Warn on coloniarity problem

thehyve · Nov 30, 2023 · 6936bed · 6936bed
1 parent d6367e9
commit 6936bed
Showing 1 changed file with 3 additions and 0 deletions.
diff --git 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)