen: 229236096
    sz: 57309024
    bwtSz: 57309024
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 7163628
    offsSz: 28654512
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 511688
    numSides: 1023376
    numLines: 1023376
    ebwtTotLen: 65496064
    ebwtTotSz: 65496064
Total time for backward call to driver() for mirror index: 00:11:00