Open code12412f opened 5 years ago
Hi Kim / @code12412f!
Sorry no one else caught this on here...can you help me recreate the error?
I am able to run this on my machine:
mhctools --mhc-predictor netmhc4 --mhc-alleles H2-Kb,H2-Db --sequence SIINFEKL
What happens when you run the same command on yours?
2019-07-03 09:18:51,494 - mhctools.cli.args - INFO - Building MHC binding prediction type for alleles ['H-2-Kb', 'H-2-Db'] and epitope lengths None 2019-07-03 09:18:53,592 - mhctools.base_commandline_predictor - INFO - Skipping allele BoLA-D18.4: The suffix '.4' of 'D18.4' was not parsed 2019-07-03 09:18:53,593 - mhctools.base_commandline_predictor - INFO - Skipping allele BoLA-JSP.1: The suffix 'SP.1' of 'JSP.1' was not parsed 2019-07-03 09:18:53,593 - mhctools.base_commandline_predictor - INFO - Skipping allele BoLA-T2C: The suffix 'C' of 'T2C' was not parsed 2019-07-03 09:18:53,593 - mhctools.base_commandline_predictor - INFO - Skipping allele BoLA-T2a: The suffix 'a' of 'T2a' was not parsed 2019-07-03 09:18:53,593 - mhctools.base_commandline_predictor - INFO - Skipping allele BoLA-T2b: The suffix 'b' of 'T2b' was not parsed 2019-07-03 09:18:56,455 - mhctools.process_helpers - INFO - Ran 2 commands in 2.8485 seconds 2019-07-03 09:18:56,467 - mhctools.cli.script - INFO - source_sequence_name offset peptide allele affinity percentile_rank prediction_method_name length 0 PEPLIST 0 SIINFEKL H-2-Kb 19.37 0.06 netMHC 8 1 PEPLIST 0 SIINFEKL H-2-Db 3220.94 0.90 netMHC 8
OK, so the MHC binding predictor works.
I tried running on some small mouse data locally and this command succeeded:
vaxrank --vcf b16.expressed.vcf --bam b16.combined.bam --output-neoepitope-report test.xlsx --genome GRCm38 --mhc-predictor netmhc4 --mhc-alleles H2-Kb,H2-Db
So...it must be something data dependent.
What happens if you run varcode --vcf 303Aligned.sortedByCoord.out.bam_dup.bam.vcf --one-per-variant --only-coding
? How many coding effects are predicted?
Alternatively, if you want to upload the data somewhere I can access, I'll try running Vaxrank with it.
I emailed you the VCF file
Varcode
Version: 0.9.1
Path: /home/kam9898/.local/lib/python3.6/site-packages/varcode
Traceback (most recent call last):
File "/home/kam9898/.local/bin/varcode", line 10, in
If the reference isn't obvious in the VCF then you need to add --genome GRCm38
to the arguments for Varcode.
Can you also send me a link to the BAM? I won't be able to run Vaxrank without both.
2041
I'm running Vaxrank and I'm getting two errors. I'm trying to get a XLSX neoepitope report as output: vaxrank --vcf 303Aligned.sortedByCoord.out.bam_dup.bam.vcf --bam 303Aligned.sortedByCoord.out.bam_dup.bam --output-neoepitope-report test.csv --genome GRCm38 --mhc-predictor netmhc4 --mhc-alleles H2-Kb,H2-Db
with traceback: Traceback (most recent call last): File "/home/kam9898/.local/lib/python3.6/site-packages/vaxrank/epitope_prediction.py", line 110, in predict_epitopes {protein_fragment.gene_name: protein_fragment.amino_acids}) File "/home/kam9898/.local/lib/python3.6/site-packages/mhctools/base_predictor.py", line 208, in predict_subsequences binding_predictions = self.predict_peptides(peptide_list) File "/home/kam9898/.local/lib/python3.6/site-packages/mhctools/base_commandline_predictor.py", line 326, in predict_peptides temp_dir_list=dirs) File "/home/kam9898/.local/lib/python3.6/site-packages/mhctools/base_commandline_predictor.py", line 271, in _run_commands_and_collect_predictions process_limit=self.process_limit) File "/home/kam9898/.local/lib/python3.6/site-packages/mhctools/process_helpers.py", line 114, in run_multiple_commands_redirect_stdout assert len(multiple_args_dict) > 0 AssertionError
Traceback (most recent call last): File "/home/kam9898/.local/bin/vaxrank", line 10, in
sys.exit(main())
File "/home/kam9898/.local/lib/python3.6/site-packages/vaxrank/cli.py", line 407, in main
excel_report_path=args.output_neoepitope_report)
File "/home/kam9898/.local/lib/python3.6/site-packages/vaxrank/report.py", line 506, in make_minimal_neoepitope_report
'%.2f nM' % epitope_prediction.wt_ic50),
TypeError: must be real number, not NoneType