Settings:
  Output files: "/scratch/8792779.1.linga/tophat2/tmp/segment_juncs.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  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:
  /scratch/8792779.1.linga/tophat2/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 2530012
Using parameters --bmax 1897509 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 1897509 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  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: 00:00:01
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 8; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
  Binary sorting into buckets
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  100%
  Binary sorting into buckets time: 00:00:01
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: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.44572e+06 (target: 1897508)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 1825041
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1825042
Getting block 2 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 1534319
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1534320
Getting block 3 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 1054905
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1054906
Getting block 4 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
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  Block accumulator loop time: 00:00:00
  Sorting block of length 1811649
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1811650
Getting block 5 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 1879760
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1879761
Getting block 6 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 1310691
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1310692
Getting block 7 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 703679
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 703680
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 2506051
fchr[G]: 5059666
fchr[T]: 7603954
fchr[$]: 10120050
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 21225858 bytes to primary EBWT file: /scratch/8792779.1.linga/tophat2/tmp/segment_juncs.1.bt2
Wrote 2530020 bytes to secondary EBWT file: /scratch/8792779.1.linga/tophat2/tmp/segment_juncs.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 10120050
    bwtLen: 10120051
    sz: 2530013
    bwtSz: 2530013
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 632504
    offsSz: 2530016
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 52709
    numLines: 52709
    ebwtTotLen: 3373376
    ebwtTotSz: 3373376
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:11
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:01
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 2530012
Using parameters --bmax 1897509 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 1897509 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  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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  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:01
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 8; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:01
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.44572e+06 (target: 1897508)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 1397442
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1397443
Getting block 2 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 1497009
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1497010
Getting block 3 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 1467928
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1467929
Getting block 4 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 1536367
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1536368
Getting block 5 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 1438484
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1438485
Getting block 6 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 918812
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 918813
Getting block 7 of 7
  Reserving size (1897509) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 1864002
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1864003
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 2506051
fchr[G]: 5059666
fchr[T]: 7603954
fchr[$]: 10120050
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 21225858 bytes to primary EBWT file: /scratch/8792779.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2
Wrote 2530020 bytes to secondary EBWT file: /scratch/8792779.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 10120050
    bwtLen: 10120051
    sz: 2530013
    bwtSz: 2530013
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 632504
    offsSz: 2530016
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 52709
    numLines: 52709
    ebwtTotLen: 3373376
    ebwtTotSz: 3373376
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:09