conditions that makes the pre-processing procedure freeze
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.