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geronimp / enrichM

Toolbox for comparative genomics of MAGs
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AttributeError: 'Databases' object has no attribute 'REF_DIR' #101

Open Thexiyang opened 4 years ago

Thexiyang commented 4 years ago

Thank for the nice tool! I downloaded the database manually and specified its location. However, I when used enirchm annotate, there is one error message come out. It reads as follows. Could you give me some hints on how I can solve it? Thanks! 

-bash-4.2$ enrichm annotate --genome_files reference.faa
[2020-03-30 06:44:36 AM] INFO: Command:enrichm annotate --genome_files reference.faa
[2020-03-30 06:44:36 AM] INFO: Running the annotate pipeline
Traceback (most recent call last):
  File "/enrichm/bin/enrichm", line 342, in <module>
    run.run_enrichm(args, sys.argv)
  File "/enrichm/lib/python3.7/site-packages/enrichm/run.py", line 305, in run_enrichm
    args.threads, args.parallel, args.suffix, args.light)
  File "/enrichm/lib/python3.7/site-packages/enrichm/annotate.py", line 122, in __init__
    self.databases = Databases()
  File "/enrichm/lib/python3.7/site-packages/enrichm/databases.py", line 98, in __init__
    self.KO_DB = os.path.join(self.REF_DIR, self.KO_DB_NAME + self.DMND_SUFFIX)
AttributeError: 'Databases' object has no attribute 'REF_DIR'
geronimp commented 4 years ago

Hi there,

Thank you for using enrichm!

Apologies for the unclear error message, would you be able to try and run enrichm annotate with an annotate option (either --ko --cazy --tigrfam or --pfam) and let me know if this error still occurs?

Thanks,

Joel

Thexiyang commented 4 years ago

Thanks for the reply. I tried. Same issue.

geronimp commented 4 years ago

Would you please be able to confirm for me that you are using version 0.5.0?

Thexiyang commented 4 years ago

Yes. I installed using conda and then upgraded to 0.5.0 using pip. It looks it did not look for the database.

jianshu93 commented 4 years ago

I have the same issue with 0.5.0 but. Is it solved?Thanks

liupfskygre commented 3 years ago

Hi, the same issue here, is this being solved? thanks.

Version: 0.5.0

Traceback (most recent call last):
  File "/home/dell/.conda/envs/enrichm/bin/enrichm", line 342, in <module>
    run.run_enrichm(args, sys.argv)
  File "/home/dell/.conda/envs/enrichm/lib/python3.7/site-packages/enrichm/run.py", line 305, in run_enrichm
    args.threads, args.parallel, args.suffix, args.light)
  File "/home/dell/.conda/envs/enrichm/lib/python3.7/site-packages/enrichm/annotate.py", line 122, in __init__
    self.databases = Databases()
  File "/home/dell/.conda/envs/enrichm/lib/python3.7/site-packages/enrichm/databases.py", line 98, in __init__
    self.KO_DB = os.path.join(self.REF_DIR, self.KO_DB_NAME + self.DMND_SUFFIX)
AttributeError: 'Databases' object has no attribute 'REF_DIR'
jianshu93 commented 3 years ago

i do not think it's solved. Still cannot use it.

mengyuan09876 commented 11 months ago

AttributeError: 'Databases' object has no attribute 'REF_DIR' same problem