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NBISweden / GenErode

GitHub repository for GenErode, a Snakemake pipeline for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.
GNU General Public License v3.0
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Problems running pipeline in Uppmax using the rhinos test dataset and slurm profile #50

Closed apfuentes closed 3 months ago

apfuentes commented 1 year ago

Dear GenErode team,

First of all, thank you for developing this great tool.

I have been trying to run the pipeline in Uppmax on the test dataset of rhinos provided in the Wiki and the slurm profile, but it fails. I have examined various things, and even deleted and reinstalled both the pipeline and the condo environment several times, without luck. Thus I wonder if any of you could help me identify the source of the problem to fix it?

Attached, please find a PDF (markdown) summarising the steps followed, as well as the input and output/log files of the pipeline.

Thanks in advance for any help!

Best regards,

Angela

Troubleshooting_problem_running_test_dataset_GenErode_in_Uppmax.pdf help_files.zip

johnne commented 1 year ago

Hi Angela, As a first step, could you run conda list > generode.packages.txt (with your generode environment activated) and upload that txt file with conda package versions here?

johnne commented 1 year ago

Can you also run (with generode environment activated):

which python

and 

module list

and supply the output here please