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mmundy42 / mackinac

Mackinac: A bridge between ModelSEED and COBRApy
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Problems retrieving models from PATRICK/RAST #3

Open hakonda opened 6 years ago

hakonda commented 6 years ago

Hi I'm not able to genereat/retrieve models in PATRICK using mackinac. Any help would be appreciated.

This is what I've done: -installed mackinac 0.8.4 in a virtual environment with python 3.5.0 -uploeaded a genome to PATRICK and annotated it. -uploaded the geome to RAST and annotated it (and made metabolic model) -made a metabolic model in modelseed with genome retrieved from RAST. -made a metabolic model in PATRICK.

attempts to use mackinac

1) mackinac.reconstruct_modelseed_model('928852.5') ## this is the id listed for my genome in PATRICK Output: nothing happens for a long time until I get a long error meassage which ends with: read timeout=1800. Besides, I see that a job has been qued in my patrick workspace (RunProbModelSeedjob).

2) mackinac.reconstruct_modelseed_model('928852.3') ## this is the id of my genome in RAST Output: same as for 1)

3) mackinac.reconstruct_modelseed_model('226186.12') ## this is the id for a publically avilable genome in PATRICK Output: same as for 1)

4) various attemts using mackinac.create_cobra_model_from_modelseed_model(id) # where id is the id listed in http://modelseed.org/my-models/, or RAST id or PATRICK id Output: long error message ending with "mackinac.SeedClient.ObjectNotFoundError: An object was not found in workspace: "/hakonda@patricbrc.org/modelseed/id" (so how do I get my model into /hakonda@patricbrc.org/modelseed?)

What am I doing wrong?

Cheers Hakonda

mmundy42 commented 6 years ago

You are not doing anything wrong. The reconstruct function in the ModelSEED server is not working and that is why you are having trouble.

I'm adding support for the PATRIC server but I'm not quite ready to release a new version of mackinac. If you look in the devel branch on GitHub there is a new patric.py module that has the support for using the PATRIC server. I'm hoping to release a new version soon but feel free to try the code from the devel branch.

hakonda commented 6 years ago

Thanks for the info. I'm looking forward to the new release :)