HLAthena Predict returns Error

Darwin Kwok

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Oct 21, 2020, 6:11:39 PM10/21/20

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Hi Sarkizova S.,

Amazing work with your publication and it seems from the history of conversations that this algorithm has gained tremendous traction - congratulations! I am emailing in regards to a similar error that one member has already addressed. It is the Error: "An error has occurred. Check your logs or contact the app author for clarification."

I am trying to use the Predict function with a .txt file with only one column of 8-11mers. Analysis was set with "ranks", "threshold" = 0, "peptide column name" = nmer, "log-transform expr" = no, "context available" = no, and "aggregate by peptide" = yes.

Fiddled with removing the header, removing peptides until it was < 10,000 per file, but no luck. Looking forward to any suggestions!

Regards,

Darwin

Sisi Sarkizova

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Oct 22, 2020, 11:42:57 AM10/22/20

to Darwin Kwok, HLAthena

Hi Darwin, thank you, glad you are finding the work useful.

Could you try to run the prediction with the provided sample input file and see if that works ok for you?

As described in the 'How to' tab, the header row is required and the name of the peptide column must match what you specify in the"Peptide column name" input field. I suspect a mismatch between your provided file and the string in the input field is what's causing the error you see. For further assistance I would need a snippet of your input file.

Sisi

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Darwin Kwok

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Oct 22, 2020, 2:43:39 PM10/22/20

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Hi Sisi,

Thank you for the fast reply - I really appreciate that. I realized that in the How To, when it said that the peptide sequence is all that is needed, it meant that the other column headers still had to be present for the code to work. Everything went smoothly once I did that! I would love to integrate this into my R pipeline, so I was wondering if the standalone version is available and fully functional? I was reading some of the other questions people were asking, and I'm assuming it involves utilizing Docker. Would there be any ReadMe for the standalone version that you can direct me to?

Thank you again for the fast and informative response! Hope you're doing well.

Regards,

Darwin

Sisi Sarkizova

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Oct 23, 2020, 7:31:50 PM10/23/20

to Darwin Kwok, HLAthena

Hi Darwin, glad it worked out. Here are the instructions for running the dockerized version:

Please pull the following docker image (assuming you already have docker installed):
docker pull ssarkizova/hlathena-external

Then run:
docker run -v `pwd`:`pwd` -w `pwd` ssarkizova/hlathena-external predict --help

You should see help output with run examples and descriptions of the available options. The parameters are very similar to those on the website and the examples should hopefully explain how to build up the command for your use case. More details on the input and output formats are available on the website: Predict -> How to.

Let me know if you run into any issues,

Sisi

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Darwin Kwok

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Oct 26, 2020, 2:40:54 PM10/26/20

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Hey Sisi!

This is awesome, thank you! I will give it a shot over the course of this week (just need to redo some input parameters and files before running it again). I will let you know here if I have anymore issues or if it runs perfectly well! Thank you so much in advance!