Settings:
  Output files: "/scratch/6136164.1.p16/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/6136164.1.p16/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: 00:00:01
bmax according to bmaxDivN setting: 2463812
Using parameters --bmax 1847859 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 1847859 --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: 00:00:00
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: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.40789e+06 (target: 1847858)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (1847859) 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 1622288
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1622289
Getting block 2 of 7
  Reserving size (1847859) 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 1286625
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1286626
Getting block 3 of 7
  Reserving size (1847859) 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 1644312
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1644313
Getting block 4 of 7
  Reserving size (1847859) 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 1679087
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1679088
Getting block 5 of 7
  Reserving size (1847859) 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 1324850
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1324851
Getting block 6 of 7
  Reserving size (1847859) 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 1361724
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1361725
Getting block 7 of 7
  Reserving size (1847859) 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 936358
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 936359
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 2445420
fchr[G]: 4924595
fchr[T]: 7408556
fchr[$]: 9855250
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 20781802 bytes to primary EBWT file: /scratch/6136164.1.p16/tophat2/tmp/segment_juncs.1.bt2
Wrote 2463820 bytes to secondary EBWT file: /scratch/6136164.1.p16/tophat2/tmp/segment_juncs.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 9855250
    bwtLen: 9855251
    sz: 2463813
    bwtSz: 2463813
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 615954
    offsSz: 2463816
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 51330
    numLines: 51330
    ebwtTotLen: 3285120
    ebwtTotSz: 3285120
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:04
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
  Time to reverse reference sequence: 00:00:01
bmax according to bmaxDivN setting: 2463812
Using parameters --bmax 1847859 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 1847859 --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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  100%
  Binary sorting into buckets time: 00:00:00
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: 00:00:00
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: 00:00:00
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: 00:00:01
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: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
Avg bucket size: 1.23191e+06 (target: 1847858)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (1847859) 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 1434331
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1434332
Getting block 2 of 8
  Reserving size (1847859) 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 1489261
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1489262
Getting block 3 of 8
  Reserving size (1847859) 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 1619084
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1619085
Getting block 4 of 8
  Reserving size (1847859) 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 1425387
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1425388
Getting block 5 of 8
  Reserving size (1847859) 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 587996
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 587997
Getting block 6 of 8
  Reserving size (1847859) 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 276760
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 276761
Getting block 7 of 8
  Reserving size (1847859) 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 1755605
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1755606
Getting block 8 of 8
  Reserving size (1847859) 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 1266819
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1266820
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 2445420
fchr[G]: 4924595
fchr[T]: 7408556
fchr[$]: 9855250
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 20781802 bytes to primary EBWT file: /scratch/6136164.1.p16/tophat2/tmp/segment_juncs.rev.1.bt2
Wrote 2463820 bytes to secondary EBWT file: /scratch/6136164.1.p16/tophat2/tmp/segment_juncs.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 9855250
    bwtLen: 9855251
    sz: 2463813
    bwtSz: 2463813
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 615954
    offsSz: 2463816
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 51330
    numLines: 51330
    ebwtTotLen: 3285120
    ebwtTotSz: 3285120
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:05