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>
Twitter for server news
twitter.com/phyre2server <http://twitter.com/phyre2server>


On 13/02/2025, 00:34, "ph...@googlegroups.com on behalf of Jason" <ph...@googlegroups.com on behalf of 13437...@gmail.com> wrote:

This email from 13437...@gmail.com originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address.

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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[Jason]

Hi Harry,

Thank you for your kind reply! Apologies for not responding sooner - I rarely hear back from developers so I've come to not expect it.

I'm very glad to be of some help, corrupted libraries must be hard to catch.

I'll be sure to use the same email in the future!

Cheers,

Jason

-----------------------------------------------------------------
Jason D. Shao
Roger Lab & Beiko Lab
Department of Biochemistry & Molecular Biology

Institute for Comparative Genomics

Dalhousie University
-----------------------------------------------------------------

[Powell, Harry]

Hi Jason

I had a quick look at the date on my original email to you and wondered why I couldn't remember doing something last week - then I noticed that it was a little before then!

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>
Twitter for server news
twitter.com/phyre2server <http://twitter.com/phyre2server>

On 19/02/2026, 15:18, "ph...@googlegroups.com on behalf of Jason" <ph...@googlegroups.com on behalf of 13437...@gmail.com> wrote:

Hi Harry,
Thank you for your kind reply! Apologies for not responding sooner - I rarely hear back from developers so I've come to not expect it.

I'm very glad to be of some help, corrupted libraries must be hard to catch.

I'll be sure to use the same email in the future!

Cheers,
Jason
-----------------------------------------------------------------
Jason D. Shao
Roger Lab & Beiko Lab
Department of Biochemistry & Molecular Biology

Institute for Comparative Genomics <https://icgenomics.ca/>

Dalhousie University
-----------------------------------------------------------------


On Thursday, February 13, 2025 at 7:10:23 a.m. UTC-4 Powell, Harry wrote:


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> <http://www.imperial.ac.uk/phyre2>
Twitter for server news
twitter.com/phyre2server <http://twitter.com/phyre2server> <http://twitter.com/phyre2server>

On 13/02/2025, 00:34, "ph...@googlegroups.com <> on behalf of Jason" <ph...@googlegroups.com <> on behalf of 13437...@gmail.com <>> wrote:

This email from 13437...@gmail.com <> originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address.

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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