failed analyses: potential input validation issue?

[Jason]

Hi,

I have been trying to run Phyre2 on this amino acid sequence. However, it seems that if "ref" is used in the description, the analyses will fail.

Here are the IDs for the two runs that failed:

37548dcf5e281579

2e9d02fd2ecd8992

Here is the run that succeeded under a different description "good":

c7c971d57034848b

With my rather limited CS experience, I sense that this may be an edge case for input validation that went under the radar.

Hopefully this was helpful.

Best,

Jason

[Powell, Harry]

Hi Jason

Thanks for getting in touch - far too many people encounter problems and then keep it to themselves.

It doesn't look like it's an edge case for validation - I ran your job with a variety of names and they all failed on only one of our computing nodes. I noticed that your job that did complete successfully was run on our node020, and the other two ran on node024. Node024 seems to have a corrupted version of our fold library - and I would not have noticed if you had not drawn this to my attention.

I've re-run the job and it looks okay now - if you look at the "hostname" file you'll see that our scheduler ran it on node001, so I didn't get the chance to check that the corrupted library is actually okay now.

By the way, it's very helpful if you contact me using the e-mail used for your job (e.g. jason...@dal.ca) rather than another e-mail address (e.g. 1343759275s@gmail) so that I can easily make the connection between your query and the job that was actually run!

Best wishes

Harry Powell
—
Dr Harry Powell
Structural Bioinformatics Group
Dept. Life Sciences
Imperial College London
harold...@imperial.ac.uk

Phyre2 Developer
www.imperial.ac.uk/phyre2 <http://www.imperial.ac.uk/phyre2>
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Hi,
I have been trying to run Phyre2 on this amino acid sequence <https://www.ncbi.nlm.nih.gov/protein/NP_461804.1?report=fasta>. However, it seems that if "ref" is used in the description, the analyses will fail.

Here are the IDs for the two runs that failed:
37548dcf5e281579
2e9d02fd2ecd8992

Here is the run that succeeded under a different description "good":
c7c971d57034848b

With my rather limited CS experience, I sense that this may be an edge case for input validation that went under the radar.

Hopefully this was helpful.

Best,
Jason

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