Error in step "Estimating functional enrichment using S LDSC"

[KPIYUSHA7]

Hi Omer, I am trying to run the Step5: Estimating functional enrichment using S LDSC on the example data provided in the manual. However, I am getting this error:

Traceback (most recent call last): File "ldsc.py", line 40, in module pd.set_option('precision', 4) File "/.conda/envs/polyfun/lib/python3.8/site-packages/pandas/_config/config.py", line 256, in call return self.func(*args, **kwds) File "/.conda/envs/polyfun/lib/python3.8/site-packages/pandas/_config/config.py", line 149, in _set_option key = _get_single_key(k, silent) File "/.conda/envs/polyfun/lib/python3.8/site-packages/pandas/_config/config.py", line 116, in _get_single_key raise OptionError("Pattern matched multiple keys") pandas._config.config.OptionError: 'Pattern matched multiple keys'

The command used is : mkdir -p temp

python ldsc.py \ --h2 example_data/sumstats.parquet \ --ref-ld-chr example_data/annotations. \ --w-ld-chr example_data/weights. \ --out temp/enrichment \ --overlap-annot \ --not-M-5-50

Please let me know what is the issue, as all the files being used are that of the example data folder, already provided in the github repository.

Thanks!

[omerwe]

Hi @KPIYUSHA7, thanks for the bug report. It looks like newer versions of pandas broke backwards compatibility for some settings. I just updated the code to fix this. Can you please git pull and let me know if the problem is fixed?

[KPIYUSHA7]

Thanks Omer. I am now able to run the Step 5 and produce the enrichment.results file for example data provided.