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hallamlab / metapathways2

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds
http://hallam.microbiology.ubc.ca/MetaPathways/
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The bundled metacyc-v5-2011-10-21 does not seem to 'work' #77

Closed gwilymh closed 7 years ago

gwilymh commented 9 years ago

I am running MetaPatways 2.5 in OS 10.6.8. Although my analyses consistently return functional categories for the SEED, CAZY and COG databases, for some reason no annotations are produced for the MetaCyc database. I.e. the ORF count is 0 for each Pathway/Reaction. I am using the metaCyc database that was bundled with the program, metacyc-v5-2011-10-21.

gwilymh commented 9 years ago

NB: I am selecting metacyc-v5-2011-10-21 from the Functional Annotation Parameters menu under Parameters.

ariahahn commented 9 years ago

Are you building pgdbs? The metacyc page in the GUI is different in that it actually displays pathways not annotations directly from the database like the other pages. In order to have annotations you must have successfully built a pathway genome database with pathway tools (one the final stages in MP 2.5). If yes, are there any errors?

Aria On 1 Sep 2015 10:11, "Gwilym Haynes" notifications@github.com wrote:

I am running MetaPatways 2.5 in OS 10.6.8. Although my analyses consistently return functional categories for the SEED, CAZY and COG databases, for some reason no annotations are produced for the MetaCyc database. I.e. the ORF count is 0 for each Pathway/Reaction. I am using the metaCyc database that was bundled with the program, metacyc-v5-2011-10-21.

— Reply to this email directly or view it on GitHub https://github.com/hallamlab/metapathways2/issues/77.

gwilymh commented 9 years ago

I don't think I was. That could well be the problem. I will run it now and see how it goes.

gwilymh commented 8 years ago

I have run an analysis on fasta file, selecting the metacyc-v5-2011-10-21 database and the ePGDB option. Metapathways ran to completion. While running, some gene pathway maps popped up on the screen. There were still no MetaCyc results under the results tab, or any errors in the log file that I could link with a lack of MetaCyc annotations. Any suggestions?

hallamlab commented 7 years ago

MetaCyc results only appear if a ePGDB was built - we are releasing a new version shortly that should help with these issues