adeno_modified_reads_mates1.fa
adeno_modified_reads_mates2.fa
Database file   : adeno.fa
Query file      : adeno_modified_reads_mates1.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 paired-end read sequences... Loaded 1 mate pair 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
 Getting STELLAR matches from file, not calling STELLAR
Importing STELLAR matches from file stellar_joinedMates_l30.gff
done
TIME importing stellar matches 0.000439771s
Getting match distance...
Constructing graphs... done
Analyzing graphs... done
 completed gff writing pairedEnd_st1_l30.gff
 completed vcf writing pairedEnd_st1_l30.vcf
TIME all 0.0891324s
