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Error: KB is NIL in GET-SLOT-VALUE

asked 2021-06-16 17:12:18 -0500

anonymous user

Anonymous

Hello,

I was trying to create a new PGDB in Pathologic and got the following error:

Error: KB is NIL in GET-SLOT-VALUE

I'm using Pathway Tools 24.5 on a Mac Catalina 10.15.7

Thanks for any advice you can provide!

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answered 2022-03-14 11:35:14 -0500

pbourceau gravatar image

updated 2022-03-14 11:40:12 -0500

Had the same problem with gbk files from RAST. Absolutely weird but working solution: Download gff files from RAST, then choose those to import. Pathway tools gives a warning there are no sequences but you can add them later. Then after setting up the new database go to Build > Specify Replicons and there select the gbk file as the annotation file. No need to specify a sequence file, it is all in the gbk file, and for some reason it now works fine with the exact same files which gave the error when trying to import them directly.

https://iili.io/EsPTle.md.png (image description)

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answered 2021-06-19 17:12:10 -0500

Suzanne Paley gravatar image

Hi, it's impossible to debug this without a stack backtrace. In the terminal window, you should see a debugger prompt. Type

:zoom :count :all

to the debugger prompt, and send the output, plus a description of the problem to ptools-support@ai.sri.com.

One possible other thing to try: before invoking PathoLogic, select MetaCyc as your current database. You could also try upgrading to PTools 25.0. Assuming neither of those help, follow the reporting instructions above.

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Asked: 2021-06-16 17:12:18 -0500

Seen: 581 times

Last updated: Mar 14