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'
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'