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

[riederd]

Can you post the vcf.gz files from the c5 dir, e.g. create the tar.gz with the --dereference tar option.

[DecodeGenome]

Hi Riederd, please see the attachment. Thanks. c5_vcf_contents.tar.gz

[riederd]

It seems that you are lacking the Frameshift.pm and the Wildtype.pm plugins in vep_cache/Plugins . They should have been installed on the first run of the pipeline, see:

https://github.com/icbi-lab/nextNEOpi/blob/fe7b21cdc0b97aae38195e5f5ac1b9851674f6b1/nextNEOpi.nf#L3255-L3291

Did you notice any error message regarding the installVEPplugins proccess?

Anyway, you may try to copy them manually from the assets folder of nextNEOpi to the vep_cache/Plugins dir, or you can delete the /wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/resources/databases/.110_plugins_ok.chck file and rerun the pipeline.

[DecodeGenome]

Hi Riederd, Thank you very much. For installVEPplugins process, I did not see any error messages. I now copies these two files, and hopefully everything is ok. Best Regards!

[riederd]

Seems to be fixed. Closing it.