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SystemsGenetics / GEMmaker

A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction
https://gemmaker.readthedocs.io/en/latest/
MIT License
33 stars 16 forks source link

Permission denied #244

Open spficklin opened 2 years ago

spficklin commented 2 years ago

I'm getting the following error message when running GEMmaker

WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  #TRACE n_remote_run_ids=1
  Traceback (most recent call last):
    File "/opt/conda/envs/systemsgenetics-gemmaker-2.0.0/lib/python3.9/pathlib.py", line 1312, in mkdir
      self._accessor.mkdir(self, mode)
  FileNotFoundError: [Errno 2] No such file or directory: '/local/Projects/GEMmaker-test/work/GEMmaker/SRA_META/SRR/649/944'

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "/opt/conda/envs/systemsgenetics-gemmaker-2.0.0/lib/python3.9/pathlib.py", line 1312, in mkdir
      self._accessor.mkdir(self, mode)
  FileNotFoundError: [Errno 2] No such file or directory: '/local/Projects/GEMmaker-test/work/GEMmaker/SRA_META/SRR/649'

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "/opt/conda/envs/systemsgenetics-gemmaker-2.0.0/lib/python3.9/pathlib.py", line 1312, in mkdir
      self._accessor.mkdir(self, mode)
  FileNotFoundError: [Errno 2] No such file or directory: '/local/Projects/GEMmaker-test/work/GEMmaker/SRA_META/SRR'

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "/opt/conda/envs/systemsgenetics-gemmaker-2.0.0/lib/python3.9/pathlib.py", line 1312, in mkdir
      self._accessor.mkdir(self, mode)
  FileNotFoundError: [Errno 2] No such file or directory: '/local/Projects/GEMmaker-test/work/GEMmaker/SRA_META'

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "/home/ficklin/.nextflow/assets/systemsgenetics/gemmaker/bin/retrieve_sra_metadata.py", line 286, in <module>
      missing_runs = find_downloaded_runs(meta_dir, run_ids)
    File "/home/ficklin/.nextflow/assets/systemsgenetics/gemmaker/bin/retrieve_sra_metadata.py", line 212, in find_downloaded_runs
      run_dir = get_accession_directory(meta_dir, run_id)
    File "/home/ficklin/.nextflow/assets/systemsgenetics/gemmaker/bin/retrieve_sra_metadata.py", line 193, in get_accession_directory
      pathlib.Path(dir).mkdir(parents=True, exist_ok=True)
    File "/opt/conda/envs/systemsgenetics-gemmaker-2.0.0/lib/python3.9/pathlib.py", line 1316, in mkdir
      self.parent.mkdir(parents=True, exist_ok=True)
    File "/opt/conda/envs/systemsgenetics-gemmaker-2.0.0/lib/python3.9/pathlib.py", line 1316, in mkdir
      self.parent.mkdir(parents=True, exist_ok=True)
    File "/opt/conda/envs/systemsgenetics-gemmaker-2.0.0/lib/python3.9/pathlib.py", line 1316, in mkdir
      self.parent.mkdir(parents=True, exist_ok=True)
    [Previous line repeated 1 more time]
    File "/opt/conda/envs/systemsgenetics-gemmaker-2.0.0/lib/python3.9/pathlib.py", line 1312, in mkdir
      self._accessor.mkdir(self, mode)
  PermissionError: [Errno 13] Permission denied: '/local/Projects/GEMmaker-test/work/GEMmaker'

I only get this message when I run GEMmaker in a filesystem other than the directory where nextflow is caching the workflows. This goes away when I run it in the same file system. This is only happening on my local machine and needs more investigation...