[Bug report title]NoneType Error Encountered with NetMHCpan and Exception When Calling MHCflurry

Installation Type

Docker

pVACtools Version / Docker Image

griffithlab/pvactools:4.4.1

Python Version

No response

Operating System

No response

Describe the bug

Hello! After pulling the latest version of the Docker image, I followed the pVACtools 4.4.1 documentation to test with the example data. When the algorithm was specified as 'all', I encountered this error.

_During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/local/bin/pvacseq", line 8, in sys.exit(main()) File "/usr/local/lib/python3.7/site-packages/pvactools/tools/pvacseq/main.py", line 130, in main args[0].func.main(args[1]) File "/usr/local/lib/python3.7/site-packages/pvactools/tools/pvacseq/run.py", line 142, in main pipeline.execute() File "/usr/local/lib/python3.7/site-packages/pvactools/lib/pipeline.py", line 451, in execute self.call_iedb(chunks) File "/usr/local/lib/python3.7/site-packages/pvactools/lib/pipeline.py", line 358, in call_iedb p.print("Making binding predictions on Allele %s and Epitope Length %s with Method %s - File %s - Completed" % (a, epl, method, filename)) File "/usr/local/lib/python3.7/site-packages/pymp/init.py", line 148, in exit raise exc_t(excval) Exception: An error occurred while calling MHCflurry:

After adjusting the command and specifying the algorithm as NetMHCpan, I encountered this error.

_Making binding predictions on Allele HLA-A29:02 and Epitope Length 10 with Method NetMHCpan - File /pvacseq_output_data/MHC_Class_I/tmp/HCC1395_TUMOR_DNA.netmhcpan.HLA-A29:02.10.tsv_1201-1400 Illegal instruction 2024-09-27:12:01:18,780 WARNING [init.py:662] did not find allele distance info from netmhcpan_output An exception occured in thread 0: (<class 'TypeError'>, a bytes-like object is required, not 'NoneType'). Traceback (most recent call last): File "/usr/local/lib/python3.7/site-packages/pvactools/lib/pipeline.py", line 357, in call_iedb pvactools.lib.call_iedb.main(arguments) File "/usr/local/lib/python3.7/site-packages/pvactools/lib/call_iedb.py", line 53, in main tmp_output_filehandle.write(responsetext) TypeError: a bytes-like object is required, not 'NoneType'

_During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr/local/bin/pvacseq", line 8, in sys.exit(main()) File "/usr/local/lib/python3.7/site-packages/pvactools/tools/pvacseq/main.py", line 130, in main args[0].func.main(args[1]) File "/usr/local/lib/python3.7/site-packages/pvactools/tools/pvacseq/run.py", line 142, in main pipeline.execute() File "/usr/local/lib/python3.7/site-packages/pvactools/lib/pipeline.py", line 451, in execute self.call_iedb(chunks) File "/usr/local/lib/python3.7/site-packages/pvactools/lib/pipeline.py", line 358, in call_iedb p.print("Making binding predictions on Allele %s and Epitope Length %s with Method %s - File %s - Completed" % (a, epl, method, filename)) File "/usr/local/lib/python3.7/site-packages/pymp/init.py", line 148, in exit raise exc_t(excval) TypeError: a bytes-like object is required, not 'NoneType'

How to reproduce this bug

docker run --rm -v /Users/anomibo/Downloads/pvactools/example_data/pvacseq_example_data:/pvacseq_example_data -v /Users/anomibo/Downloads/pvactools/output:/pvacseq_output_data -it griffithlab/pvactools

pvacseq run \
> /pvacseq_example_data/annotated.expression.vcf.gz \
> HCC1395_TUMOR_DNA \
> HLA-A*29:02,HLA-B*45:01,DRB1*04:05 \
> all \
> /pvacseq_output_data \
> -e1 8,9,10 \
> -e2 15 \
> --normal-sample-name HCC1395_NORMAL_DNA \
> --iedb-install-directory /opt/iedb

Input files

pvacseq_example_data

Log output

I did not receive the expected TSV file. Here are the complete results, including the log file. Thank you in advance for your response.

MHC_Class_I.zip

Output files

No response

griffithlab / pVACtools