Benjamin Wingfield

The file I'm trying to work with is a variant information file from [plink2](https://www.cog-genomics.org/plink/2.0/) (`.pvar.zst` or `.bim.zst`). plink is a popular toolkit used in genome wide association studies and related...

That fixes my problem 😁 thank you!

pretty sure this was fixed in https://github.com/PGScatalog/pygscatalog/pull/15 but we haven't integrated it yet

@lemieuxl released now https://github.com/PGScatalog/pgsc_calc/releases/tag/v2.0.0-alpha.6 sorry for the delay, the update ended up including more things than expected

Sorry you're having trouble. I don't normally see problems with this process. A few questions: * Are you able to run the workflow OK without `--run_ancestry`? * What does `nextflow_ancestry.yaml`...

That's strange. The only thing that looks odd to me is `sudo`. Our tests never run nextflow as root - only on user accounts - so perhaps there's a problem...

Sorry, I'm not sure what's going wrong. Our test suite is passing and we're able to run the ancestry calculations in quite a few different environments. Tracking down the precise...

@mireklzicar It also might be worth trying again [with the latest release](https://github.com/PGScatalog/pgsc_calc/releases/tag/v2.0.0-alpha.5)

Our ancestry VCF test [wasn't testing VCFs](https://github.com/PGScatalog/pgsc_calc/commit/7345cdd879e8edce97800bbcdb40ab2ecc556025) 👀 It was accidentally using plink2 files as input. When I fixed the test it reproduced the reported error. After making some changes...

Thanks for the bug report! Sorry, I can't reproduce on the dev branch. Here's what I tried: ``` $ cd /path/to/pgsc_calc $ rm -r work results # guarantee a fresh...