[BUG] anvi-setup-kegg-data encountered an error

[Zerong0513]

Short description of the problem

anvi-setup-kegg-data encountered an error when running anvi-setup-kegg-data --download-from-kegg -D -T 4 --reset

anvi'o version

Anvi'o .......................................: marie (v8)
Python .......................................: 3.10.15
Profile database .............................: 38
Contigs database .............................: 21
Pan database .................................: 16
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 4
tRNA-seq database ............................: 2

System info

Windows 11. Anvio installed followed the instructions by conda.

Detailed description of the issue

Traceback (most recent call last):
File "/home/zerong/miniconda3/envs/anvio-8/bin/anvi-setup-kegg-data", line 179, in
main(args, unknown_args)
File "/home/zerong/miniconda3/envs/anvio-8/lib/python3.10/site-packages/anvio/terminal.py", line 915, in wrapper
program_method(*args, **kwargs)
File "/home/zerong/miniconda3/envs/anvio-8/bin/anvi-setup-kegg-data", line 126, in main
KODatabase.set_up(num_threads = args.num_threads, dir = setup_directory, reset = args.reset)
File "/home/zerong/miniconda3/envs/anvio-8/lib/python3.10/site-packages/anvio/biochemistry/reactionnetwork.py", line 1262, in set_up
if line[0] == ' ':
IndexError: string index out of range

[semiller10]

Hi @Zerong0513, sorry for the delayed response. Here is my recommendation of what to do.

First, I notice that you have two redundant flags in your command, --download-from-kegg and -D. -D is just the abbreviated version of --download-from-kegg.

If you wish to use the most advanced anvi'o capabilities for manipulating KEGG data, I suggest using the development version, which you can find installation instruction for here. I expect that downloading the current version of the KEGG database with your command will work fine in dev since we have recently tested that. New additions for manipulating KEGG data include anvi-draw-kegg-pathways and a better version of the reaction network. A drawback to switching from v8 to dev is that you will have to remake your databases.

If you wish to continue using v8, I recommend using the following command to download the most recent KEGG data without the files needed for the reaction network: anvi-setup-kegg-data -D -T 4 --reset --mode KOfam modules. This will still download the files needed for KOfam annotation of contigs databases, calculating module completeness, and a few other functions.

Let me know how that works.
Best of luck,
Sam