I swear i've fixed this bug like three times now. Changed the order of dirs & files in os.walk.

chipathlon/run_data.py

@@ -170,7 +170,7 @@ class RunData(object):
                 self.genomes[assembly]["chr_fasta"] = []
                 # Load chromosome files here:
                 base_dir = os.path.dirname(os.path.dirname(self.data["genomes"][assembly]["chrom.sizes"] + "/"))
-                for root, files, dirs in os.walk(base_dir):
+                for root, dirs, files in os.walk(base_dir):
                     for f in files:
                         if f.startswith("chr"):
                             self._add_file(f, root + "/" + f, "local")