PGScatalog / pgscatalog_utils

(superseded by pygscatalog) Utilities for working with PGS Catalog API and scoring files
Apache License 2.0
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Make sure ancestry_analysis works on single samples #57

Closed smlmbrt closed 8 months ago

smlmbrt commented 11 months ago
          @AWS-crafter are you by any chance running the pipeline on a single sample?

_Originally posted by @smlmbrt in https://github.com/PGScatalog/pgsc_calc/issues/177#issuecomment-1737035019_

Current fails on the Mann-whitney U test stage when there is only 1 sample

AWS-crafter commented 11 months ago

Thanks for looking into this. I've previously ran the pipeline successfully with --run_ancestry on a single sample, so having 1 sample probably is not sufficient in and of itself to cause a failure, but does under certain circumstances (i.e, single sample + some other unknown factor).

smlmbrt commented 9 months ago

Also mentioned here https://github.com/PGScatalog/pgsc_calc/issues/174#issuecomment-1775321744

smlmbrt commented 9 months ago

Thanks for looking into this. I've previously ran the pipeline successfully with --run_ancestry on a single sample, so having 1 sample probably is not sufficient in and of itself to cause a failure, but does under certain circumstances (i.e, single sample + some other unknown factor).

This is helpful to know - I just tried it with one sample and it didn't fail.

smlmbrt commented 9 months ago

This bug might not actually be specific to single-samples (re: https://github.com/PGScatalog/pgsc_calc/issues/177#issuecomment-1804847942)

smlmbrt commented 9 months ago

65 will likely fix this bug that happens when there are only samples with numeric identifiers.

nebfield commented 8 months ago

https://github.com/PGScatalog/pgscatalog_utils/releases/tag/v0.4.3