griffithlab / griffithlab/pVACtools
Add retry when NetMHCstabpan fails
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- Dominant language
- Python
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- 9d 17h
- Merged PRs (30d)
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Description
Sometimes NetMHCstabpan fails in the following way but restarts of the pipeline will succeed:
Traceback (most recent call last):
File "/usr/local/bin/pvacseq", line 8, in <module>
sys.exit(main())
File "/usr/local/lib/python3.7/site-packages/pvactools/tools/pvacseq/main.py", line 116, in main
args[0].func.main(args[1])
File "/usr/local/lib/python3.7/site-packages/pvactools/tools/pvacseq/run.py", line 132, in main
pipeline.execute()
File "/usr/local/lib/python3.7/site-packages/pvactools/lib/pipeline.py", line 506, in execute
PostProcessor(**post_processing_params).execute()
File "/usr/local/lib/python3.7/site-packages/pvactools/lib/post_processor.py", line 38, in execute
self.call_netmhc_stab()
File "/usr/local/lib/python3.7/site-packages/pvactools/lib/post_processor.py", line 121, in call_netmhc_stab
NetMHCStab(self.net_chop_fh.name, self.netmhc_stab_fh.name, self.file_type, self.top_score_metric).execute()
File "/usr/local/lib/python3.7/site-packages/pvactools/lib/netmhc_stab.py", line 86, in execute
raise Exception("NetMHCstabpan encountered an error during processing.\n{}".format(response.content.decode()))
Exception: NetMHCstabpan encountered an error during processing.
<html><head><title>635A40E9000078ABEBEE3CAB failed</title></head>
<body>
<H1>Failed run</H1>
<P>Unfortunately, your job failed. It responded with this:</P>
<PRE>
Content-Type: text/html; charset=ISO-8859-1
<BODY LINK="#0000ff" BGCOLOR="#ffffff">
<script language=JavaScript type = "text/javascript">
var loc = window.top.location.search.substring(1);
if (loc != null && loc !== "" && loc.length > 1) {
document.write('<center><h2>',loc,' Server Output - DTU Health Tech</h2></center>');}
</script>
<hr>
<pre>
</pre>
<hr>
Go <a href="javascript:history.back()"><b>back</b></a>.
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This may indicate that a retry (after some appropriate amount of wait) for this error condition would succeed. We should also do the same for NetChop
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with pvactools/lib/netmhc_stab.py and its execute path shown in the traceback, then inspect the NetChop call in the post-processing pipeline. Determine how this transient failure is identified and what wait interval is appropriate; done means the pipeline retries failed NetMHCstabpan and NetChop jobs instead of requiring a restart.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100