pVACtools_generate_protein_seq (test_sample)` terminated with an error exit status (1)

[DecodeGenome]

Hi nextNEOpi developer,

While I ran command line for test sample, it gave me an error as followings, I attached contents from /wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/c5/4d38fd64e93256a050d78f2774d3dd and file from .nextflow.log for your information. Please help to resolve this issue.

Thanks,

Wei

################################## Error message #################### Error executing process > 'pVACtools_generate_protein_seq (test_sample)'

Caused by: Process pVACtools_generate_protein_seq (test_sample) terminated with an error exit status (1)

Command executed:

pvacseq generate_protein_fasta
-p test_sample_vep_phased.vcf.gz
-s test_sample_tumor
-d full
test_sample_vep_somatic_gx.vcf.gz
31
test_sample_long_peptideSeq.fasta

Command exit status: 1

Command output: Converting VCF to TSV

Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred Converting VCF to TSV VCF doesn't contain VEP FrameshiftSequence annotations. Please re-annotate the VCF with VEP and the Wildtype and Frameshift plugins.

Work dir: /wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/c5/4d38fd64e93256a050d78f2774d3dd

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

April_29_nextflow.log c5_contents.tar.gz vep_cache_plugins.tar.gz