Settings:
  Output files: "A3CO_13059_CGATGT/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:
  A3CO_13059_CGATGT/tmp/segment_juncs.fa
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: 00:00:04
bmax according to bmaxDivN setting: 41723418
Using parameters --bmax 31292564 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 31292564 --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
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:06
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: 00:00:05
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:05
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.08617e+07 (target: 31292563)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:02
  Sorting block of length 29306486
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 29306487
Getting block 2 of 8
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:02
  Sorting block of length 6320860
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 6320861
Getting block 3 of 8
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:02
  Sorting block of length 29609081
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 29609082
Getting block 4 of 8
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:02
  Sorting block of length 7788970
  (Using difference cover)
  Sorting block time: 00:00:03
Returning block of 7788971
Getting block 5 of 8
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:02
  Sorting block of length 24162417
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 24162418
Getting block 6 of 8
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:02
  Sorting block of length 29678165
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 29678166
Getting block 7 of 8
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:02
  Sorting block of length 22925347
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 22925348
Getting block 8 of 8
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:02
  Sorting block of length 17102340
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 17102341
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 52015713
fchr[G]: 84069842
fchr[T]: 116029795
fchr[$]: 166893673
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 275065577 bytes to primary EBWT file: A3CO_13059_CGATGT/tmp/segment_juncs.1.bt2
Wrote 41723424 bytes to secondary EBWT file: A3CO_13059_CGATGT/tmp/segment_juncs.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 166893673
    bwtLen: 166893674
    sz: 41723419
    bwtSz: 41723419
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 10430855
    offsSz: 41723420
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 869238
    numLines: 869238
    ebwtTotLen: 55631232
    ebwtTotSz: 55631232
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:02:26
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: 00:00:04
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 41723418
Using parameters --bmax 31292564 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 31292564 --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: 00:00:02
  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
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:06
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: 00:00:04
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:06
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.3842e+07 (target: 31292563)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:01
  Sorting block of length 30859494
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 30859495
Getting block 2 of 7
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:02
  Sorting block of length 3386946
  (Using difference cover)
  Sorting block time: 00:00:02
Returning block of 3386947
Getting block 3 of 7
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:02
  Sorting block of length 30579504
  (Using difference cover)
  Sorting block time: 00:00:16
Returning block of 30579505
Getting block 4 of 7
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:02
  Sorting block of length 18444097
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 18444098
Getting block 5 of 7
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:02
  Sorting block of length 30955368
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 30955369
Getting block 6 of 7
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:03
  Sorting block of length 31088603
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 31088604
Getting block 7 of 7
  Reserving size (31292564) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:02
  Sorting block of length 21579655
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 21579656
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 52015713
fchr[G]: 84069842
fchr[T]: 116029795
fchr[$]: 166893673
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 275065577 bytes to primary EBWT file: A3CO_13059_CGATGT/tmp/segment_juncs.rev.1.bt2
Wrote 41723424 bytes to secondary EBWT file: A3CO_13059_CGATGT/tmp/segment_juncs.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 166893673
    bwtLen: 166893674
    sz: 41723419
    bwtSz: 41723419
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 10430855
    offsSz: 41723420
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 869238
    numLines: 869238
    ebwtTotLen: 55631232
    ebwtTotSz: 55631232
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:02:27