Merge branch 'development'

phac-nml · Oct 26, 2022 · 3f32f49 · 3f32f49
2 parents 0088d49 + 4e2e245
commit 3f32f49
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,7 @@
 # Version 0.9.1
 
-* Fixed a bug that occured when parsing some plasmid FASTA record IDs.
+* Fixed a bug that occured when parsing some plasmid FASTA record IDs ([PR 159](https://github.com/phac-nml/staramr/pull/159)).
+* Fixed issue where sometimes the extraction of error messages from `makeblastdb` was crashing leading to less useful errors ([PR 160](https://github.com/phac-nml/staramr/pull/160)).
 
 # Version 0.9.0
 

diff --git a/staramr/blast/JobHandler.py b/staramr/blast/JobHandler.py
@@ -286,5 +286,7 @@ def _make_blast_db(self, path: str, file: str) -> None:
             subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True)
         except subprocess.CalledProcessError as e:
             err_msg = str(e.stderr.strip())
-            err_msg = re.findall('REF\|(.*?)\'', err_msg)[0]
+            err_msg_match = re.findall('REF\|(.*?)\'', err_msg)
+            if len(err_msg_match) > 0:
+                err_msg = err_msg_match[0]
             raise Exception('Could not run makeblastdb on file {}, error {}'.format(file, err_msg))