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SNP and COG association with fixed effects model #271
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Try without |
@johnlees |
That looks ok to me, the likelihoods in your file should be ignored. To debug further we would need you to make a minimal reproducible example, including input files and ideally with a single variant which triggers this error. |
@johnlees |
Hi, everyone
I encounter an issue when I run with my laptop (macbook pro, M3 max, using iterm with rosetta x86 simulation)
SNP and COG association with fixed effects model :
pyseer --phenotypes a.pheno --vcf change.vcf.gz --load-m a_mds.pkl --lineage --print-samples --cpu 8 > SNPs_amox_all.txt
it showed a lot of logs like:
error:
/Users/Ycchen/miniforge3/envs/Pyseer/lib/python3.10/site-packages/statsmodels/discrete/discrete_model.py:2385: RuntimeWarning: overflow encountered in exp
return 1/(1+np.exp(-X))
/Users/Ycchen/miniforge3/envs/Pyseer/lib/python3.10/site-packages/statsmodels/discrete/discrete_model.py:2443: RuntimeWarning: divide by zero encountered in log
return np.sum(np.log(self.cdf(q * linpred)))
does anyone ever encounter such an issue ?
many thanks
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