Settings:
  Output files: "/scratch/8793276.1.p8/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/8793276.1.p8/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: 2618612
Using parameters --bmax 1963959 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 1963959 --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 2, 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
Avg bucket size: 1.49635e+06 (target: 1963958)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (1963959) 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 1942763
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1942764
Getting block 2 of 7
  Reserving size (1963959) 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 1519177
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1519178
Getting block 3 of 7
  Reserving size (1963959) 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 1862732
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1862733
Getting block 4 of 7
  Reserving size (1963959) 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 1553640
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1553641
Getting block 5 of 7
  Reserving size (1963959) 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 1092588
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1092589
Getting block 6 of 7
  Reserving size (1963959) 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 1188190
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1188191
Getting block 7 of 7
  Reserving size (1963959) 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 1315354
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1315355
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 2602212
fchr[G]: 5227894
fchr[T]: 7852978
fchr[$]: 10474450
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 21818881 bytes to primary EBWT file: /scratch/8793276.1.p8/tophat2/tmp/segment_juncs.1.bt2
Wrote 2618620 bytes to secondary EBWT file: /scratch/8793276.1.p8/tophat2/tmp/segment_juncs.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 10474450
    bwtLen: 10474451
    sz: 2618613
    bwtSz: 2618613
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 654654
    offsSz: 2618616
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 54555
    numLines: 54555
    ebwtTotLen: 3491520
    ebwtTotSz: 3491520
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:05
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: 2618612
Using parameters --bmax 1963959 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 1963959 --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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  50%
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  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.49635e+06 (target: 1963958)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (1963959) 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 1839711
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1839712
Getting block 2 of 7
  Reserving size (1963959) 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 1550122
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1550123
Getting block 3 of 7
  Reserving size (1963959) 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 1210411
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1210412
Getting block 4 of 7
  Reserving size (1963959) 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 1394782
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1394783
Getting block 5 of 7
  Reserving size (1963959) 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 1302108
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1302109
Getting block 6 of 7
  Reserving size (1963959) 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 1782920
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1782921
Getting block 7 of 7
  Reserving size (1963959) 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 1394390
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1394391
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 2602212
fchr[G]: 5227894
fchr[T]: 7852978
fchr[$]: 10474450
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 21818881 bytes to primary EBWT file: /scratch/8793276.1.p8/tophat2/tmp/segment_juncs.rev.1.bt2
Wrote 2618620 bytes to secondary EBWT file: /scratch/8793276.1.p8/tophat2/tmp/segment_juncs.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 10474450
    bwtLen: 10474451
    sz: 2618613
    bwtSz: 2618613
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 654654
    offsSz: 2618616
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 54555
    numLines: 54555
    ebwtTotLen: 3491520
    ebwtTotSz: 3491520
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:04