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command line Ncbi Blast SRA remote

I am willing to make a bunch of blast queries in ncbi hosted SRA datasets.

The blast query is fast, I want to search for two short sequences X and Y in SARS-CoV-2 datasets, Y is a mutated version of X, and stop when 100 reads are found, in order to find if sometimes Y appears as a minority variant of X, and conversely.

It seems this is not allowed (anymore?), neither by the blast Web API nor by the blastn command line executable.

So this fails blastn -db SRX10000025 -query XY.fasta -remote -out blast_output.out as well as github/srablast and blast/Web API.

On the other hand the blast interface allows to do it for one SRA.

Is there any way to get over this?

ncbi blast sra

Sometimes the SRA request works too, but more frequently it fails with

Non-interactive SRA BLAST searches not supported. User IP address: 235.175.46.207

1 answer

NCBI moved SRA database into amazon/google cloud last year. That may be one of the reasons why one can't do a remote blast against entries in SRA database.

NCBI's blast web application is likely using a private link to enable web based SRA blast searches.

Clearly blasting SRA is more computationally expensive, no it is natural that there are some restrictions, but I don't understand what ncbi is wanting me to do. Ncbi mentions blasting on the amazon cloud but I don't understand how it works. I think I am just going to make a chrome extension faking to be clicking on the buttons of the web interface..

(by the way some SRA seem to lack a blast DB, we can see the reads but not blast. A blast DB is just the list of the 8-letters words and where they are appearing in the NGS data?)

This does come with a risk that NCBI may flag your IP and your computer may be banned from using web blast.

NCBI makes a special database available for SARS-CoV-2 data (LINK, look under BLAST_DB). Perhaps you can download that database and use it locally.

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