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Old 03-29-2012, 09:54 AM   #1
Junior Member
Location: Germany

Join Date: Mar 2012
Posts: 4
Exclamation using blast+ for remote blasting

Hi I'm trying to run a remote blastn search from linux command line.
Here's my working syntax for doing this with blastcl3, which is now deprecated:

blastcl3 -p blastn -i seqs.fasta -p blastn -d nr -o blast.out -T -K 1

I'm trying to translate this to the new blast+ syntax.
This is what I thought should work:

blastn -task blastn -remote -db nr -query suspected.seqs.fasta -evalue 0.00001 -dust no -max_target_seqs 1 -html -out output.blastn.html

but what happens is that the computer hangs for about 20 min and then spews the following error about 100 times:

Error: Error: internal_error: (Severe Error) Blast search error: Details: search failed. # Informational Message: [blastsrv4.REAL]: Error: CPU usage limit was exceeded, resulting in SIGXCPU (24).

any suggestions?

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Old 03-29-2012, 11:02 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

How many query sequences do you have? If lots, that explains the NCBI CPU limit. You might be better off running it locally.
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Old 03-29-2012, 03:30 PM   #3
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Location: Germany

Join Date: Mar 2012
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The query file contains about a 100 sequences, which doesn't sound a lot to me.
the old blastcl3 doesn't seem to have any problem with that.
In any case I tried running blastn with 1 sequence and I get the right restult, but if the new function isn't working as well as the old one why are the people at NCBI deprecating it?!

Is my syntax wrong maybe? is there a way to optimise it?

thanks again
rangel is offline   Reply With Quote

blast, blast+, command line

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