lbcb-sci/ra

Cannot find minimap2

Opened this issue · 2 comments

nadegeguiglielmoni commented

Hello,

I am having trouble to run Ra on a cluster. I tried on two different clusters, and get this:
[Ra::run] preconstruction overlap stage [Ra::run] error: unable to run minimap2!
But minimap2 is in my PATH. How can I make sure it finds minimap2?

rvaser commented

Hi Nadege,
it is probably due to Ra being a python script connecting Minimap2, Rala and Racon. Try manually editing the ra.py script you are running by setting the right paths for all three tools. Add full paths at lines 13-15.

If I may ask, why are you using Ra instead of Raven?:)

Best regards,
Robert

nadegeguiglielmoni commented

Seems to work better. I have to wait for the job to run though.
I am using Ra and Raven because I still get sometimes on some genomes better results with Ra, so I test both.

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