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geronimp / enrichM

Toolbox for comparative genomics of MAGs
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AttributeError: 'Databases' object has no attribute 'M2DEF' #126

Closed wdp9966 closed 3 years ago

wdp9966 commented 3 years ago

Thanks for your nice tool. When I used enrichm_0.6.3, the database was manually downloaded. But there is one error message come out. I don't know how to solve it.

[2021-04-20 00:16:21 AM] INFO: Running command: /home/wdp/.conda/envs/enrichm_0.6.3/bin/enrichm annotate --output enrichm --protein_directory /usr/local/usrdata_16T/wdp/home/test_protein/ --ko --pfam --tigrfam --hypothetical --cazy --threads 36 --parallel 36 --force [2021-04-20 00:16:21 AM] INFO: Loading databases Traceback (most recent call last): File "/home/wdp/.conda/envs/enrichm_0.6.3/bin/enrichm", line 357, in r.main(args, sys.argv) File "/home/wdp/.conda/envs/enrichm_0.6.3/lib/python3.7/site-packages/enrichm/run.py", line 319, in main args.light) File "/home/wdp/.conda/envs/enrichm_0.6.3/lib/python3.7/site-packages/enrichm/annotate.py", line 120, in init self.databases = Databases() File "/home/wdp/.conda/envs/enrichm_0.6.3/lib/python3.7/site-packages/enrichm/databases.py", line 97, in init self.m2def = self.load_pickle(self.M2DEF) AttributeError: 'Databases' object has no attribute 'M2DEF'

Thanks very much!

wdp9966 commented 3 years ago

I have automatically downloaded the database with the "enrichm data", and resolved this issue. While no folder "26-11-2018" was found in the automatically database, and all files in the "26-11-2018" were listed in the "/databases/enrichm_database_v10/" together with the folder "databases", "gtdb" and "ids". Meanwhile, the file "uniref100.KO.dmnd" in the databases was renamed as "uniref100.dmnd", beacuse of the issue " INFO: - BLASTing genomes No such file or directory Error: Error opening file /databases/enrichm_database_v10/databases/uniref100.dmnd" Thanks very much!