read_reference2.fa
Database file   : adeno.fa
Query file      : read_reference2.fa

Thresholds:
  overlap threshold (oth)          : 0.5
  gap threshold (gth)              : 5
  initial gap threshold (ith)      : 15
Penalties:
  translocation penalty (tp)       : 5
  inversion penalty (ip)           : 5
  order penalty (op)               : 0
  required read support (st)       : 1
Loading query sequences... Loaded 1 query sequence.
done
Loading reference sequences... Loaded 2 database sequences.
Loaded db seq with length: 4718
Loaded db ID: gi|9632547|ref|NC_002077.1|
Loaded db seq with length: 1148
Loaded db ID: gi|1234567|
done
Calling STELLAR...
Stellar options:
Database file   : adeno.fa
Query file      : read_reference2.fa

User specified parameters:
  minimal match length             : 30
  maximal error rate (epsilon)     : 0.05
  maximal x-drop                   : 5
  search forward strand            : yes
  search reverse complement        : yes

  verification strategy            : exact
  maximal number of matches        : 50
  duplicate removal every          : 500

Calculated parameters:
  k-mer length: 13
  s^min       : 13
  threshold   : 2
  distance cut: 40
  delta       : 16
  overlap     : 2

Constructing index...

TIME stellar 0.31517s
done
Getting match distance...
Constructing graphs... done
Analyzing graphs... done
 completed gff writing reference2_st1_l30.gff
 completed vcf writing reference2_st1_l30.vcf
TIME all 1.81999s
