anthony-aylward
commented
6 years ago For me this was caused by pandas version 0.21.0, and I solved the problem by downgrading to pandas 0.20.1
pip uninstall pandas
pip install pandas==0.20.1Open skanoni opened 6 years ago
anthony-aylward
commented
6 years ago For me this was caused by pandas version 0.21.0, and I solved the problem by downgrading to pandas 0.20.1
pip uninstall pandas
pip install pandas==0.20.1
Hi,
I am testing LDSC with the example files and I am getting the following errors. Could you please help me troubleshoot?
Call: ./munge_sumstats.py \ --out scz \ --merge-alleles w_hm3.snplist \ --N 17115.0 \ --sumstats pgc.cross.SCZ17.2013-05.txt
Interpreting column names as follows: info: INFO score (imputation quality; higher --> better imputation) snpid: Variant ID (e.g., rs number) a1: Allele 1, interpreted as ref allele for signed sumstat. pval: p-Value a2: Allele 2, interpreted as non-ref allele for signed sumstat. or: Odds ratio (1 --> no effect; above 1 --> A1 is risk increasing)
Reading list of SNPs for allele merge from w_hm3.snplist Read 1217311 SNPs for allele merge. Reading sumstats from pgc.cross.SCZ17.2013-05.txt into memory 5000000 SNPs at a time. Read 1237958 SNPs from --sumstats file. Removed 137131 SNPs not in --merge-alleles. Removed 0 SNPs with missing values. Removed 256286 SNPs with INFO <= 0.9. Removed 0 SNPs with MAF <= 0.01. Removed 0 SNPs with out-of-bounds p-values. Removed 2 variants that were not SNPs or were strand-ambiguous. 844539 SNPs remain. Removed 0 SNPs with duplicated rs numbers (844539 SNPs remain). Using N = 17115.0 Median value of or was 1.0, which seems sensible. Removed 39 SNPs whose alleles did not match --merge-alleles (844500 SNPs remain).
ERROR converting summary statistics:
Traceback (most recent call last): File "./munge_sumstats.py", line 701, in munge_sumstats dat = allele_merge(dat, merge_alleles, log) File "./munge_sumstats.py", line 439, in allele_merge dat.loc[~jj, [i for i in dat.columns if i != 'SNP']] = float('nan') File "/python2/lib/python2.7/site-packages/pandas/core/indexing.py", line 193, in setitem indexer = self._get_setitem_indexer(key) File "/python2/lib/python2.7/site-packages/pandas/core/indexing.py", line 171, in _get_setitem_indexer return self._convert_tuple(key, is_setter=True) File "/python2/lib/python2.7/site-packages/pandas/core/indexing.py", line 242, in _convert_tuple idx = self._convert_to_indexer(k, axis=i, is_setter=is_setter) File "/python2/lib/python2.7/site-packages/pandas/core/indexing.py", line 1269, in _convert_to_indexer .format(mask=objarr[mask])) KeyError: '[-1 -1 -2 ..., -1 -1 -1] not in index'
Conversion finished at Fri Nov 3 11:52:40 2017 Total time elapsed: 40.27s