rsx-rs
Troubleshooting¶
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Troubleshooting¶
Build¶
minimap2-sys fails to build¶
The map command links minimap2, which needs a C toolchain and does not build
on Windows MSVC. Build the other commands without it:
cargo build --release --no-default-features
Linker error building the Python extension on macOS¶
The pyrsx extension is a pyo3 extension-module; a plain workspace build
needs the dynamic-lookup linker flag. The repository ships a .cargo/config.toml
that sets -undefined dynamic_lookup for macOS targets; build from the workspace
root so it is picked up, or use maturin directly.
Running¶
Output does not match RADSex¶
Specify the groups explicitly with -G (for example -G M,F). Without an
explicit group order, tie-breaking and column order can differ; with it, the
frequentist calls are identical to RADSex v1.2.0.
A command uses more memory than expected¶
signif with FDR correction materializes per-marker rows because global ranking
is intrinsic to the procedure. For strictly bounded memory use Bonferroni or the
uncorrected streaming mode. depth on inputs above a few GB switches to external
sort automatically; force spill testing with RSX_FORCE_SPILL=1.
map reports no alignments¶
Check that -g/--genome points to a FASTA the reference index can be built
from, and that the marker tags are long enough to align. map is feature-gated;
confirm the binary was built with the default map feature.
Statistics¶
Bayesian output is empty or all markers look “Bayes-factor-only”¶
The posterior layer reports evidence under explicit priors and a fixed heterogametic-sex prevalence. If many markers are Bayes-factor-only, the data support enrichment but not above the posterior threshold; treat those as hypotheses to validate by mapping, PCR, or independent genomic evidence rather than as calls.
Which sex system should I assume (XY vs ZW)?¶
You do not have to choose: the posterior mixes symmetrically over both directions. Male-biased markers surface as candidate Y-linked under XY; female-biased markers as candidate W-linked under ZW.
Reporting a problem¶
Open an issue on GitHub with the command, the input shape (individuals, markers, depth), and the exact message. For reproducibility questions, point to the Zenodo archive.