Fixed missing nreads when using sam as input file

biobakery · Aug 27, 2020 · 9059751 · 9059751
1 parent 446ee61
commit 9059751
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/metaphlan/metaphlan.py b/metaphlan/metaphlan.py
@@ -1001,6 +1001,7 @@ def main():
         os.remove( pars['inp'] )
 
     if ESTIMATE_UNK and pars['input_type'] == 'sam':
+        n_metagenome_reads = pars['nreads']
         if not n_metagenome_reads and not pars['nreads']:
             sys.stderr.write(
                     "Please provide the size of the metagenome using the "