Ignore rmtree errors and log when results are written #298

Author: rafelafrance

lib/assemblers/base.py

@@ -224,6 +224,10 @@ def write_filtered_contigs(self, prefix):
             self.state['cxn'],
             self.args['bit_score'],
             self.args['contig_length'])
+
+        self.log.info('Writing {} filtered contigs after iteration {}'.format(
+            count, self.state['iteration']))
+
         if not count:
             return
 
@@ -241,6 +245,10 @@ def write_filtered_contigs(self, prefix):
     def write_all_contigs(self, prefix):
         """Write all contigs to a final output file."""
         count = db_atram.all_assembled_contigs_count(self.state['cxn'])
+
+        self.log.info('{} total contigs after iteration {}'.format(
+            count, self.state['iteration']))
+
         if not count:
             return
 

lib/assemblers/none.py

@@ -15,6 +15,8 @@ def __init__(self, args, cxn, log):
 
     def write_final_output(self, blast_db, query):
         """Output this file if we are not assembling the contigs."""
+        self.log.info('Writing blast hits.')
+
         prefix = self.final_output_prefix(blast_db, query)
 
         file_name = '{}.fasta'.format(prefix)

lib/util.py

@@ -55,7 +55,7 @@ def make_temp_dir(where=None, prefix=None, keep=False):
         yield temp_dir
     finally:
         if not keep or not where:
-            rmtree(temp_dir)
+            rmtree(temp_dir, ignore_errors=True)
 
 
 @contextmanager