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Error when processing somatic variants: Column 'GLOBAL_ASSOC_RANK' not found #256

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Kowen-Angenmed opened this issue Dec 13, 2024 · 6 comments
Closed

Error when processing somatic variants: Column 'GLOBAL_ASSOC_RANK' not found #256

Kowen-Angenmed opened this issue Dec 13, 2024 · 6 comments

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@Kowen-Angenmed
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I encountered an error while running PCGR 2.1.2 (grch38) during the somatic variant processing step. The error occurs when the system tries to rank variants according to clinical significance.
Error message:

Error in `dplyr::mutate()`:
In argument: `GLOBAL_ASSOC_RANK = dplyr::if_else(...)`.
Caused by error in `.data$GLOBAL_ASSOC_RANK`:
! Column `GLOBAL_ASSOC_RANK` not found in `.data`.

Steps to reproduce:

Running PCGR with somatic variants data
Error occurs during step 6 (Generation of output files)
Specifically during the assignment of variants to tiers of clinical significance

Environment:

Using conda environment: pcgrr
Command run:
export CONDA_PREFIX=/opt/mambaforge/envs/pcgrr && export PATH=/opt/mambaforge/envs/pcgrr/bin:"$PATH" && /opt/mambaforge/envs/pcgrr/bin/Rscript /opt/mambaforge/envs/pcgr/bin/pcgrr.R /mnt/pcgr/T001-COAD_docker/test_T001-COAD.grch38.pcgr.grch38.conf.yaml /opt/mambaforge/envs/pcgrr/etc/conda/activate.d/quarto.sh

Thank you a lot.
KW
@sigven
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sigven commented Dec 13, 2024

Hi @Kowen-Angenmed,

thanks a lot for reporting this! Would it be possible for you to share the input file (somatic VCF) so I can reproduce the error also on my side?

best,
Sigve

@Kowen-Angenmed
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Hi @sigven ,

I've tried running both the conda and docker versions, but get the same error. The input files used are from the example directory in this repository.
https://github.com/sigven/pcgr/blob/main/examples/T001-COAD.grch38.vcf.gz

docker container run -it --rm \ -v /media/hunglab/DATA/kowen/workspace/_pipelineDB/vep_cache:/mnt/vep \ -v /media/hunglab/DATA/kowen/workspace/_pipelineDB/pcgr_bundle:/mnt/bundle \ -v ~/workspace/project/pcgr/AG002:/mnt/pcgr \ sigven/pcgr:2.1.2 \ pcgr \ --input_vcf "/mnt/pcgr/vcf_files/T001-COAD.grch38.vcf.gz" \ --input_cna "/mnt/pcgr/vcf_files/T001-COAD.cna.tsv" \ --vep_dir "/mnt/vep" \ --refdata_dir "/mnt/bundle" \ --output_dir "/mnt/pcgr/T001-COAD_docker" \ --genome_assembly "grch38" \ --sample_id "test_T001-COAD.grch38" \ --tumor_dp_tag "TDP" \ --tumor_af_tag "TVAF" \ --tumor_purity 0.9 \ --tumor_ploidy 2.0 \ --assay "WES" \ --debug --force_overwrite

Could you please advise on how to resolve this issue?
Thanks,
KW

@sigven
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sigven commented Dec 16, 2024

Thanks for the info , I'll have a look.

@sigven
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sigven commented Dec 16, 2024

Just tried the v2.1.2 Conda version on my Mac, and unable to reproduce your error, it processed T001-COAD.grch38.vcf.gz fine. So bit unsure how to proceed with respect to your error. What does pcgr --version give you? Can you provide the full log?

@Kowen-Angenmed
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I re-downloaded all the data, including the vep_cache and PCGR bundle. The test results are fine now. Previously, I may have mistakenly used the human_sapins_merged version from the vep_cache. Everything is working correctly now. Thank you for your help!

@sigven
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sigven commented Dec 23, 2024

Glad you figured it out:) Enjoy the holiday season.

kind regards,
Sigve

@sigven sigven closed this as completed Dec 23, 2024
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@sigven @Kowen-Angenmed