BigMHC prediction not working
Closed this issue · 3 comments
Installation Type
Standalone
pVACtools Version / Docker Image
4.2.1
Python Version
3.10.8
Operating System
Linux
Describe the bug
The error occurs when pvactools run BigMHC prediction. It seems that there is no tool named bigmhc_predict, that is installed with pvactools. Should I install it separately from this repo ?
How to reproduce this bug
pvacseq run \
input.vcf.gz \
sample_name \
HLA-A*01:01,HLA-A*68:02,HLA-B*08:01,HLA-B*37:01,HLA-C*06:03,HLA-C*07:01 \
all \
output \
--normal-sample-name normal_sample_name \
-e1 8,9,10 \
-e2 15 \Input files
No response
Log output
The full log file is :
pvactools.log
Output files
No response
BigMHC, as well as DeepImmuno, need to be installed separately. Please follow the instructions in our documentation to install these predictors. Please note, that these instructions are different from the installation instructions provided by BigMHC and DeepImmuno directly. pVACtools will only be able to use BigMHC and DeepImmuno if it is installed as instructed in our documentation.
Thank you for your quick response. I installed pvactools using pip and wonder if the Docker image of pvactools already includes BigMHC or DeepImmuno, or if I need to install them separately ?
Our Docker image comes with both BigMHC and DeepImmuno pre-installed.