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Check for errors from calling DIAMOND #108

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Check for errors from calling DIAMOND #108

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4 changes: 2 additions & 2 deletions checkm2/diamond.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ def check_for_diamond(self):
# else returns something non-zero

try:
subprocess.call(['diamond', 'help'], stdout=open(os.devnull, 'w'), stderr=subprocess.STDOUT)
subprocess.check_call(['diamond', 'help'], stdout=open(os.devnull, 'w'), stderr=subprocess.STDOUT)
except:
logging.error("Make sure diamond is on your system path.")
sys.exit(1)
Expand Down Expand Up @@ -98,7 +98,7 @@ def __call_diamond(self, seq_object, diamond_output):
diamond_working_dir.name)

logging.debug(cmd)
subprocess.call(cmd, shell=True)
subprocess.check_call(cmd, shell=True)
logging.debug('Finished Running DIAMOND')
except Exception as e:
logging.error('An error occured while running DIAMOND: {}'.format(e))
Expand Down
4 changes: 1 addition & 3 deletions checkm2/prodigal.py
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Original file line number Diff line number Diff line change
Expand Up @@ -196,10 +196,8 @@ def areORFsCalled(self, bNucORFs):
def checkForProdigal(self):
"""Check to see if Prodigal is on the system before we try to run it."""

# Assume that a successful prodigal -h returns 0 and anything
# else returns something non-zero
try:
subprocess.call(['prodigal', '-h'], stdout=open(os.devnull, 'w'), stderr=subprocess.STDOUT)
subprocess.check_call(['prodigal', '-h'], stdout=open(os.devnull, 'w'), stderr=subprocess.STDOUT)
except:
logging.error("Make sure prodigal is on your system path.")
sys.exit(1)
Expand Down