Settings:
  Output files: "/scratch/8793017.1.c/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/8793017.1.c/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: 2499962
Using parameters --bmax 1874972 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 1874972 --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
Avg bucket size: 1.24998e+06 (target: 1874971)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (1874972) 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 1791893
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1791894
Getting block 2 of 8
  Reserving size (1874972) 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 425550
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 425551
Getting block 3 of 8
  Reserving size (1874972) 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 1481634
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1481635
Getting block 4 of 8
  Reserving size (1874972) 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 1594156
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1594157
Getting block 5 of 8
  Reserving size (1874972) 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 582273
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 582274
Getting block 6 of 8
  Reserving size (1874972) 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 1507289
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1507290
Getting block 7 of 8
  Reserving size (1874972) 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 1642934
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1642935
Getting block 8 of 8
  Reserving size (1874972) 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 974114
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 974115
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 2482793
fchr[G]: 4995766
fchr[T]: 7512162
fchr[$]: 9999850
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 21023991 bytes to primary EBWT file: /scratch/8793017.1.c/tophat2/tmp/segment_juncs.1.bt2
Wrote 2499968 bytes to secondary EBWT file: /scratch/8793017.1.c/tophat2/tmp/segment_juncs.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 9999850
    bwtLen: 9999851
    sz: 2499963
    bwtSz: 2499963
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 624991
    offsSz: 2499964
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 52083
    numLines: 52083
    ebwtTotLen: 3333312
    ebwtTotSz: 3333312
    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: 00:00:00
bmax according to bmaxDivN setting: 2499962
Using parameters --bmax 1874972 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 1874972 --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 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 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
Split 1, merged 1; iterating...
  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
Avg bucket size: 1.42855e+06 (target: 1874971)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (1874972) 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 642655
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 642656
Getting block 2 of 7
  Reserving size (1874972) 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 1468149
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1468150
Getting block 3 of 7
  Reserving size (1874972) 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 1396983
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1396984
Getting block 4 of 7
  Reserving size (1874972) 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 1779119
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1779120
Getting block 5 of 7
  Reserving size (1874972) 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 1424650
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1424651
Getting block 6 of 7
  Reserving size (1874972) 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 1560849
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1560850
Getting block 7 of 7
  Reserving size (1874972) 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 1727439
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1727440
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 2482793
fchr[G]: 4995766
fchr[T]: 7512162
fchr[$]: 9999850
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 21023991 bytes to primary EBWT file: /scratch/8793017.1.c/tophat2/tmp/segment_juncs.rev.1.bt2
Wrote 2499968 bytes to secondary EBWT file: /scratch/8793017.1.c/tophat2/tmp/segment_juncs.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 9999850
    bwtLen: 9999851
    sz: 2499963
    bwtSz: 2499963
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 624991
    offsSz: 2499964
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 52083
    numLines: 52083
    ebwtTotLen: 3333312
    ebwtTotSz: 3333312
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:05