gravatar for DR

2 hours ago by

European Union

Hi there!

So I have this problem I have been struggling with the entire day and I am running out of ideas to test what's going on. Let's see if you have any suggestion..

I am trying to blast some genomes and I want to do it in parallel by using a snakemake pipeline.

Here the basic command:

blastn -db plsdb.fna -out {output} -query {input}

And here the error:

Error:  (CArgException::eSynopsis) Too many positional arguments (1), the offending value: 2.blastn

I feel like I've tried everything. I changed the order of the arguments. I had modified the name of the input-output files to make sure there is no funny character. I put everything on the same folder where I run the blast...

Now, here it comes the interesting part: when I do type the command without the wildcards (let's say in the example this would be blastn -db plsdb.fna -out 2.blastn -query 2.fna, it will work just fine.

I have no idea whatsoever what may be happening here. If someone has encountered the same problem or has any suggestion it would be highly appreciated.



modified 2 hours ago



2 hours ago


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