error in anvi'o tool

Question

[Kumar]

I have installed anvi'o in my miniconda3 (Ubuntu 18.04 LTS) laptop computer and successfully executed anvi-self-test. I intended to execute anvi-setup-ncbi-cogs to annotate my contigs, but whenever I run this command, it throws errors as follows,

(anvio-7) dinesh@dinesh7k:~$ anvi-setup-ncbi-cogs
COG version ..................................: COG20
COG data source ..............................: The anvi'o default.
COG base directory ...........................: /home/dinesh/miniconda3/envs/anvio-7/lib/python3.6/site-packages/anvio/data/misc/COG

WARNING
===============================================
This program will first check whether you have all the raw files, and then will
attempt to regenerate everything that is necessary from them.

Press ENTER to continue, or press CTRL + C to cancel...

Downloaded successfully ......................: /home/dinesh/miniconda3/envs/anvio-7/lib/python3.6/site-packages/anvio/data/misc/COG/COG20/RAW_DATA_FROM_NCBI/cog-20.cog.csv
Downloaded successfully ......................: /home/dinesh/miniconda3/envs/anvio-7/lib/python3.6/site-packages/anvio/data/misc/COG/COG20/RAW_DATA_FROM_NCBI/cog-20.def.tab
Downloaded successfully ......................: /home/dinesh/miniconda3/envs/anvio-7/lib/python3.6/site-packages/anvio/data/misc/COG/COG20/RAW_DATA_FROM_NCBI/fun-20.tab
Downloaded successfully ......................: /home/dinesh/miniconda3/envs/anvio-7/lib/python3.6/site-packages/anvio/data/misc/COG/COG20/RAW_DATA_FROM_NCBI/cog-20.fa.gz
Traceback (most recent call last):
  File "/home/dinesh/miniconda3/envs/anvio-7/bin/anvi-setup-ncbi-cogs", line 47, in <module>
    setup.create()
  File "/home/dinesh/miniconda3/envs/anvio-7/lib/python3.6/site-packages/anvio/cogs.py", line 617, in create
    self.setup_raw_data()
  File "/home/dinesh/miniconda3/envs/anvio-7/lib/python3.6/site-packages/anvio/cogs.py", line 831, in setup_raw_data
    self.files[file_name]['func'](file_path, J(self.COG_data_dir, self.files[file_name]['formatted_file_name']))
  File "/home/dinesh/miniconda3/envs/anvio-7/lib/python3.6/site-packages/anvio/cogs.py", line 659, in format_p_id_to_cog_id_cPickle
    p_id = fields[2].replace('.', '_')
IndexError: list index out of range

I reported this error to anvi'o issues section, but did not get any response. If anybody knows how to solve this issue please help me. Thanks in advance

Answer 1

[Iva]

This is an ongoing bug in anvi'o that we are still trying to solve, as it has been difficult for us to reproduce. It has been discussed extensively in the anvi'o issues here, here, and here. If anyone else is coming here to look for a solution to this problem, I am sorry to say that we still don't have anything besides running anvi-setup-ncbi-cogs --reset many times to see if it works. We would appreciate your reporting of this problem in this issue as it may help us finally solve it.

One final note, it is a good idea to report anvi'o errors like this in the anvi'o Slack, our dedicated forum for questions and technical help, since it is much less likely to fall through the cracks there.