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XPRESSyourself / XPRESSpipe

An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data
https://xpresspipe.readthedocs.io/en/latest/
GNU General Public License v3.0
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P-site QC not processing #36

Closed j-berg closed 4 years ago

j-berg commented 4 years ago

Describe the bug Pipeline gets stuck on p-site QC. These seems to be a recurrent issue where the pipeline runs into issues with running riboWaltz consistently. Will try to get to the issue this weekend.

To Reproduce Steps to reproduce the behavior:

  1. Run general riboseq pipeline

Screenshots

Generating P-site meta profiles...
Traceback (most recent call last):
  File "/uufs/chpc.utah.edu/common/home/$USER/miniconda3/bin/xpresspipe", line 11, in <module>
    load_entry_point('XPRESSpipe', 'console_scripts', 'xpresspipe')()
  File "/uufs/chpc.utah.edu/common/home/$USER/XPRESSpipe/xpresspipe/__main__.py", line 734, in main
    make_periodicity(args_dict)
  File "/uufs/chpc.utah.edu/common/home/$USER/XPRESSpipe/xpresspipe/periodicity.py", line 149, in make_periodicity
    index_col=0)
  File "/uufs/chpc.utah.edu/common/home/$USER/miniconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 685, in parser_f
    return _read(filepath_or_buffer, kwds)
  File "/uufs/chpc.utah.edu/common/home/$USER/miniconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 457, in _read
    parser = TextFileReader(fp_or_buf, **kwds)
  File "/uufs/chpc.utah.edu/common/home/$USER/miniconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 895, in __init__
    self._make_engine(self.engine)
  File "/uufs/chpc.utah.edu/common/home/$USER/miniconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 1135, in _make_engine
    self._engine = CParserWrapper(self.f, **self.options)
  File "/uufs/chpc.utah.edu/common/home/$USER/miniconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 1917, in __init__
    self._reader = parsers.TextReader(src, **kwds)
  File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.__cinit__
  File "pandas/_libs/parsers.pyx", line 689, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] File b'/scratch/general/lustre/$USER/7794015/output/p_site_qc/metrics/annotation.txt' does not exist: b'/scratch/general/lustre/$USER/7794015/output/p_site_qc/metrics/annotation.txt'

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Additional context Add any other context about the problem here.

j-berg commented 4 years ago

Works perfectly fine with R 3.5.1, doesn't like 3.6. May need to restrict R version allowed on install

j-berg commented 4 years ago

For whatever reason, it does not like having all row subplots filled for the periodicity graphs. Currently adding a filler row which seems to keep it happy for now. Will need to look into this further at a later time to get past this issue. Seems to not be an issue for single-column multi-row plots. See 5751fc6 for fixes.