documented_errors.txt

#check our errors report
1- Github API Rate Limit Exceeded when installing SCDC, bseqsc etc.:
  Reason: Gıthub API limit is ~60 downloads, this crash only happens in the first
  run of a new workflow
  
  

  Action: Generated public PAT token integrated to scripts, 
  In case of errors, contact repo owner.



2- Cannot solve least square algorithms, singular
  Reason: Random sampling creates very similar bulk samples (mean cosine 0.99)
  therefore, there is not enough variance inbetween columns to solve the system

  Action: Either remove crashing method & restart, or use mode 2 with high
  propvar.



3- Cluster exits job with code 120 after stopping for no apparent reason

  Action (Not consistent): Remove all outputs after cell splits manually before
  restarting the run.



4- DWLS dims dont match
  Reason (Most likely): No significant genes found during MAST DGE tests in
  DWLS, returns NA with no dims.

  Action: Use sqrt transform instead of log, or remove method through config.



5- Errors in environments
  Reason (Most likely): A package has been moved from CRAN or github to another
  location

  Action: Download source and build package from source within pipeline.



6- Methods making use of C2 fail
  Reason (Most likely): No differentially expressed genes could be found for
  a cell type.

  Action: Remove failed methods or change dge tests in config. Changing norm
  method could also help.
  


7- Conda checksum error during first run
  Reason: One of the packages in the environment where the crash occurs is corrupt
  
  Action: Remove build info + version info, if still fails downgrade.



8- Mamba error cannot lock package cache
  Reason: First time running more than one pipeline, one of them cant lock the pkgs
  because the other already locked it
  
  Action: First runs should be done one by one.