Grenepipe gets stuck in qualimap step about grenepipe HOT 5 CLOSED

We found this error message in the log file:
WARNING: out of memory!
Qualimap allows to set RAM size using special argument: --java-mem-size
Check more details using --help command or read the manual.

That is how we figured it out :)
Sure, it can be closed, thanks!

from grenepipe.

Hi Florian,

glad to hear that you find grenepipe useful!

I am not entirely sure what is going on there and what the issue actually is - so no, this one in particular is not a known problem. It most likely is some snakemake/conda issue, and has nothing to do with grenepipe itself. These things happen from time to time, but that would be up to snakemake and conda to fix...

Firstly, I am not entirely sure what the issue actually is. You write that it comes from the Java command that runs qualimap, but the screenshot shows the merge call step. How did you extract/infer that Java command?

Secondly, if it is due to conda, you could try to remove all conda environments, and have snakemake download them again. For this, do rm -rf /lv01/home/hahn/downloads/grenepipe-0.2.0/.snakemake/conda, and then try again.

Hope these hints help - if not, we will have to dig deeper.
Lucas

from grenepipe.

Thanks for the feedback! Seems it was a RAM size problem of Qualimap. We could solve it by assigning more RAM space in the config.yaml file to Qualimap (see below). Thanks a lot!

from grenepipe.

Oh interesting, thanks for the feedback! Yeah, Java can be weird... May I ask how you figured this out? Might be interesting for future reference!

from grenepipe.

Also, can this issue be closed then?

from grenepipe.