Different blast results between CLCBio and local blast

[arundurvasula]

Hi,

I've been using CLCBio to blast assembled contigs, but it's really slow. I decided to try setting up a local blast database and using that to blast my contigs, but I'm getting different results even though I'm using the same parameters. The parameters are below:

CLCBio:

Query genetic code: 1 Standard
Limit by entrez query: All organisms
Filter low complexity
Expect: 10
Word Size: 3
Matrix: BLOSUM62
Gap cost: Existrence 11, Extension 1
Max number of hit sequences: 3

Local Blast:

blastx -db nr -query ../results/contigs/CLC-contigs.fa -evalue 10 -matrix 'BLOSUM62' -word_size 3 -gapopen 11 -gapextend 1 -max_target_seqs 3 -outfmt "10 std stitle" -out ../results/blast/blast-005.csv -num_threads 4

Since CLCBio and blast+ are using the same parameters and the same query sequence and the same database, I should the same results right? But I'm getting 226 hits in CLCBio that aren't in the local blast. Of these species, 2 are extremely important and are known to be in the query sequence.

Any ideas?

Thanks!