AssertionError: Allele "HLA-B*07:02" not stated in NetMHCpan output

[mimifp]

I'm trying to run MuPeXI pipeline with test data. There seems to be a problem with NetMHCpan, but I can't seem to fix it. I have checked the paths requested by the tool in its installation, as well as the MuPeXI config.ini file. I have also changed the permissions to the $NETMHCpan/data/version file, giving write and read permissions for other users. Moreover, I hace also added netmhcpan executable to my user $PATH.

I am working with a conda eviroment to be able to use Python 2.7 and the required versions of pandas, numpy, vep and biopython, since I am running on an HPC with Slurm as task manager. The NetMHCpan-4.0 tool is out of this enviroment, but works separately.

The data/allelenames file does contain the allele HLA-B07:02 it says it cannot find.

Any idea what might be happening? Thanks in advance

(mupexi) [uscmgmfp@login209-18 data]$ ../MuPeXI.py -v example.vcf -c /mnt/lustre/scratch/nlsas/home/usc/mg/translational_oncology/1_tools/24_mupexi/MuPeXI/config.ini -e example_expression.tsv -a HLA-A*01:01,HLA-A*11:01,HLA-B*07:02,HLA-B*35:01 -t

Reading in data
    Creating expression file dictionary
    Creating proteome reference dictionary
    Creating genome reference dictionary
    Creating cancer genes list

VEP: Starting process for running the Ensembl Variant Effect Predictor
    Detecting variant caller
        MuTect2
    Change VCF to the VEP compatible
    Extracting allele frequencies
    Running VEP
    Creating mutation information dictionary

MuPeX: Starting mutant peptide extraction
    Extracting all possible peptides from reference
        Peptides of 9 aa are being extracted
    Peptide extraction begun
        Running 9 aa normal peptide match

MuPeI: Starting mutant peptide informer
    Writing temporary peptide file
    Running NetMHCpan eluted ligand prediction
Unable to open(r) file $NETMHCpan/data/version
    Creating NetMHCpan eluted ligand prediction file dictionary
    Writing output file
Traceback (most recent call last):
  File "../MuPeXI.py", line 1800, in <module>
    main(sys.argv[1:])
  File "../MuPeXI.py", line 101, in main
    output_file = write_output_file(peptide_info, expression, net_mhc_BA, net_mhc_EL, unique_alleles, cancer_genes, tmp_dir, input_.webserver, input_.print_mismatch, allele_fractions, input_.expression_type, transcript_info, reference_peptides, proteome_reference, protein_positions, version)
  File "../MuPeXI.py", line 1261, in write_output_file
    assert hla in net_mhc_EL, 'Allele "{}" not stated in NetMHCpan output'.format(hla)
AssertionError: Allele "HLA-B*07:02" not stated in NetMHCpan output

[levinyi]

I encountered a similar issue and resolved it by ensuring the netMHCpan configuration was correctly set up. Please check the following in your configuration:

1. Verify the correct path to the netMHCpan home directory. It should look like this in your configuration file: setenv NMHOME /path/to/netMHC/netMHCpan-4.0/

2. Ensure the path to the temporary directory (TMPDIR) is correctly specified. You might want to create a 'tmp' folder in your netMHCpan installation directory for this purpose: setenv TMPDIR /path/to/netMHCpan-4.0/tmp/

3. Check the netMHCpan path in the MuPeXI's config file. It should be specified like this: MHC = /path/to/netMHCpan-4.0/netMHCpan

Make sure these paths are accurate and reflect your actual directory structure.