Question: blastn --remote option skipping sequences
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gravatar for eli_bayat
4 months ago by
eli_bayat20
eli_bayat20 wrote:

I am using the below command line to run blast on my sequences:

blastn -db nt -query $inputfile -outfmt "6 qseqid evalue bitscore stitle" -out $outputfile -remote

However, when I run blast on multiple files at the same time, some of the sequences are skipped and I end up with lower number of sequences than there are in my original file. I assumed there should be some CPU limit issue, or max requests issue. Is there anyway to know the limits? How can I ensure I stay under them? Thanks

blast command-line • 202 views
ADD COMMENTlink written 4 months ago by eli_bayat20

I don't know if the new limits put in place for web blast apply to the -remote option (they likely do). You can see them here : https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews

You can try setting the e-value explicitly to a higher value (default is now 0.05).

ADD REPLYlink modified 4 months ago • written 4 months ago by GenoMax95k

Thank you for the link. It is very helpful. Do you mean if I set the e-value higher, the probability that the blast skip sequences is lower?

ADD REPLYlink written 4 months ago by eli_bayat20

How many sequences were you passing to blast? And incidentally, what version of blast are you using?

ADD REPLYlink written 4 months ago by Dunois490

I have multiple Fasta files and I blast each in parallel. So over all I passed 6845 sequences each has around 6000 positions. The version is 2.9.0. When I do blast individually, meaning I blast one file and wait till its done and then blast the next one, it skips a lot less compare to when I run all of the in parallel.

ADD REPLYlink modified 4 months ago • written 4 months ago by eli_bayat20

That's really strange that anything's getting skipped at all. These sequences that get skipped, do they have matches when they're blasted individually? What database are you searching against, by the way?

ADD REPLYlink written 4 months ago by Dunois490
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