Print error even if blast error message does not match pattern

[apetkau]

Fix for #155

Error message

  File "/usr/local/tools/_conda/envs/__staramr@0.7.2/lib/python3.7/site-packages/staramr/blast/JobHandler.py", line 289, in _make_blast_db
    err_msg = re.findall('REF\|(.*?)\'', err_msg)[0]
IndexError: list index out of range

Cause

While we weren't able to reproduce the issue, the error itself is triggered because we are parsing the output of makeblastdb and searching for particular patterns to extract an appropriate error message (re.findall('REF\|(.*?)\''). Perhaps either STDERR of makeblastdb was empty for the above issue, or different versions of blast print different messages. See below code

staramr/staramr/blast/JobHandler.py

Lines 287 to 290 in 6e8ded8

	except subprocess.CalledProcessError as e:
	err_msg = str(e.stderr.strip())
	err_msg = re.findall('REF\|(.*?)\'', err_msg)[0]
	raise Exception('Could not run makeblastdb on file {}, error {}'.format(file, err_msg))

Solution

The fix works by defaulting to just printing the full STDERR of makeblastdb if we can't pull out a more specific error message (rather than crashing).