Benjamin Wingfield

The variant IDs are missing from the log because no matching variant is found in your target genomes. For example, the unmatched variant in PGS000119 at chromosome 16 / position...

Which Nextflow process fails? Could you please copy the output from your terminal and upload `.command.log` / `.command.err` / `.command.run` from the working directory of the failed process? Does the...

This is definitely broken, sorry! We set up a unified data model for all PGS Catalog Python packages in https://github.com/PGScatalog/pygscatalog/pull/46 which broke support for multiple columns. This isn't easy to...

Hi, thanks for reporting the issue. I think the problem might be the extra `.` in your filename. Try renaming your files to remove `.dose` (or use a different delimiter...

> I am able to get the pipeline to run if I use vcf files instead of pfiles for my imputed chromosomes. This does have the downside of being a...

Are you able to use the conda profile? These problems are caused by the way apptainer is set up on your cluster - perhaps your cluster admins can help.

`/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/6c/e7f9e4905b61e1f67635c5d9a607ac/.command.run` will contain a bash script generated by Nextflow for the failing process. The `nxf_launch()` function should contain the apptainer command that's failing, which might be enough for a minimal...

Closing this now. Please feel free to reopen or create a new issue or discussion if you have any more questions.

I'd suggest converting your VCF into plink2 files before using the workflow. Your VCF file seems complicated and big! [See here for more details](https://pgsc-calc.readthedocs.io/en/latest/how-to/prepare.html). In particular it would be probably...

8GB RAM isn't enough for a big target genome. You can allocate more memory to the APPLY_SCORE stage by [changing your configuration](https://pgsc-calc.readthedocs.io/en/latest/how-to/bigjob.html#high-performance-computing-cluster): ``` process { withName: 'APPLY_SCORE' { cpus =...