Question: Remote Blast sometimes failing
2
gravatar for aenigma
23 months 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 • 562 views
ADD COMMENTlink modified 23 months ago • written 23 months ago by aenigma20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 755 users visited in the last hour