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Trying to create PGDB and getting "Object is not coercible to a frame for KB UNBASE"

asked 2016-03-25 10:46:59 -0500

Avid gravatar image

updated 2016-03-25 13:06:24 -0500

Version of Pathway Tools: 19.5 Platform: Ubuntu 14.04.4 Error message: Object G18PS-6734 is not coercible to a frame for KB UNBASE

I have a genome split up into two .gbk-files and need to create a unified PGDB using PathoLogic, but when I try to build the database, after parsing it, I get an error in the console saying "Object G18PS-6734 is not coercible to a frame for KB UNBASE"

I'm throwing stuff at the wall to see what sticks now, I might be off on a completely wrong tangent, but this is what I've been looking into, and hopefully this could help you understand what I've been doing:

These are the settings I'm using:

Pathologic Project window: Create Organism: Yes, because I'm using an unpublished genome.

Everything else set to default except for the taxonomic class, full species name and abbreviated species name.

Specify Replicons window:

Type: Chromosome

Circular: Yes

Code: Bacterial

Then I click "Add contig", I do not click "New", add the second .gbk-file and use the exact same settings as above, the rest is set to default.

I can run a trial parse successfully, and when I run "Automated Build" I get to set the Pathway Scoring Parameters, I leave them untouched, and then this error message appears in the terminal window, I added a backtrace too:

[Indexed class Growth-Media of 1 frames yielding hash table of 2 entries]
[Indexed class Extragenic-Sites of 3 frames yielding hash table of 4 entries]
[Indexed class Organisms of 27 frames yielding hash table of 110 entries]
[Indexed class Transcription-Units of 0 frames yielding hash table of 1 entries]
[Indexed class Gene-Ontology-Terms of 3 frames yielding hash table of 13 entries]

[Indexed class DNAs of 14 frames yielding hash table of 26 entries]
[Indexed class Reactions of 40 frames yielding hash table of 51 entries]
[Indexed class Pathways of 591 frames yielding hash table of 893 entries]
[Indexed class Enzymatic-Reactions of 0 frames yielding hash table of 0 entries]
[Indexed class RNAs of 200 frames yielding hash table of 425 entries]
[Indexed class All-Genes of 252 frames yielding hash table of 492 entries]
100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000 2100 2200 2300 2400 2500 2600 2700 2800 2900 3000 100 200 300 400 500 600 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000 2100 2200 2300 2400 2500 2600 2700 2800 2900 3000 100 200 300 400 500 600 500 500 
1000 500 
Error: Object G18PS-6734 is not coercible to a frame for KB UNBASE
  [condition type: NOT-COERCIBLE-TO-FRAME]

Restart actions (select using :continue):
 0: Return to PathoLogic command level
 1: PathoLogic top level
 2: Exit PathoLogic
 3: Abort entirely from this (lisp) process.

[changing package from "COMMON-LISP-USER" to "ECOCYC"]
[Current process: PathoLogic GUI]

[1] EC(1): :zoom :count :all
Evaluation stack:

   (ERROR NOT-COERCIBLE-TO-FRAME :FRAME ...)
 ->((METHOD OCELOT::OCELOTFR ...
(more)
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answered 2016-04-05 13:08:54 -0500

latendresse gravatar image

We are working to find a solution.

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answered 2016-09-02 14:53:04 -0500

latendresse gravatar image

Hello,

Could you try again and let us know the result? Version 20.0 of Pathway Tools might also have a more complete fix as it was more difficult to fix it in version 19.5.

Best regards,

-- Mario Latendresse

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Asked: 2016-03-25 10:46:59 -0500

Seen: 475 times

Last updated: Sep 02 '16