-
Notifications
You must be signed in to change notification settings - Fork 141
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Error running anvi-reaction-network
#2142
Comments
Hey @semiller10 , I think this error is occuring because the |
We used to solve similar situations with migration scripts that add new keys with None values. Perhaps that would be a better way to do it to ensure it is a constant part of every contigs-db? |
I set a value of None for that self variable in the migration script, and her contigs database has apparently been updated to v21, so I'm a little confused. |
Oh! Sorry for missing that! I wonder if there was a manual update of versions in the SQlite database :p |
For posterity, I see it here that it is indeed required to be a part of any contigs-db that is upgraded to https://github.com/merenlab/anvio/blob/master/anvio/migrations/contigs/v20_to_v21.py But is the variable also set for new contigs-db files that are not upgraded? The answer to that seems to be a No :) |
Exactly, I have since fixed that in a branch which I will now merge into master. I'll have her rerun with anvi'o dev and test. |
@IsabelFE Sorry for the bug. Would you mind installing the anvi'o development branch and regenerating your contigs database and rerunning If everything works, you can close out this issue. Thank you! |
Thank you, @semiller10. And thank you very much for the detailed report and helping us identify these problems, @IsabelFE. |
@IsabelFE I just fixed one other related thing in the development branch, so make sure the codebase is fully updated to this point before running |
I do have 117 contig databases fully annotated with all databases. Do I need to regenerate them? Or only redo the KEGG annotation? |
@IsabelFE In that case, I'll spare you the pain and waste of regenerating all of them. I'll post a little script here in a minute that you can run on each database to update it. It's a very simple fix involving three database "metavariables" that were not initialized with empty values when the databases were created. Then you can run |
@semiller10, a better solution may be to increase the version number of the contigs-db once again, and have a matching migration script so anyone who may have suffered from this would be forced to have the right version. My 2 cents. |
@meren Yes, I think that would be appropriate, so that other people working in v8 can be pointed to the dev branch rather than an ad hoc script. |
Hey @semiller10, just a heads up that |
@Mild-High the issue with the directory name was just fixed by Meren via commit bdfb50e and will be good to go in anvi'o dev :) |
@IsabelFE @Mild-High Very sorry for the delay in returning to this issue. Please find fixes in the anvi'o development branch to both of your problems: see pull request #2151 |
Hi @semiller10 I installed the development branch, ran |
@IsabelFE The two tables of reactions and metabolites hypothesized from the genome that are stored in the database may be more convenient to work with than a model file for your purposes. If you want to do this yourself now, they are called |
I was wondering if there was a way to export those tables. They get mentioned on the documentation, but I didn't know how to access them. |
I've just realized that anvio databases can be accessed via SQL, so I got hold of those tables. It will be useful to have a small description about what is encoded in each table and their corresponding columns. Thanks! |
@semiller10 I was able to get the tables from the anvio contig databases. Any recommendations on how to get started on visualizing the models. Maybe some pointers on how to get the files imported into Escher or any other recommended next steps? |
Thank you! I'm currently reaction networking away :) |
Short description of the problem
KeyError: 'reaction_network_ko_annotations_hash' when running
anvi-reaction-network
anvi'o version
System info
Mac Sonoma 14.0 (Chip M1). Anvio installed followed the instructions
Detailed description of the issue
I have a contigs.db file and when I try to run
anvi-reaction-network
I get this error:anvi-setup-kegg-data and anvi-setup-modelseed-database were run already
The text was updated successfully, but these errors were encountered: