Settings:
  Output files: "/scratch/7534469.1.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/7534469.1.linga/tophat2/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:01
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: 6750462
Using parameters --bmax 5062847 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 5062847 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:01
  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: 00:00:01
  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
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.70018e+07 (target: 5062846)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 1
  No samples; assembling all-inclusive block
  Sorting block of length 27001850 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 27001851 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 6904551
fchr[G]: 13275553
fchr[T]: 19610231
fchr[$]: 27001850
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 49397034 bytes to primary EBWT file: /scratch/7534469.1.linga/tophat2/tmp/segment_juncs.1.bt2
Wrote 6750468 bytes to secondary EBWT file: /scratch/7534469.1.linga/tophat2/tmp/segment_juncs.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 27001850
    bwtLen: 27001851
    sz: 6750463
    bwtSz: 6750463
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 1687616
    offsSz: 6750464
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 140635
    numLines: 140635
    ebwtTotLen: 9000640
    ebwtTotSz: 9000640
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:32
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: 6750462
Using parameters --bmax 5062847 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 5062847 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:01
  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
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.70018e+07 (target: 5062846)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 1
  No samples; assembling all-inclusive block
  Sorting block of length 27001850 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 27001851 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 6904551
fchr[G]: 13275553
fchr[T]: 19610231
fchr[$]: 27001850
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 49397034 bytes to primary EBWT file: /scratch/7534469.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2
Wrote 6750468 bytes to secondary EBWT file: /scratch/7534469.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 27001850
    bwtLen: 27001851
    sz: 6750463
    bwtSz: 6750463
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 1687616
    offsSz: 6750464
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 140635
    numLines: 140635
    ebwtTotLen: 9000640
    ebwtTotSz: 9000640
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:27