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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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surprising Permission denied #24

Closed kobejamescurry closed 5 years ago

kobejamescurry commented 5 years ago

1

ambj commented 5 years ago

Dear ? You have made full permission to the input file - since the program runs the first half this is not where the permission error occurs.
Have you looked at your permission to NetMHCpan 4.0? Since you are running with the print temp file option (-t) it looks like the input file to netMHCpan is generated but not the output files. have you stated the correct path in the config.ini file? Best, Anne-Mette

ambj commented 5 years ago

HG19 is the same as GRCh37. If you are not using GRCh38 you need to liftover your vcf file from GRCh37 to GRCh38. you need to make sure that the functioning path to NetMHCpan is stated correctly in the config.ini file. Best, /AM

ambj commented 5 years ago

Dear ? It is difficult for me to help you when you change or edit your original question. It is not clear to me what you problem is now - did you succeed with the permission error? Best, Anne-Mette

ambj commented 5 years ago

Yes the output change when you use the full netMHCpan run - getting both the eluted ligand rank score output and the binding affinity output. unfortunately i have not change the explanation for this in user manual yet.

The references you are referring to are not necessary to be stated in the config.ini file. they are generated for each run if not stated there - you can save a bit of processing time by using the -t option to get them printed and then save then and state the paths in the config.ini file.

ambj commented 5 years ago

I kindly refer to reading the MuPeXI paper, user manual and NetMHCpan paper i detail - this does not seem to be an issue with the software.