Error: No command specified

[Geneece]

Installation Type

Docker

pVACtools Version / Docker Image

Docker container, version 4.4.1

Python Version

No response

Operating System

No response

Describe the bug

I am getting an output message from pvacseq stating that no command was specified after it starts running. It stops before converting .vcf to TSV. I was able to run the test data successfully. I used the same command format for my own data and didn't receive any other error messages.

How to reproduce this bug

apptainer exec /home/containers/pvactools.sif pvacseq run \
${OUTDIR}/VEP_ANNOTATED.genotype.dna.somatic.sv.vcf \
${TUMOR} \
${VALID_ALLELES} \
all \
${OUTDIR} \
--normal-sample-name ${NORMAL} \
--iedb-install-directory /opt/iedb

Log output

Executing MHC Class I predictions
Converting .vcf to TSV
usage: pvacseq [-h]
{run,binding_filter,coverage_filter,transcript_support_level_filter,top_score_filter,net_chop,netmhc_stab,calculate_reference_proteome_similarity,generate_protein_fasta,generate_aggregated_report,identify_problematic_amino_acids,download_example_data,install_vep_plugin,valid_alleles,valid_algorithms,allele_specific_cutoffs}
...

positional arguments:
{run,binding_filter,coverage_filter,transcript_support_level_filter,top_score_filter,net_chop,netmhc_stab,calculate_reference_proteome_similarity,generate_protein_fasta,generate_aggregated_report,identify_problematic_amino_acids,download_example_data,install_vep_plugin,valid_alleles,valid_algorithms,allele_specific_cutoffs}
run Run the pVACseq pipeline.
binding_filter Filter variants processed by IEDB by binding score.
coverage_filter Filter variants processed by IEDB by coverage, vaf,
and gene expression.
transcript_support_level_filter
Filter variants processed by IEDB by transcript
support level.
top_score_filter Pick the best neoepitope for each variant.
net_chop Run NetChop on existing pVACseq output .tsv to predict
cleavage sites on the neoepitopes.
netmhc_stab Run NetMHCStabPan on existing pVACseq output .tsv to
add stability predictions to the neoepitopes.
calculate_reference_proteome_similarity
Blast peptides against the reference proteome on
existing pVACseq output .tsv.
generate_protein_fasta
Generate an annotated fasta file from a VCF with
protein sequences of mutations and matching wildtypes.
generate_aggregated_report
Generate an aggregated report from a pVACseq
.all_epitopes.tsv report file.
identify_problematic_amino_acids
Mark problematic amino acid positions in each epitope
or filter entries that have problematic amino acids.
download_example_data
Download example input and output files.
install_vep_plugin Install the Wildtype and Frameshift VEP plugins into
your VEP_plugins directory.
valid_alleles Show a list of valid allele names.
valid_algorithms Show a list of algorithms supported given the
specified species and/or allele
allele_specific_cutoffs
Show the allele specific cutoffs.

optional arguments:
-h, --help show this help message and exit
Error: No command specified

[susannasiebert]

Thank you for this bug report and my apologies that you are running into issues with using pVACtools. Can you please attach your input VCF so I can try to debug this issue further? It's most likely that your VCF is either malformed in some way or the code is running into some sort of edge case but I would need to see the file to confirm this.

[Geneece]

Thank you for your prompt response, however, I cannot share the VCF file. It did contain structural variants as an output from Manta. Could this be related to the issue? As I have been able to run SNVs through pVACseq. Thank you again.

…

________________________________ From: Susanna Kiwala ***@***.***> Sent: Tuesday, November 19, 2024 2:20 PM To: griffithlab/pVACtools ***@***.***> Cc: Geneece Gilbert ***@***.***>; Author ***@***.***> Subject: Re: [griffithlab/pVACtools] Error: No command specified (Issue #1158) [△EXTERNAL] Thank you for this bug report and my apologies that you are running into issues with using pVACtools. Can you please attach your input VCF so I can try to debug this issue further? It's most likely that your VCF is either malformed in some way or the code is running into some sort of edge case but I would need to see the file to confirm this. — Reply to this email directly, view it on GitHub<#1158 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BMMUEPRBPTK6C5FERMS24V32BOTQNAVCNFSM6AAAAABSC6J4MKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOBWG43TKMJSHA>. You are receiving this because you authored the thread.

[susannasiebert]

I'm not entirely sure.

Can you try running the pvacseq generate_protein_fasta command on your VCF? That command runs the same code under the hood for the step that is failing in the full pVACseq pipeline. I'm hoping that this will generate some additional error messages. Otherwise I would need a minimal VCF to replicate this issue. You don't need to share the full VCF but if you could share one with even just a single variant that is causing this behavior, that would be sufficient.

[susannasiebert]

@Geneece have you had a chance to run the pvacseq generate_protein_fasta command on your input VCF to see if that outputs additional error information?

[Geneece]

Yes, unfortunately I received the same error message. As a test I removed predicted SVs with breakend notation from the VCF file, this resolved the error message. The output .fa file, however, remains empty even with this edit. Perhaps the remaining SVs are not appropriate inputs for this tool. Thank you for your help.

…

________________________________ From: Susanna Kiwala ***@***.***> Sent: Wednesday, December 18, 2024 7:25 AM To: griffithlab/pVACtools ***@***.***> Cc: Geneece Gilbert ***@***.***>; Mention ***@***.***> Subject: Re: [griffithlab/pVACtools] Error: No command specified (Issue #1158) [△EXTERNAL] @Geneece<https://github.com/Geneece> have you had a chance to run the pvacseq generate_protein_fasta command on your input VCF to see if that outputs additional error information? — Reply to this email directly, view it on GitHub<#1158 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BMMUEPUZERUVUUH6KLKB2QL2GGAWPAVCNFSM6AAAAABSC6J4MKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNJRGQ2TMMZSG4>. You are receiving this because you were mentioned.

[susannasiebert]

This does indeed point to at least one of the SVs being the culprit of this issue. Would you be able to create and share a single-variant VCF that creates an example SV that breaks the commands? This would greatly help us in improving pVACseq to handle this edge case.