failed on field 'sebeta' attempting to convert value 'Inf' to type <class 'float'>

Open Shicheng-Guo opened this issue 4 years ago • 1 comments

Regenie have 'inf' in sebeta column which will cause error for Pheweb parse. Maybe we can add one step to remove such records from regenie summary statistics output.

pheweb.utils.PheWebError: failed on field 'sebeta' attempting to convert value 'Inf' to type <class 'float'> with constraints {'aliases': ['se'], 'type': <class 'float'>, 'nullable': True, 'sigfigs': 2, 'tooltip_underscoretemplate': False, 'tooltip_lztemplate': False, 'required': False, 'from_assoc_files': True} in '/expanse/projects/janssen4/dsci-csb/user/sguo2/pheweb2/input/UKB.phecode.v1.WGS.additive.SVA_X1013.regenie.gz' on line with values ['X', '155984365', 'C', 'T', 'NA', '0.5', 'NA', 'Inf', '120964']

Sep 03 '21 16:09 Shicheng-Guo

Could you send the full error message? One of those NAs is the pvalue, right?

Sep 03 '21 17:09 pjvandehaar