Settings:
  Output files: "/Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/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:
  /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:24
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:08
bmax according to bmaxDivN setting: 33691522
Using parameters --bmax 25268642 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 25268642 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:05
  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: 00:00:02
  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: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.92523e+07 (target: 25268641)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:02
  Sorting block of length 18759775
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 18759776
Getting block 2 of 7
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 22291802
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 22291803
Getting block 3 of 7
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 18633529
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 18633530
Getting block 4 of 7
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 24032920
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 24032921
Getting block 5 of 7
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 10319523
  (Using difference cover)
  Sorting block time: 00:00:05
Returning block of 10319524
Getting block 6 of 7
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 16540351
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 16540352
Getting block 7 of 7
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 24188182
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 24188183
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 48781561
fchr[G]: 67485220
fchr[T]: 86167224
fchr[$]: 134766088
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 222140004 bytes to primary EBWT file: /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment_juncs.1.bt2
Wrote 33691528 bytes to secondary EBWT file: /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment_juncs.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 134766088
    bwtLen: 134766089
    sz: 33691522
    bwtSz: 33691523
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 8422881
    offsSz: 33691524
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 701907
    numLines: 701907
    ebwtTotLen: 44922048
    ebwtTotSz: 44922048
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:02:50
Reading reference sizes
  Time reading reference sizes: 00:00:02
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:06
  Time to reverse reference sequence: 00:00:02
bmax according to bmaxDivN setting: 33691522
Using parameters --bmax 25268642 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 25268642 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:04
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  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
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:09
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: 00:00:08
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: 00:00:08
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.68458e+07 (target: 25268641)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:02
  Sorting block of length 15746092
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 15746093
Getting block 2 of 8
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 14073156
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 14073157
Getting block 3 of 8
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 14447011
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 14447012
Getting block 4 of 8
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 19157510
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 19157511
Getting block 5 of 8
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 12517288
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 12517289
Getting block 6 of 8
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 19073221
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 19073222
Getting block 7 of 8
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:04
  Sorting block of length 23061192
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 23061193
Getting block 8 of 8
  Reserving size (25268642) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:03
  Sorting block of length 16690611
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 16690612
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 48781561
fchr[G]: 67485220
fchr[T]: 86167224
fchr[$]: 134766088
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 222140004 bytes to primary EBWT file: /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment_juncs.rev.1.bt2
Wrote 33691528 bytes to secondary EBWT file: /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/segment_juncs.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 134766088
    bwtLen: 134766089
    sz: 33691522
    bwtSz: 33691523
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 8422881
    offsSz: 33691524
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 701907
    numLines: 701907
    ebwtTotLen: 44922048
    ebwtTotSz: 44922048
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:02:43