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ambj / MuPeXI

MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.
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IndexError: list index out of range #7

Closed Phorutai closed 6 years ago

Phorutai commented 6 years ago

Hi, I run MuPeXI with VCF file called from mutect2, but I got this error

MuPeI: Starting mutant peptide informer Writing temporary peptide file Running NetMHCpan Creating NetMHCpan file dictionary Traceback (most recent call last): File "/apps/MuPeXI/MuPeXI.py", line 1637, in main(sys.argv[1:]) File "/apps/MuPeXI/MuPeXI.py", line 98, in main net_mhc = build_netMHC(netMHCfile, input.webserver) File "/apps/MuPeXI/MuPeXI.py", line 1092, in build_netMHC rank = float(line[13]) IndexError: list index out of range

How should I fix this problem?

Phorutai commented 6 years ago

Even if I tried to run your example file, I got the same error.

ambj commented 6 years ago

Which version of NetMHCpan and MuPeXI er you running? It looks like you are trying to run NetMHCpan4.0 with MuPeXI 1.1.3. MuPeXI have been updated in the development (dev) branch to work with NetMHCpan 4.0 the new MePeXI version will soon be merged into the master branch, until then you can clone the dev branch.

Best, /AM

Phorutai commented 6 years ago

Thank you for a quick reply. Yes, I used NetMHCpan4.0, I will try with the new version, but actually if I use NetMHCpan3.0 instead, would it be ok?

Best, Phorutai

ambj commented 6 years ago

Yes it should work with 3.0