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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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Error in loadNamespace(x) #304

Closed xiaoyuppp closed 2 years ago

xiaoyuppp commented 2 years ago

Hi Team, congrats on the awesome software! I am working on the analysis of a skin single cell sequencing dataset utilizing 10X Genomic. I am having issues with the counting step of the zUMIs pipeline.

I created a virtual environment for R3.6.0 using Conda and “plyranges” was successfully installed. When I activated the virtual environment and tried “library (‘Plyranges’)”, these processes didn't have any problem.

library plyranges

But when I actually run zUMIs.sh, the nohup.out file tells me: “Error in loadNamespace(x) : There is no package called 'Plyranges'.” I don't know how to solve this problem. And there are also error messages: “Error in gzfile(file, "rb") : Unable to open the link.” I suspect this problem may be related to the error above. I was hoping you could help me troubleshoot this issue. Would appreciate any input.

My nohup.output files look like this: nohup.out.txt

yaml file: Skin-T-F-1_zUMIs_run.txt

Some basic information:

basic information
cziegenhain commented 2 years ago

Hi,

Sorry for the slow reply - I missed this post.

Instead of setting up a conda environment yourself, I recommend using the integrated one within zUMIs. It could otherwise be a configuration issue of your system depending on which binary "Rscript" you default to.

so, please use the -c flag for the zUMIs integrated miniconda. /data/pxyy/workspace/zUMI/zUMIs/zUMIs.sh -c -y Skin-T-F-1_zUMIs_run.yaml

Best, Christoph