observed issues with omission of '--dna ,-o' option in command about carveme

[cdanielmachado]

Hi @rdmtinez,

Thanks for the detailed description. Why are you using the -r option with a single genome file?

Would you mind just trying again without the -r and see if the problem persists ?

Also, if you are using .fna files (i.e. nucleotide sequences) you must always use the --dna option.

[rdmtinez]

Greetings @cdanielmachado,

I used -r because it was a batch process I was running when I noticed the errors and forgot to delete it during my post--just a typo really.

-Ricardo

[cdanielmachado]

Hi Ricardo,

I am not sure if I understand what is the issue you are trying to submit here...

If I understand correctly, you are saying if the correct options are not provided, things do not work as expected.

If you give the program nucleotide sequences without the --dna flag it fails.

If you do not give the -o option, things don't go into the expected output folder.

Is that correct?

[rdmtinez]

That exactly right @cdanielmachado ... I had some typos in my code and then I realized these things so I decided to post about it. It was just surprising to see the "output" being a folder with the given name rather than some file when '-o' is omitted and decided to mention it.

[cdanielmachado]

Ok, I think I understand it a bit better now.

All arguments which are not preceded by a flag are considered to be input files. Therefore, when you omit the -o flag, it will take your second argument, and assume it is a second genome file.

If you don't use the -r option, you get the following error:

carve: error: Use -r when specifying more than one input file

But because you used -r, it assumed you were giving it multiple genome files to run in parallel. Diamond will receive your output folder as a genome file to process, and it will fail.

I think there is really nothing that can be done here. It is normal for command line tools to fail when you don't specify the arguments correctly.