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WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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DRAM-setup.py prepare_databases issue #242

Closed YilingWang1997 closed 1 year ago

YilingWang1997 commented 1 year ago

Hello

I installed DRAM using miniconda and tried to download databases. However, I got the following error:

2022-12-14 14:45:34,409 - dbCAN database processed 2022-12-14 14:45:34,411 - Moved dbcan to final destination, configuration updated 2022-12-14 14:45:34,413 - Moved dbcan_fam_activities to final destination, configuration updated 2022-12-14 14:45:34,415 - Moved dbcan_subfam_ec to final destination, configuration updated 2022-12-14 14:45:34,417 - Moved vog_annotations to final destination, configuration updated 2022-12-14 14:45:34,417 - Processing viral 2022-12-14 14:45:41,871 - RefSeq viral database processed Traceback (most recent call last): File "/home/ec2-user/miniconda3/envs/DRAM/bin/DRAM-setup.py", line 184, in <module> args.func(**args_dict) File "/home/ec2-user/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 619, in prepare_databases db_handler.set_database_paths(**{f"{k}_loc":v}) TypeError: DatabaseHandler.set_database_paths() got an unexpected keyword argument 'viral_loc'

Do you know how to solve this problem? Thank you!

rmFlynn commented 1 year ago

For you, I would install dram_bio 1.4.0 I introduced a bug in 1.4.2 trying to fix a bug in 1.4.0 I am fixing it now but 1.4.0 bug will not stop you in your case. conda install -c bioconda dram==1.4.0

rmFlynn commented 1 year ago

All bugs seem to be corrected for this issue