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MDU-PHL / bohra

A pipeline for bioinformatics analysis of bacterial genomes
GNU General Public License v3.0
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"bohra run" no params is a traceback mess #35

Closed tseemann closed 4 years ago

tseemann commented 4 years ago 
bohra run
[INFO:03/05/2020 05:13:47 PM] Starting bohra pipeline using /home/linuxbrew/.linuxbrew/bin/bohra run
[INFO:03/05/2020 05:13:47 PM] You are running bohra in preview mode.
Traceback (most recent call last):
  File "/home/linuxbrew/.linuxbrew/bin/bohra", line 8, in <module>
    sys.exit(main())
  File "/home/linuxbrew/.linuxbrew/opt/python/lib/python3.7/site-packages/bohra/bohra.py", line 136, in main
    args.func(args)
  File "/home/linuxbrew/.linuxbrew/opt/python/lib/python3.7/site-packages/bohra/bohra.py", line 32, in run_pipeline
    R = RunSnpDetection(args)
  File "/home/linuxbrew/.linuxbrew/opt/python/lib/python3.7/site-packages/bohra/SnpDetection.py", line 65, in __init__
    self.log_messages('warning', 'Input file can not be empty, please set -i path_to_input to try again')
AttributeError: 'RunSnpDetection' object has no attribute 'log_messages'