KeyError: u"None of [Int64Index

[wanghf0501]

I get error message "KeyError: u"None of [Int64Index([-2, -2, -2, -2, -2, -2, -2, -2, -2, -1,\n ...\n -1, -2, -2, -2, -2, -2, -2, -2, -2, -2],\n dtype='int64', length=1217311)] are in the [index]"", when I run mtag_munge.py on the example data ( python ldsc/mtag_munge.py --sumstats example/GWAS_EA_excl23andMe.txt --merge-alleles data/ldsc/w_hm3.snplist --n-value 766345 --keep-pval --p PVAL --out example/EA3_Lee2018).
Does anyone know how to fix it?

[dangxiao21]

I met the same problem, I changed the line:

dat.loc[~jj, [i for i in dat.columns if i != 'SNP']] = float('nan')

to the following in the mtag_munge.py script and run successfully:

dat.loc[~jj.astype('bool'), [i for i in dat.columns if i != 'SNP']] = float('nan')