adeno_modified_reads.fa
Database file   : adeno.fa
Query file      : adeno_modified_reads.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 6 query sequences.
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
 Getting STELLAR matches from file, not calling STELLAR
Importing STELLAR matches from file stellar.gff
done
TIME importing stellar matches 0.00103426s
Getting match distance...
Constructing graphs... done
Analyzing graphs... done
 completed gff writing st1_l30_m.gff
 completed vcf writing st1_l30_m.vcf
TIME all 0.174012s
