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microbiomedata / metaMS

GC-MS Based Metabolomics Workflow
BSD 2-Clause "Simplified" License
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Issue with running MetaMS and minwidl #7

Closed Michal-Babins closed 3 years ago

Michal-Babins commented 3 years ago

For metaMS:

After following standard install procedure, when I run:

metaMS dump_json_template MetamsFile.json

Error:

Traceback (most recent call last):
  File "/home/mbabinski/miniconda3/bin/metaMS", line 5, in <module>
    from metaMS.cli import cli
ModuleNotFoundError: No module named 'metaMS'

For miniwdl:

After following installation, when I run:

miniwdl run wdl/metaMS.wdl -i wdl/metams_input.json --verbose --no-cache --copy-input-files:

Error:

task runMetaMS (wdl/metaMS.wdl Ln 5 Col 1) failed :: dir: "/panfs/biopan04/scratch-mbabinski/metaMS/20210624_134633_gcmsMetabolomics/call-runMetaMS", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied'))"

With docker image there was no issue.

Thanks! Michal

corilo commented 3 years ago

@Michal-Babins

for the min-wdl error: error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied'))

looks like you are having issues pulling the docker image from the registry, make sure you are logged on docker registry

for the metaMS cli error,

I confirmed that PyPi package release is not working, but the installation from source works. The recommendation is to install it from source, clone codebase and install (pip3 install --editable .), until a solution for the PyPi package is found.

Regards,

Yuri

corilo commented 3 years ago

PyPi package has been fixed, setup code has been update and and a new version uploaded of the package release on PyPi (2.1.3),

Michal-Babins commented 3 years ago

Command works when installing from source. But looks like I am getting back an issue with sql database:

With:

metaMS run-gcms-workflow /panfs/biopan04/scratch-mbabinski/metaMS/data/MetamsFile.json

Error: sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) unable to open database file

corilo commented 3 years ago

Yes, that is expected, the database is not yet provided, since it contains proprietary data. We are working and expect to provide the open source molecular reference data early next year.

You can change to point to you sqlite file here: data\CoremsFile.json here:

"url_database": "sqlite:///db/pnnl_lowres_gcms_compounds.sqlite",

details of the db structure is here:

https://github.com/EMSL-Computing/CoreMS/blob/stable/corems/molecular_id/factory/EI_SQL.py