blastn --remote option skipping sequences

Question

[eli_bayat]

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

[GenoMax]

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).

[eli_bayat]

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?

[Dunois]

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

[eli_bayat]

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.

[Dunois]

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?