Settings:
  Output files: "Ct_1//tmp/segment_juncs.*.ebwt"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 5 (one in 32)
  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:
  Ct_1//tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:08
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:13
bmax according to bmaxDivN setting: 33355075
Using parameters --bmax 25016307 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 25016307 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:10
  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: 00:00:20
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
  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: 1.906e+07 (target: 25016306)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (25016307) 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 19279310
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 19279311
Getting block 2 of 7
  Reserving size (25016307) 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 23753645
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 23753646
Getting block 3 of 7
  Reserving size (25016307) 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 11733579
  (Using difference cover)
  Sorting block time: 00:00:13
Returning block of 11733580
Getting block 4 of 7
  Reserving size (25016307) 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 20837432
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 20837433
Getting block 5 of 7
  Reserving size (25016307) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 21077482
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 21077483
Getting block 6 of 7
  Reserving size (25016307) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 24857802
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 24857803
Getting block 7 of 7
  Reserving size (25016307) 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 11881045
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 11881046
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 40990739
fchr[G]: 66756152
fchr[T]: 92614341
fchr[$]: 133420301
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 236398213 bytes to primary EBWT file: Ct_1//tmp/segment_juncs.1.ebwt
Wrote 16677544 bytes to secondary EBWT file: Ct_1//tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 133420301
    bwtLen: 133420302
    sz: 33355076
    bwtSz: 33355076
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4169385
    offsSz: 16677540
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 297814
    numSides: 595628
    numLines: 595628
    ebwtTotLen: 38120192
    ebwtTotSz: 38120192
    reverse: 0
Total time for call to driver() for forward index: 00:05:08
Reading reference sizes
  Time reading reference sizes: 00:00:06
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:15
bmax according to bmaxDivN setting: 33355075
Using parameters --bmax 25016307 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 25016307 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:10
  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: 00:00:05
  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%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:14
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:08
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.906e+07 (target: 25016306)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (25016307) 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 24464270
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 24464271
Getting block 2 of 7
  Reserving size (25016307) 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 17272295
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 17272296
Getting block 3 of 7
  Reserving size (25016307) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  100%
  Block accumulator loop time: 00:00:06
  Sorting block of length 14598987
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 14598988
Getting block 4 of 7
  Reserving size (25016307) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 21434126
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 21434127
Getting block 5 of 7
  Reserving size (25016307) 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 18186914
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 18186915
Getting block 6 of 7
  Reserving size (25016307) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:07
  Sorting block of length 23475529
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 23475530
Getting block 7 of 7
  Reserving size (25016307) 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 13988174
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 13988175
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 40990739
fchr[G]: 66756152
fchr[T]: 92614341
fchr[$]: 133420301
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 236398213 bytes to primary EBWT file: Ct_1//tmp/segment_juncs.rev.1.ebwt
Wrote 16677544 bytes to secondary EBWT file: Ct_1//tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 133420301
    bwtLen: 133420302
    sz: 33355076
    bwtSz: 33355076
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4169385
    offsSz: 16677540
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 297814
    numSides: 595628
    numLines: 595628
    ebwtTotLen: 38120192
    ebwtTotSz: 38120192
    reverse: 0
Total time for backward call to driver() for mirror index: 00:04:54