Trying to run ShortStack with the --knownRNAs argument, it does not work

[ozambadam]

Hi, I am trying to run this package using the --knownRNAs function and It is not recognized:

`Unknown option: knownrnas

Unknown arguments: 6 ../sly_miRBase.fa`

[MikeAxtell]

The option is --knownRNAs with capital letters for RNA.

[ozambadam]

I am using capital letters.

My command is:

ShortStack --genomefile ../TPMVd_genome.fa --readfile *.fq --threads 6 --outdir with_DB --knownRNAs ../sly_miRBase.fa

Still doesn´t work

[MikeAxtell]

You are running ShortStack version 3.8.5, as the output that you pasted says ShortStack version 3.8.5. You have not installed version 4.0.0. Only version 4.0.0 has the option --knownRNAs.

Conda and bioconda can be a challenge sometimes especially if conda is cacheing repo lists and not checking for updates.

Assuming you were using conda, try:

• double check your conda config. You need to have the channel priority settings as described by Bioconda https://bioconda.github.io
• ensure that conda search shortstack lists version 4.0.0
• try specifying the version of ShortStack : conda create --name ShortStack4 shortstack=4.0.0

[MikeAxtell]

This is likely part of an ongoing issue / defect in conda (not ShortStack) ... there are cases where just calling conda install [tool] does not give the latest version of the tool. There are lots of discussions about this conda issue. For instance:

https://github.com/bioconda/bioconda-recipes/issues/24199

https://github.com/conda/conda/issues/9905

You can also try two steps, and specifying the release you wish to obtain:

conda create --name ShortStack4 conda install shortstack=4.0.0

[ozambadam]

Thanks a lot, it is working now