feat(fix merging with 540):

Ecogenomics · Apr 24, 2024 · 3e1cc69 · 3e1cc69
1 parent b1096b8
commit 3e1cc69
Showing 1 changed file with 12 additions and 17 deletions.
diff --git a/gtdbtk/main.py b/gtdbtk/main.py
@@ -1160,23 +1160,18 @@ def parse_options(self, options):
             if all_classified_ani:
                 self.logger.info('All genomes have been classified by the ANI screening step, Identify and Align steps will be skipped.')
             else:
-                reports  = self.identify(options,classified_genomes)
-                if reports is None:
-                    self.logger.info(
-                        'No genomes could pass the Identify step, Align and Classify steps will be skipped.')
-                    all_classified_ani = True
-                else:
-                    options.taxa_filter = None
-                    options.custom_msa_filters = False
-                    # Added here due to the other mutex argument being included above.
-                    options.skip_trimming = False
-                    options.min_consensus = None
-                    options.min_perc_taxa = None
-                    options.skip_gtdb_refs = False
-                    options.cols_per_gene = None
-                    options.max_consensus = None
-                    options.rnd_seed = None
-                    options.skip_trimming = False
+                self.identify(options, classified_genomes)
+                options.taxa_filter = None
+                options.custom_msa_filters = False
+                # Added here due to the other mutex argument being included above.
+                options.skip_trimming = False
+                options.min_consensus = None
+                options.min_perc_taxa = None
+                options.skip_gtdb_refs = False
+                options.cols_per_gene = None
+                options.max_consensus = None
+                options.rnd_seed = None
+                options.skip_trimming = False
 
                 all_failed_prodigal = self.align(options)