Settings:
  Output files: "/work/smaman/oct2021_intronSeeker/rerunFRS//hisat2_genomeRef/frs_n1000_r100_mix_cov100X_am_tr_d1_contigs-modified.fa.*.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:
  /work/smaman/oct2021_intronSeeker/rerunFRS/frs_n1000_r100_mix_cov100X_am_tr_d1_contigs-modified.fa
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 292973 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 292973 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  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
Avg bucket size: 195314 (target: 292972)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Getting block 1 of 8
  Reserving size (292973) 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 238577 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 238578 for bucket 1
Getting block 2 of 8
  Reserving size (292973) 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 166560 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 166561 for bucket 2
Getting block 3 of 8
  Reserving size (292973) 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 175632 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 175633 for bucket 3
Getting block 4 of 8
  Reserving size (292973) 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 182880 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 182881 for bucket 4
Getting block 5 of 8
  Reserving size (292973) 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 190595 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 190596 for bucket 5
Getting block 6 of 8
  Reserving size (292973) 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 232085 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 232086 for bucket 6
Getting block 7 of 8
  Reserving size (292973) 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 129380 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 129381 for bucket 7
Getting block 8 of 8
  Reserving size (292973) 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 246807 for bucket 8
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 246808 for bucket 8
Exited GFM loop
fchr[A]: 0
fchr[C]: 391246
fchr[G]: 782175
fchr[T]: 1172149
fchr[$]: 1562523
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 4813623 bytes to primary GFM file: /work/smaman/oct2021_intronSeeker/rerunFRS//hisat2_genomeRef/frs_n1000_r100_mix_cov100X_am_tr_d1_contigs-modified.fa.1.ht2
Wrote 390636 bytes to secondary GFM file: /work/smaman/oct2021_intronSeeker/rerunFRS//hisat2_genomeRef/frs_n1000_r100_mix_cov100X_am_tr_d1_contigs-modified.fa.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 12890749 bytes to primary GFM file: /work/smaman/oct2021_intronSeeker/rerunFRS//hisat2_genomeRef/frs_n1000_r100_mix_cov100X_am_tr_d1_contigs-modified.fa.5.ht2
Wrote 392332 bytes to secondary GFM file: /work/smaman/oct2021_intronSeeker/rerunFRS//hisat2_genomeRef/frs_n1000_r100_mix_cov100X_am_tr_d1_contigs-modified.fa.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
    len: 1562523
    gbwtLen: 1562524
    nodes: 1562524
    sz: 390631
    gbwtSz: 390632
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 97658
    offsSz: 390632
    lineSz: 64
    sideSz: 64
    sideGbwtSz: 48
    sideGbwtLen: 192
    numSides: 8139
    numLines: 8139
    gbwtTotLen: 520896
    gbwtTotSz: 520896
    reverse: 0
    linearFM: Yes
Total time for call to driver() for forward index: 00:00:01