From 6936beda100179612861e532cac9994f7f3fa321 Mon Sep 17 00:00:00 2001 From: RobinM-code Date: Thu, 30 Nov 2023 12:46:57 +0100 Subject: [PATCH] Warn on coloniarity problem --- scripts/gcta.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/scripts/gcta.py b/scripts/gcta.py index 612b032..d600da9 100644 --- a/scripts/gcta.py +++ b/scripts/gcta.py @@ -80,6 +80,9 @@ def perform_conditional_adjustment(sumstats, in_plink, temp_dir, index_var, if "Error: none of the given SNPs can be matched to the genotype and summary data." in gcta_error: logger.warning(' GCTA error:\n\n{0}\n'.format(gcta_error)) sys.exit(0) + if "Error: there is a collinearity problem of the given list of SNPs." in gcta_error: + logger.warning(' GCTA error:\n\n{0}\n'.format(gcta_error)) + sys.exit(0) if logger: logger.error(' GCTA error:\n\n{0}\n'.format(gcta_error)) sys.exit(1)