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moiexpositoalonsolab / grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.
http://grene-net.org
GNU General Public License v3.0
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Grenepipe gets stuck in qualimap step #1

Closed florianhahn87 closed 3 years ago

florianhahn87 commented 3 years ago

Hey, looks like grenepipe would be super useful for us. Unfortunately, it seems to always get stuck in one of the final steps, namely in this command: java -Xms32m -Xmx1200M -classpath /lv01/home/hahn/downloads/grenepipe-0.2.0/.snakemake/conda/683a3dfbf01aef5bbb47865a237a8afc/share/qualimap-2.2.2a-1/* org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain bamqc -bam dedup/WT-1.bam -nt 2 -outdir qc/qualimap/WT-1 -outformat HTML

I attached a screenshot of the part where it gets stuck image

Is this a known problem and do you know a solution?

Cheers, Florian

lczech commented 3 years ago

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

florianhahn87 commented 3 years ago

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! image

lczech commented 3 years ago

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!

lczech commented 3 years ago

Also, can this issue be closed then?

florianhahn87 commented 3 years ago

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!