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Open workflow definitions for genomic analysis from MGI at WUSM.
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KeyError: 'WildtypeProtein' #164

Closed xuxue1986 closed 7 years ago

xuxue1986 commented 7 years ago

Hi,

I meet a new error when I used pvac-seq, I use :pvacseq run TUMOR.vcf test1 HLA-G01:09,HLA-E01:01,H2-IAb NetMHC PickPocket NNalign /home/xuexu/Documents/melanoma_project/neoantigene/IEDB/pvacseq-4.1.0b0/pvacseq/example_data/result4 -e 9,10

TUMOR.vcf originally consists of tumor and normal samples, and I use vcftools to seperate them. Then I use pvacseq to meet this error.

Could you help me to work out the problem? Executing MHC Class I predictions Converting VCF to TSV Traceback (most recent call last): File "/home/xuexu/miniconda2/envs/snakes/bin/pvacseq", line 11, in sys.exit(main()) File "/home/xuexu/miniconda2/envs/snakes/lib/python3.5/site-packages/pvacseq/pvacseq.py", line 84, in main args[0].func.main(args[1]) File "/home/xuexu/miniconda2/envs/snakes/lib/python3.5/site-packages/pvacseq/lib/main.py", line 291, in main pipeline.execute() File "/home/xuexu/miniconda2/envs/snakes/lib/python3.5/site-packages/pvacseq/lib/pipeline.py", line 292, in execute self.convert_vcf() File "/home/xuexu/miniconda2/envs/snakes/lib/python3.5/site-packages/pvacseq/lib/pipeline.py", line 133, in convert_vcf lib.convert_vcf.main(convert_params) File "/home/xuexu/miniconda2/envs/snakes/lib/python3.5/site-packages/pvacseq/lib/convert_vcf.py", line 264, in main 'wildtype_amino_acid_sequence' : transcript['WildtypeProtein'], KeyError: 'WildtypeProtein'

susannasiebert commented 7 years ago

Hi,

This is the incorrect repository for this issue. Please re-submit your issue to the pVAC-Seq repository.

Thanks, Susanna