Description
Hello, I recently encountered an Warning message after running xpclr using the software xpclr v1.1.2
My Code:
xpclr
--format vcf
--input keep.recode.vcf
--samplesA pinyuan.txt
--samplesB gaoyuan.txt
-C 1
--ld 0.95 --maxsnps 200 --size 50 --step 50
--out ./test2
My Warning :
2024-06-08 19:41:36 : INFO : running xpclr v1.1.2
2024-06-08 19:41:36 : INFO : Loading VCF
2024-06-08 19:42:58 : INFO : VCF loading complete
2024-06-08 19:42:58 : INFO : 59,263 SNPs in total are in the provided input files
2024-06-08 19:42:58 : INFO : 0 SNPs excluded as multiallelic
2024-06-08 19:42:58 : INFO : 0 SNPs excluded as missing in all samples in a population
2024-06-08 19:42:58 : INFO : 625 SNPs excluded as invariant or singleton in population 2
2024-06-08 19:42:58 : INFO : 58,638/59,263 SNPs included in the analysis (98.95%)
2024-06-08 19:42:58 : INFO : Done dropping above SNPs from analysis. XP-CLR algorithm starting.
2024-06-08 19:42:59 : INFO : No genetic distance provided; using rrate of 1e-08/bp
2024-06-08 19:42:59 : INFO : Omega estimated as : 0.053405
/home/limaoshi/mambaforge/envs/liftover/lib/python3.12/site-packages/xpclr/util.py:160: RuntimeWarning: Mean of empty slice
out["xpclr_norm"] = (out.xpclr - np.nanmean(out.xpclr))/np.nanstd(out.xpclr)
/home/limaoshi/mambaforge/envs/liftover/lib/python3.12/site-packages/numpy/lib/nanfunctions.py:1879: RuntimeWarning: Degrees of freedom <= 0 for slice.
var = nanvar(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
2024-06-08 20:05:46 : INFO : Analysis complete. Output file ./test2
Subsequently, when I opened the result file, I found that the columns for xpclr and xpclr-norm were empty. I don't know what the reason is, and my input files were all prepared according to the requirements.
Could you give me some suggestions? Thank you very much.