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Getting "Object is not coercible to a frame for KB METACYC 22.0" Error when creating PGDB using Pathologic

asked 2019-12-26 01:28:13 -0500

Chris gravatar image

Version of Pathway Tools: 23.0 Platform: Windows 10 Error Message: Object "D-Tryptophanyl-tRNA-Trp" is not coercible to a frame for KB METABASE-22.0

I am trying to create a PGDB using PlantCyc13.0 database as reference using Pathologic. After parsing the GenBank file of the organism, specifying PlantCyc as reference and running the "Trial Parse", I encountered this warning:

"The PGDB PlantCyc (PlantCyc) was built with, or at last upgraded to Pathway Tools version 21.5, and may be incompatible with the current Pathway Tools version 23.0. Do you wish to upgrade now? Before upgrading, the current stat of the PGDB will be saved and a new PGDB version created. A log of changes will be saved to ... Alternatively, you may choose to upgrade for the current session only, but not create a new version, log changes or save the upgraded PGDB."

Upon choosing either of the available options "Upgrade Now (Recommended)" or "Upgrade for Current Session Only", I encountered the error 'Object "D-Tryptophanyl-tRNA-Trp" is not coercible to a frame for KB METABASE-22.0'.

Here's the log of what I did:

--- Starting upgrade process for PLANTBASE: Start version: 21.5 Target version: 22.0

--- Upgrading PLANTBASE from version 21.5 to version 22.0. [Loading Ocelot KB from C:\Program Files\Pathway Tools\aic-export\old-metacyc-versions\22.0\metabase-22.0.ocelot KB name=METABASE, format=V4-FASL 230456 frames loaded]

Current metacyc: C:\Program Files\Pathway Tools\aic-export\old-metacyc-versions\22.0\metabase-22.0.ocelot (#'UPGRADE-V21.5-KB-TO-V22.0-KB) [Upgrading PLANTBASE to Pathway Tools 22.0]

-- Updating PLANTBASE with respect to METABASE-22.0

Converting CPD0-1104 from an instance to a class Importing the following 1241 classes:

Printing 1241 objects

"Activated-tRNA"
'activated' tRNA
"DMNT-Biosynthesis"
(3E)-4,8-dimethylnona-1,3,7-triene biosynthesis "5Z-Dodec-5-enoate-Biosynthesis" (5Z)-dodecenoate Biosynthesis .... "YHAV-DEGRADATION-SUBSTRATE-MRNA" YhaV endonuclease degradation substrate mRNA "YHAV-DEGRADATION-SUBSTRATE-RRNA" YhaV endonuclease degradation substrate rRNA

Error: Object "D-Tryptophanyl-tRNA-Trp" is not coercible to a frame for KB METABASE-22.0 [condition type: NOT-COERCIBLE-TO-FRAME]

I'm wondering if there's any fix to this? Or is it possible to specify the MetaCyc version run by Pathologic such that I can circumvent upgrading my database entirely?

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answered 2019-12-27 02:35:12 -0500

Suzanne Paley gravatar image

updated 2020-01-02 19:02:24 -0500

Hi Chris, SRI is currently shut down for the holidays, so most likely no-one will be able to look into this until after Jan 1. I will see if I can reproduce the problem then, and then hopefully make a fix available. If I can't reproduce the problem myself, I will need a stack backtrace from you. Was an error.tmp file generated in your home directory? If so, can you please send it to us at ptools-support@ai.sri.com. Or did the software break into the debugger, and leave you at a debugger prompt in your terminal window? If so, please type :zoom to the debugger prompt and send us the output.

Suzanne

Edit: Back again. I don't have access to a Windows machine, but I was successfully able to upgrade plantcyc on both linux and mac without encountering this error using both pathway-tools version 23.0 and our latest 23.5 (I did encounter a different later error, which has now been patched). I suggest you install the latest pathway-tools version (23.5), and open plantcyc immediately upon startup (i.e. before invoking pathologic) and do the upgrade from there. If you still encounter the same problem, send us the debugging information I requested above.

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Asked: 2019-12-26 01:28:13 -0500

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Last updated: Jan 02