search

databio / peppro

A modular, containerized pipeline for PRO-seq data processing
http://peppro.databio.org/
BSD 2-Clause "Simplified" License
9 stars 2 forks source link

invalid error message when assets not found #72

Open stolarczyk opened 4 years ago

stolarczyk commented 4 years ago

The suggested CLI args are None for some reason. 

looper run examples/meta/peppro_test.yaml --compute bulker_local
...

Some assets are not found. You can update your REFGENIE config file or point directly to the file using the noted command-line arguments:

### Pipeline failed at:  (03-31 17:04:13) elapsed: 0.0 _TIME_

Total time: 0:00:01
Failure reason: Required assets not existing: fasta.chrom_sizes:default (--None), fasta.None:default (--None), bowtie2_index.None:default (--None)
Traceback (most recent call last):
  File "/Users/mstolarczyk/Uczelnia/UVA/code//peppro/pipelines/peppro.py", line 3867, in <module>
    sys.exit(main())
  File "/Users/mstolarczyk/Uczelnia/UVA/code//peppro/pipelines/peppro.py", line 1988, in main
    res, rgc = _add_resources(args, res, check_list)
  File "/Users/mstolarczyk/Uczelnia/UVA/code//peppro/pipelines/peppro.py", line 1868, in _add_resources
    pm.fail_pipeline(IOError(err_msg.format(", ".join(["{asset_name}.{seek_key}:{tag_name} (--{user_arg})".format(**x) for x in required_list]))))
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pypiper/manager.py", line 1660, in fail_pipeline
    raise exc
OSError: Required assets not existing: fasta.chrom_sizes:default (--None), fasta.None:default (--None), bowtie2_index.None:default (--None)