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griffithlab / pVACtools

http://www.pvactools.org
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KeyError: 'MHCflurry' #978

Closed brycemash closed 1 year ago

brycemash commented 1 year ago

Describe the bug After the binding predictions complete, it is having problems parsing the files.

... Parsing prediction file for Allele H-2-Kb and Epitope Length 8 - Entries 1201-1290 - Completed Parsing binding predictions for Allele H-2-Kb and Epitope Length 9 - Entries 1201-1290 Parsing prediction file for Allele H-2-Kb and Epitope Length 9 - Entries 1201-1290 Parsing prediction file for Allele H-2-Kb and Epitope Length 9 - Entries 1201-1290 - Completed Parsing binding predictions for Allele H-2-Kb and Epitope Length 10 - Entries 1201-1290 Parsing prediction file for Allele H-2-Kb and Epitope Length 10 - Entries 1201-1290 Traceback (most recent call last): File "/broad/dunnlab/BLM/conda_libraries/pvactools_conda/bin/pvacseq", line 8, in sys.exit(main()) File "/broad/dunnlab/BLM/conda_libraries/pvactools_conda/lib/python3.6/site-packages/pvactools/tools/pvacseq/main.py", line 116, in main args[0].func.main(args[1]) File "/broad/dunnlab/BLM/conda_libraries/pvactools_conda/lib/python3.6/site-packages/pvactools/tools/pvacseq/run.py", line 133, in main pipeline.execute() File "/broad/dunnlab/BLM/conda_libraries/pvactools_conda/lib/python3.6/site-packages/pvactools/lib/pipeline.py", line 434, in execute split_parsed_output_files = self.parse_outputs(chunks) File "/broad/dunnlab/BLM/conda_libraries/pvactools_conda/lib/python3.6/site-packages/pvactools/lib/pipeline.py", line 395, in parse_outputs parser.execute() File "/broad/dunnlab/BLM/conda_libraries/pvactools_conda/lib/python3.6/site-packages/pvactools/lib/output_parser.py", line 438, in execute iedb_results = self.process_input_iedb_file(tsv_entries) File "/broad/dunnlab/BLM/conda_libraries/pvactools_conda/lib/python3.6/site-packages/pvactools/lib/output_parser.py", line 363, in process_input_iedb_file iedb_results_with_metrics = self.add_summary_metrics(iedb_results) File "/broad/dunnlab/BLM/conda_libraries/pvactools_conda/lib/python3.6/site-packages/pvactools/lib/output_parser.py", line 311, in add_summary_metrics result['correspondingwt{}'.format(metric)] = result['wt_{}s'.format(metric)][best_mt_value_method] KeyError: 'MHCflurry'

To Reproduce

vcf-genotype-annotator broad/dunnlab/BLM/pvac/Mutation/INDEL/Annotation/SR_NF.GATK.indel.mm10_multianno.vcf NF_indel 0/1 -o broad/dunnlab/BLM/pvac/Mutation/INDEL/Annotation/SR_NF.GATK.indel.mm10_multianno.gt.vcf

vep \ --input_file broad/dunnlab/BLM/pvac/Mutation/INDEL/Annotation/SR_NF.GATK.indel.mm10_multianno.gt.vcf \ --output_file broad/dunnlab/BLM/pvac/Mutation/INDEL/Annotation/SR_NF.GATK.indel.mm10_multianno.gt.vep.vcf \ --format vcf --vcf --symbol --terms SO --tsl \ --hgvs --fasta broad/dunnlab/BLM/pvac/usftp21.novogene.com/mm10.fa \ --offline --cache \ --dir_cache broad/dunnlab/BLM/pvac \ --plugin Frameshift --plugin Wildtype \ --dir_plugins /broad/dunnlab/BLM/pvac/VEP_plugins \ --species mus_musculus --cache_version 102

ref-transcript-mismatch-reporter broad/dunnlab/BLM/pvac/Mutation/INDEL/Annotation/SR_NF.GATK.indel.mm10_multianno.gt.vep.vcf \ --filter hard \ -o broad/dunnlab/BLM/pvac/Mutation/INDEL/Annotation/SR_NF.GATK.indel.mm10_multianno.gt.vep.filtered.vcf

pvacseq run \ broad/dunnlab/BLM/pvac/Mutation/INDEL/Annotation/SR_NF.GATK.indel.mm10_multianno.gt.vep.filtered.vcf \ NF_indel \ H-2-Kb,H-2-Db \ MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign \ broad/dunnlab/BLM/pvac/output/NF_indel \ -e1 8,9,10 -e2 15

susannasiebert commented 1 year ago

Hi @brycemash, thank you for the error report. Could you please try with the latest version (3.1.3) just to make sure this hasn't been already fixed. Can you please also confirm that the output directory broad/dunnlab/BLM/pvac/output/NF_indel was empty when you started this pVACseq run? If this doesn't fix the problem, would it possible to share your input VCF with us for further debugging?

susannasiebert commented 1 year ago

@brycemash I noticed you closed and then reopened this issue. Are you still running into errors?

brycemash commented 1 year ago

I was able to fix this by deleting the intermediate files that were causing inconsistencies, although it took a few deletions to complete.