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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
Calling STELLAR...
Stellar options:
Database file : adeno.fa
Query file : adeno_modified_reads.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 0.104487s
done
Getting match distance...
Constructing graphs... done
Analyzing graphs... done
completed gff writing st1_l30.gff
completed vcf writing st1_l30.vcf
TIME all 0.262024s
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