GitLab

For some in put the pre-processing procedure freeze (and ctrl+C does not work).

It seems to be when the markername field has NA values (since removing those line removed the problem), but that was not a sufficient condition to reduce the size of the illustrating files. I did not manage to make a 20 line file that replicate the bug.

I put the file that bug in PCMA/1._DATA/freeze_pre_process

The procedure output is:

processing GWAS: Willer_AtrialFibri
MarkerName	rs_dbSNP147	CHR	POS_GRCh37	A1	A2	Freq_A2	Effect_A2	StdErr	Pvalue

snpid    1
a2       4
a1       5
freq     6
z        7
se       8
pval     9
dtype: int64
sys:1: DtypeWarning: Columns (1) have mixed types. Specify dtype option on import or set low_memory=False.