Question: Remote Blast sometimes failing
2
gravatar for aenigma
2.1 years ago by
aenigma20
Germany
aenigma20 wrote:

Hello,

I'm trying to find those of a subset of species without a certain protein.

For this, I tried to use blast-2.2.31+ (newest version) remote feature with an entrez queries limiting it to those species, e.g.:

blastp -query sequence.fa -db nr -remote -entrez_query "txid387662 [ORGN]" -evalue 10E-3 -outfmt "7 sseqid pident positive evalue staxids"

And sometimes it works, sometimes it doesn't terminate within an hour (usually doesn't take a minute), sometimes it only returns 

# BLAST processed 1 queries

and I don't know why... I'm guessing the remote feature isn't that stable...

 

Any help is appreciated :)

blast entrezquery genome • 604 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by aenigma20
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