cant run pvacsplice on non-human species (when using pvactools docker image 5.0.1 and 5.1.0)

[mhoang22]

im running pvacsplice using docker images pvactools:5.1.0 and 5.0.1 and got this error:

Warning: The above variant/transcript/gene combination is present in the junctions file, but not in the VEP-annotated VCF. Skipping.
Traceback (most recent call last):
  File "/usr/local/bin/pvacsplice", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.7/site-packages/pvactools/tools/pvacsplice/main.py", line 117, in main
    args[0].func.main(args[1])
  File "/usr/local/lib/python3.7/site-packages/pvactools/tools/pvacsplice/run.py", line 149, in main
    pipeline.execute()
  File "/usr/local/lib/python3.7/site-packages/pvactools/lib/splice_pipeline.py", line 46, in execute
    self.junction_to_fasta()
  File "/usr/local/lib/python3.7/site-packages/pvactools/lib/splice_pipeline.py", line 149, in junction_to_fasta
    combined_df = self.combine_inputs()
  File "/usr/local/lib/python3.7/site-packages/pvactools/lib/splice_pipeline.py", line 143, in combine_inputs
    sys.exit("Combined dataset is empty. Aborting.")
NameError: name 'sys' is not defined

I know that the variant is indeed present in the input VEP-annotated VCF. So pvacsplice wasnt running probably because of the missing 'sys' package.

command:

pvacsplice run -g -k -t 4 --normal-sample-name WT-B6-SPLEEN splice_junction.tsv P6-WCMC H-2-Kb,H-2-Db,H2-IAb all /storage1/fs1/tfehnige/Active/fehniger_lymphoma/SPORE/P1P6/wdl_runs/P6-WCMC/pvacsplice/i10e10 annotated_filtered_NoExistingVar.vcf.gz Mus_musculus.GRCm39.dna.primary_assembly.fa Mus_musculus.GRCm39.113.gtf

[mhoang22]

I have made copies of files for troubleshooting at

/storage1/fs1/mgriffit/Active/griffithlab/gc2596/hmy/pvactools_issue_missing_sys