update to hal

ComparativeGenomicsToolkit · Jun 27, 2020 · ee3cdce · ee3cdce
1 parent b1e400f
commit ee3cdce
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/cat/__init__.py b/cat/__init__.py
@@ -736,7 +736,7 @@ def output(self):
 
     def run(self):
         logger.info('Extracting fasta for {}.'.format(self.genome))
-        cmd = ['hal2fasta', os.path.abspath(self.hal), self.genome]
+        cmd = ['hal2fasta', '--onlySequenceNames', os.path.abspath(self.hal), self.genome]
         self.run_cmd(cmd)