search

MDU-PHL / bohra

A pipeline for bioinformatics analysis of bacterial genomes
GNU General Public License v3.0
18 stars 4 forks source link

An error when --kraken_db provides available kraken database path #78

Open abcdtree opened 5 months ago

abcdtree commented 5 months ago

Hi Kristy,

I was running bohra on Spartan with the conda install version.

14
Traceback (most recent call last):
  File "/data/gpfs/projects/xx/anaconda3/envs/bohra/bin/bohra", line 10, in <module>
    sys.exit(main())
  File "/data/gpfs/projects/xx/anaconda3/envs/bohra/lib/python3.8/site-packages/bohra/bohra.py", line 133, in main
    args.func(args)
  File "/data/gpfs/projects/xx/anaconda3/envs/bohra/lib/python3.8/site-packages/bohra/bohra.py", line 30, in run_pipeline
    return(R.run_pipeline())
  File "/data/gpfs/projects/xx/anaconda3/envs/bohra/lib/python3.8/site-packages/bohra/SnpDetection.py", line 663, in run_pipeline
    self._check_kraken2DB(checking = False)
  File "/data/gpfs/projects/xx/anaconda3/envs/bohra/lib/python3.8/site-packages/bohra/SnpDetection.py", line 311, in _check_kraken2DB
    self.check_kraken2_files(k2db = self.kraken_db)
AttributeError: 'RunSnpDetection' object has no attribute 'check_kraken2_files'

Got this error message. I guess the function may not be set up because bohra was more often to be run without --kraken_db parameter.

Cheers,

I love MDU . :D

Josh

tseemann commented 4 weeks ago

@kristyhoran this looks like a bug related to Kraken2 database or ENV var not being set?