Settings:
  Output files: "./tophat_out/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:
  ./tophat_out/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:05
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:07
bmax according to bmaxDivN setting: 79922014
Using parameters --bmax 59941511 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 59941511 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:07
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:02
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:03
  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: 00:00:14
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 8; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:12
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: 00:00:11
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.56697e+07 (target: 59941510)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (59941511) 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 51621316
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 51621317
Getting block 2 of 7
  Reserving size (59941511) 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 16571905
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 16571906
Getting block 3 of 7
  Reserving size (59941511) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 57264830
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 57264831
Getting block 4 of 7
  Reserving size (59941511) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 49611408
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 49611409
Getting block 5 of 7
  Reserving size (59941511) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 52673783
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 52673784
Getting block 6 of 7
  Reserving size (59941511) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 57867232
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 57867233
Getting block 7 of 7
  Reserving size (59941511) 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 34077579
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 34077580
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 110728244
fchr[G]: 159659673
fchr[T]: 208535722
fchr[$]: 319688059
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 442789021 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.1.bt2
Wrote 79922020 bytes to secondary EBWT file: ./tophat_out/tmp/segment_juncs.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 319688059
    bwtLen: 319688060
    sz: 79922015
    bwtSz: 79922015
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 19980504
    offsSz: 79922016
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1665042
    numLines: 1665042
    ebwtTotLen: 106562688
    ebwtTotSz: 106562688
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:04:27
Reading reference sizes
  Time reading reference sizes: 00:00:03
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:07
  Time to reverse reference sequence: 00:00:01
bmax according to bmaxDivN setting: 79922014
Using parameters --bmax 59941511 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 59941511 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:07
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:02
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:03
  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
  10%
  20%
  30%
  40%
  50%
  60%
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  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:14
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
  Binary sorting into buckets
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  30%
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  50%
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  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:13
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.56697e+07 (target: 59941510)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (59941511) 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 22648623
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 22648624
Getting block 2 of 7
  Reserving size (59941511) 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 51249812
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 51249813
Getting block 3 of 7
  Reserving size (59941511) 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 49404064
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 49404065
Getting block 4 of 7
  Reserving size (59941511) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 56142100
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 56142101
Getting block 5 of 7
  Reserving size (59941511) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:06
  Sorting block of length 55572853
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 55572854
Getting block 6 of 7
  Reserving size (59941511) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:05
  Sorting block of length 48849641
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 48849642
Getting block 7 of 7
  Reserving size (59941511) 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 35820960
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 35820961
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 110728244
fchr[G]: 159659673
fchr[T]: 208535722
fchr[$]: 319688059
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 442789021 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.rev.1.bt2
Wrote 79922020 bytes to secondary EBWT file: ./tophat_out/tmp/segment_juncs.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 319688059
    bwtLen: 319688060
    sz: 79922015
    bwtSz: 79922015
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 19980504
    offsSz: 79922016
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1665042
    numLines: 1665042
    ebwtTotLen: 106562688
    ebwtTotSz: 106562688
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:03:53