Comments (6)
Can you send me the log file, as shown in Run_MFAToolkit.sh:
/Users/student/Desktop/ModelSEED/Model-SEED-core/logs/fba-14.log
from model-seed-core.
Hi Sam,
I am attaching the log file.
Thanks,
Aaron
On Thu, Jun 7, 2012 at 1:10 AM, samseaver <
[email protected]
wrote:
Can you send me the log file, as shown in Run_MFAToolkit.sh:
/Users/student/Desktop/ModelSEED/Model-SEED-core/logs/fba-14.log
Reply to this email directly or view it on GitHub:
from model-seed-core.
I think I know what the problem is.
Can you double-check your model in:
/Users/student/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/MFAToolkitOutputFiles/14/Seed211586.9.1.tbl
to see if it has a biomass reaction?
I know that one problem we get is that the code seg faults if the model does not have a biomass reaction. We never did implement a check for this to say "You don't have a biomass reaction", so it just farts on you and quits.
===Update===
Allow me to correct myself. It correctly says there is no biomass reaction if you load a fresh model. However, if you re-load a model file, then it doesn't realize that a biomass reaction is missing, leading to the seg-fault.
from model-seed-core.
It appears that there is the following line in the .tbl file. This indicates biomass present, correct?
Turing:~/Desktop/ModelSEED/Model-SEED-core/workspace/AaronB/Shew5>
grep -i "bio" /Users/student/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/MFAToolkitOutputFiles/14/Seed211586.9.1.tbl
bio00170;=>;c;BOF;NONE;1;;
from model-seed-core.
It appears that the mfatoolkit was not rebuilt after an ms-update. When I did "ms-update" it said that the MFAToolkit was up to date. But I moved it out of the way (i.e., renamed to Model-SEED-core/software/mfatoolkit/Linux/mfatoolkit.bk), which forced a rebuild, and got a new mfatoolkit that is much bigger and now works.
-rwxrwxr-x 1 student staff 15564068 Jun 8 15:21 mfatoolkit
-rwxrwxr-x 1 student staff 1570392 May 22 09:31 mfatoolkit.bk
from model-seed-core.
Ah, that's interesting. I've never used ms-update, so clearly here
there's an issue with recognizing that the source files have been
updated and need to be re-compiled.
On Fri, Jun 8, 2012 at 2:26 PM, aabest
[email protected]
wrote:
It appears that the mfatoolkit was not rebuilt after an ms-update. When I did "ms-update" it said that the MFAToolkit was up to date. But I moved it out of the way (i.e., renamed to Model-SEED-core/software/mfatoolkit/Linux/mfatoolkit.bk), which forced a rebuild, and got a new mfatoolkit that is much bigger and now works.
-rwxrwxr-x 1 student staff 15564068 Jun 8 15:21 mfatoolkit
-rwxrwxr-x 1 student staff 1570392 May 22 09:31 mfatoolkit.bk
Reply to this email directly or view it on GitHub:
#159 (comment)
Postdoctoral Fellow
Mathematics and Computer Science Division
Argonne National Laboratory
9700 S. Cass Avenue
Argonne, IL 60439
http://www.linkedin.com/pub/sam-seaver/0/412/168
[email protected]
(773) 796-7144
"We shall not cease from exploration
And the end of all our exploring
Will be to arrive where we started
And know the place for the first time."
--T. S. Eliot
from model-seed-core.
Related Issues (20)
- Feature request: source of annotation for reactions
- mdl-loadbiomass has stopped working HOT 3
- mdl-autocomplete crashes HOT 6
- ./fba-checkgrowth and MetaboliteProduction.txt HOT 1
- Saved FVA results are invalid after model is changed HOT 1
- Autocomplete not filling gaps with new biomass HOT 1
- object rights not working, perhaps because of case mismatch
- Why is mdl-loadmodel having http request timeouts?
- Error Accessing Model Information HOT 7
- Behavior of the mdl-createmodel command HOT 3
- Segmentation fault with new biomass HOT 1
- ModelSEED commands aren't working HOT 3
- New fba function fails
- generating model IDs
- Use of FIGMODEL Table in MSSupport
- No argument list returned HOT 3
- Autocompletion Failing
- Install Error about MFATOOLKIT in Mac OS 10.7 HOT 1
- ms login error( 502 Bad Gateway)
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from model-seed-core.