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Troubleshooting

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Charlotte Soneson edited this page Nov 14, 2022 · 6 revisions
  • To check for errors in your inputs and parameter specifications, run
snakemake [--use-conda] --cores 1 checkinputs

  • For help with the software/R installation, please refer to the Managing software page.

  • If the snakemake error you get (typically starting with RuleException: CalledProcessError in line XXX of /ARMOR/Snakefile:) points to a Rmd file, or to a rule invoking an R script (e.g. edgeR, DRIMseq, tximeta), check the <output_folder>/Rout/ folder and look at the last .Rout or .txt file generated.

  • If you can't figure out the problem, open an issue and paste the code. We will contact you as soon as we can.

Home

  1. Preparing the input files
  2. The config.yaml configuration file
  3. Managing software
  4. Testing the setup
  5. Setting up the DGE analysis
  6. Running the analysis
  7. Expected output
  8. Visualizing results with iSEE
  9. Method description
  10. Managing multiple projects
  11. Troubleshooting
  12. Required resources
  13. Citing ARMOR
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