Error installing DB

[shlomobl]

Hello,

I am using an Ubuntu 20.02 system in which I installed ConFindr as part of the AQUAMIS pipeline. I am now trying to complete the setup of the DBs following the instructions in the ConFindr site, and I got the following error:

2023-10-30 11:04:04  Downloading BACT000065... 
 2023-10-30 11:04:17  Downloading rMLST profiles... 
 2023-10-30 11:04:18  Combining rMLST files... 
Traceback (most recent call last):
 File "/home/shlomo/Programs/miniconda3/envs/aquamis/bin/confindr_database_setup", line 10, in <module>
   sys.exit(main())
 File "/home/shlomo/Programs/miniconda3/envs/aquamis/lib/python3.7/site-packages/confindr_src/database_setup.py", line 270, in main
   args.secret_file)
 File "/home/shlomo/Programs/miniconda3/envs/aquamis/lib/python3.7/site-packages/confindr_src/database_setup.py", line 209, in setup_confindr_database
   record.seq._data = record.seq._data.replace('-', '').replace('N', '')
TypeError: a bytes-like object is required, not 'str'

Hope someone can help me figure out what's wrong and how to fix.
Thanks!

[pcrxn]

Hi @shlomobl,

The pipeline that you're using may be running an older version of ConFindr. If possible, please update the ConFindr version, but if this isn't possible without breaking things, then upgrading the BioPython version to >1.79 should fix this too.