Settings:
  Output files: "Ct_1_R2//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_R2//tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:04
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:06
bmax according to bmaxDivN setting: 32066143
Using parameters --bmax 24049608 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 24049608 --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: 00:00:01
  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: 00:00:08
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
  Binary sorting into buckets
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  100%
  Binary sorting into buckets time: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.60331e+07 (target: 24049607)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (24049608) 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 21550905
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 21550906
Getting block 2 of 8
  Reserving size (24049608) 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 13289004
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 13289005
Getting block 3 of 8
  Reserving size (24049608) 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 13347201
  (Using difference cover)
  Sorting block time: 00:00:05
Returning block of 13347202
Getting block 4 of 8
  Reserving size (24049608) 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 11066223
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 11066224
Getting block 5 of 8
  Reserving size (24049608) 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 23801552
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 23801553
Getting block 6 of 8
  Reserving size (24049608) 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 21073675
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 21073676
Getting block 7 of 8
  Reserving size (24049608) 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 19640634
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 19640635
Getting block 8 of 8
  Reserving size (24049608) 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 4495371
  (Using difference cover)
  Sorting block time: 00:00:03
Returning block of 4495372
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 37403468
fchr[G]: 63969900
fchr[T]: 90758446
fchr[$]: 128264572
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 227426859 bytes to primary EBWT file: Ct_1_R2//tmp/segment_juncs.1.ebwt
Wrote 16033076 bytes to secondary EBWT file: Ct_1_R2//tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 128264572
    bwtLen: 128264573
    sz: 32066143
    bwtSz: 32066144
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4008268
    offsSz: 16033072
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 286305
    numSides: 572610
    numLines: 572610
    ebwtTotLen: 36647040
    ebwtTotSz: 36647040
    reverse: 0
Total time for call to driver() for forward index: 00:02:18
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: 00:00:05
bmax according to bmaxDivN setting: 32066143
Using parameters --bmax 24049608 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 24049608 --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: 00:00:03
  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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  60%
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  90%
  100%
  Binary sorting into buckets time: 00:00:12
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 5; iterating...
  Binary sorting into buckets
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  30%
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  100%
  Binary sorting into buckets time: 00:00:09
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 2; iterating...
  Binary sorting into buckets
  10%
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  30%
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  50%
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  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:08
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 2; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
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  100%
  Binary sorting into buckets time: 00:00:06
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 2; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
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  100%
  Binary sorting into buckets time: 00:00:06
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 2; iterating...
Avg bucket size: 1.28265e+07 (target: 24049607)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 10
  Reserving size (24049608) 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 11208241
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 11208242
Getting block 2 of 10
  Reserving size (24049608) 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 15302778
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 15302779
Getting block 3 of 10
  Reserving size (24049608) 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 21740357
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 21740358
Getting block 4 of 10
  Reserving size (24049608) 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 5097622
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 5097623
Getting block 5 of 10
  Reserving size (24049608) 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 11471769
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 11471770
Getting block 6 of 10
  Reserving size (24049608) 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 12986754
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 12986755
Getting block 7 of 10
  Reserving size (24049608) 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 14077245
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 14077246
Getting block 8 of 10
  Reserving size (24049608) 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 24497166
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 24497167
Getting block 9 of 10
  Reserving size (24049608) 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 452862
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 452863
Getting block 10 of 10
  Reserving size (24049608) 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 11429769
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 11429770
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 37403468
fchr[G]: 63969900
fchr[T]: 90758446
fchr[$]: 128264572
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 227426859 bytes to primary EBWT file: Ct_1_R2//tmp/segment_juncs.rev.1.ebwt
Wrote 16033076 bytes to secondary EBWT file: Ct_1_R2//tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 128264572
    bwtLen: 128264573
    sz: 32066143
    bwtSz: 32066144
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4008268
    offsSz: 16033072
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 286305
    numSides: 572610
    numLines: 572610
    ebwtTotLen: 36647040
    ebwtTotSz: 36647040
    reverse: 0
Total time for backward call to driver() for mirror index: 00:03:11