Encountered an error when using expressed_neoantigen_count in the course of an analysis:
This did not occur for all patients, but did occur for approximately 3 patients.
Here is a sample of the relevant output:
expressed_neoantigen_count: 18%|████████████████████████████████████▋ | 14/79 [01:04<12:12, 11.27s/it]
Traceback (most recent call last):
File "/demeter/users/burosj01/projects/netmhc-bundle/netMHC-3.4/netMHC.py", line 536, in <module>
main()
File "/demeter/users/burosj01/projects/netmhc-bundle/netMHC-3.4/netMHC.py", line 528, in main
fulldict[allele] = printresults(NNpred, seqs, inorder, preds, allele, methodlist[allele], peplen, wwwrun)
KeyError: 'HLA-B07:02'
Traceback (most recent call last):
File "/demeter/users/burosj01/projects/netmhc-bundle/netMHC-3.4/netMHC.py", line 536, in <module>
main()
File "/demeter/users/burosj01/projects/netmhc-bundle/netMHC-3.4/netMHC.py", line 528, in main
fulldict[allele] = printresults(NNpred, seqs, inorder, preds, allele, methodlist[allele], peplen, wwwrun)
KeyError: 'HLA-B07:02'
Traceback (most recent call last):
File "/demeter/users/burosj01/projects/netmhc-bundle/netMHC-3.4/netMHC.py", line 536, in <module>
main()
File "/demeter/users/burosj01/projects/netmhc-bundle/netMHC-3.4/netMHC.py", line 528, in main
fulldict[allele] = printresults(NNpred, seqs, inorder, preds, allele, methodlist[allele], peplen, wwwrun)
KeyError: 'HLA-B07:02'
Traceback (most recent call last):
File "/demeter/users/burosj01/projects/netmhc-bundle/netMHC-3.4/netMHC.py", line 536, in <module>
main()
File "/demeter/users/burosj01/projects/netmhc-bundle/netMHC-3.4/netMHC.py", line 528, in main
fulldict[allele] = printresults(NNpred, seqs, inorder, preds, allele, methodlist[allele], peplen, wwwrun)
KeyError: 'HLA-B07:02'
Traceback (most recent call last):
File "/demeter/users/burosj01/projects/netmhc-bundle/netMHC-3.4/netMHC.py", line 536, in <module>
main()
File "/demeter/users/burosj01/projects/netmhc-bundle/netMHC-3.4/netMHC.py", line 528, in main
fulldict[allele] = printresults(NNpred, seqs, inorder, preds, allele, methodlist[allele], peplen, wwwrun)
KeyError: 'HLA-C07:02'
... etc.
The set of HLA alleles causing this error includes: 'HLA-B07:02', 'HLA-C07:02', 'HLA-A03:01', 'HLA-B44:02', 'HLA-A68:01' .
On further inspection, this occurs for patients with no expressed variants. Not sure if this is an error in the context of that analysis or not -- that's a separate issue. For now, I want to catch & address this situation appropriately.
As noted elsewhere, one limitation of our current caching strategy is that we lose potentially-informative output like this once these results have been cached. I don't yet have a good solution to this, but will create an issue for this (to capture logger output when caching items).
Encountered an error when using
expressed_neoantigen_countin the course of an analysis:This did not occur for all patients, but did occur for approximately 3 patients.
Here is a sample of the relevant output:
... etc.
The set of HLA alleles causing this error includes:
'HLA-B07:02', 'HLA-C07:02', 'HLA-A03:01', 'HLA-B44:02', 'HLA-A68:01'.On further inspection, this occurs for patients with no expressed variants. Not sure if this is an error in the context of that analysis or not -- that's a separate issue. For now, I want to catch & address this situation appropriately.
As noted elsewhere, one limitation of our current caching strategy is that we lose potentially-informative output like this once these results have been cached. I don't yet have a good solution to this, but will create an issue for this (to capture logger output when caching items).