Dear ROSIE2 team,
thank you very much to making available such a great ressource.
I used the ROSIE2 server and AlphaRed to predict protein-protein interactions. While it works most of the time, I would like to share some of the error messages which I experience regularly. Maybe they help you to improve the software.
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AlphaRed job №16676
ERROR: Job exectution was aborted!
Usually this indicates issues with the job input. Please see log files for details.back-end-error.output
ERROR: failed to validate flag line: '-parser:protocol @dock-xml-ref ' due to presence of '@', aborting...
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same error for job ids: 16675, 16674, 16600, 16598, 16597, 16476, and more.
Another error I experienced was the following:
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AlphaRed job №16505
ERROR: Some of the Rosetta processes crashed!
Usually this indicates issues with the job input. Please see log files for details.ROSETTA_CRASH.log
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error log is attached as file
this or similiar also happend for job id 16475 and 16471
Please let me know in case you need for info.
Cheers
Daniel
| Attachment | Size |
|---|---|
 ROSETTA_CRASH.log | 11.53 KB |
Hi Daniel,
The validation error is a bit misleading. The real error could be seen in `0.colab-fold.0.output` file (for example here https://r2.graylab.jhu.edu/job/16600/file/output/0.colab-fold.0.output) is due to colab-fold job not completing in allowed time limit. The only way to mitigate this would be to try to use shorter input sequence if possible.
Sergey.
Dear Sergey,
thank you for your response. That explains it.
It there a plan to increase the time limit in the future?
Best,
Daniel
It is possible that we will increase it but unlikely in the immediate future. Issue is that we have to balance our avaliable computational resources with current demand (which is high!) so some compromise is needed. We are planning to continue expanding our ROSIE cluster next year so things might change then.