CRITICAL:metage2metabo.m2m.reconstruction:Something went wrong running Pathway Tools. See the log file in /home/chencong/output3/pgdb_log/log_error.txt

[ChenCongZ]

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

[cfrioux]

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

[ChenCongZ]

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.

[cfrioux]

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

[ChenCongZ]

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.

[ChenCongZ]

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?

[cfrioux]

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.