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AuReMe / metage2metabo

From annotated genomes to metabolic screening in large scale microbiotas
https://metage2metabo.readthedocs.io
GNU Lesser General Public License v3.0
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CRITICAL:metage2metabo.m2m.reconstruction:Something went wrong running Pathway Tools. See the log file in /home/chencong/output3/pgdb_log/log_error.txt #46

Closed ChenCongZ closed 1 year ago

ChenCongZ commented 1 year ago

Hi @cfrioux, It alerted me to this problem when I used the recon pipeline.

Screenshot from 2022-11-26 15-27-49

cfrioux commented 1 year ago

Hi. It says there is no pgdb ID for fatty acid oxydation in taxon_id.tsv. So this is what you should fix.

ChenCongZ commented 1 year ago

Hi @cfrioux, Thank you! I fix the problem, but I encountered a problem of Frame name "ESCHERICHIA COLI K12 MG1655" contains the illegal character" However, I didn't find the root cause of this issue. Screenshot from 2022-11-26 19-50-17

cfrioux commented 1 year ago

The error says that the space is a problem. Try removing the spaces?

ChenCongZ commented 1 year ago

Hi @cfrioux, Thank you! I apologize for time zone issues. I will pay attention to this issue later. I'm trying to run my data and test data and having this issue. Screenshot from 2022-11-27 09-20-45 Screenshot from 2022-11-26 21-25-21

ChenCongZ commented 1 year ago

Hi @cfrioux, Hi @ArnaudBelcour, Thank you for your help. I have solved the problems I encountered before, but I didn't see this function when I created the seed file ( from metabolites file (.txt) to seed file (.sbml)). Can you teach me some command lines about it? QQ截图20221201203136

cfrioux commented 1 year ago

The command line is in the screenshot you just attached, together with the input file structure. If you solved your problems, I'll close the issue.