Settings:
  Output files: "chr9_indexed.*.ht2"
  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
  Local offset rate: 3 (one in 8)
  Local fTable chars: 6
  Local sequence length: 57344
  Local sequence overlap between two consecutive indexes: 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:
  chr9.fasta
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: 00:00:01
  Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 22526893 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 22526893 --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
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 2; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.50179e+07 (target: 22526892)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Getting block 1 of 8
  Reserving size (22526893) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 14104791 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 14104792 for bucket 1
Getting block 2 of 8
  Reserving size (22526893) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 8895241 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:06
Returning block of 8895242 for bucket 2
Getting block 3 of 8
  Reserving size (22526893) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 14532106 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:10
Returning block of 14532107 for bucket 3
Getting block 4 of 8
  Reserving size (22526893) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 20450029 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 20450030 for bucket 4
Getting block 5 of 8
  Reserving size (22526893) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 10902648 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 10902649 for bucket 5
Getting block 6 of 8
  Reserving size (22526893) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 22511944 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 22511945 for bucket 6
Getting block 7 of 8
  Reserving size (22526893) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 17244574 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 17244575 for bucket 7
Getting block 8 of 8
  Reserving size (22526893) for bucket 8
  Calculating Z arrays for bucket 8
  Entering block accumulator loop for bucket 8:
  bucket 8: 10%
  bucket 8: 20%
  bucket 8: 30%
  bucket 8: 40%
  bucket 8: 50%
  bucket 8: 60%
  bucket 8: 70%
  bucket 8: 80%
  bucket 8: 90%
  bucket 8: 100%
  Sorting block of length 11502091 for bucket 8
  (Using difference cover)
  Sorting block time: 00:00:08
Returning block of 11502092 for bucket 8
Exited GFM loop
fchr[A]: 0
fchr[C]: 35260078
fchr[G]: 60086290
fchr[T]: 84899549
fchr[$]: 120143431
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 44242818 bytes to primary GFM file: chr9_indexed.1.ht2
Wrote 30035864 bytes to secondary GFM file: chr9_indexed.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 53018681 bytes to primary GFM file: chr9_indexed.5.ht2
Wrote 30586252 bytes to secondary GFM file: chr9_indexed.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HierEbwt constructor
Headers:
    len: 120143431
    gbwtLen: 120143432
    nodes: 120143432
    sz: 30035858
    gbwtSz: 30035859
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 7508965
    offsSz: 30035860
    lineSz: 64
    sideSz: 64
    sideGbwtSz: 48
    sideGbwtLen: 192
    numSides: 625748
    numLines: 625748
    gbwtTotLen: 40047872
    gbwtTotSz: 40047872
    reverse: 0
    linearFM: Yes