Throw an error if blastn fails with non-zero exit code

bifrost_chewbbaca/rule__blast_genecall.py

@@ -34,7 +34,10 @@ def run_blastn_and_parse(query_fa, db, assembly_sequences,log):
 
     # Run BLASTN and stream output
     with subprocess.Popen(blastn_cmd, stdout=subprocess.PIPE, text=True, stderr=open(log.err_file, "w+")) as proc:
-        for line in proc.stdout:
+        stdout = proc.communicate()
+        if proc.returncode != 0:
+            raise RuntimeError(f"Command {" ".join(blastn_cmd)} failed with code {proc.returncode}.\nCheck the logs in {log.err_file}")
+        for line in stdout:
             # Parse the BLAST output line into a dictionary
             cols = line.strip().split("\t")
             record = {