[BUG] Error while running a SARS-CoV-2 analysis

[Addicted-to-coding]

Hi,
I'm trying to run a SARS-CoV-2 analysis for sequences only from Wuhan. I tried doing this by downloading the data from GISAID and then running the command
sed -n 40701,40909p metadata.tsv > COVID_Research/ncov/data/metadata.tsv
sed -n 81400,81816p sequences.fasta > COVID_Research/ncov/data/sequences.fasta
to extract only the sequences from Wuhan

When I run the command snakemake --profile profiles/default, I get the error

WARNING: only one state found for discrete state reconstruction: ['China']
Traceback (most recent call last):
File "/home/vs/anaconda3/envs/nextstrain/bin/augur", line 8, in
sys.exit(main())
File "/home/vs/anaconda3/envs/nextstrain/lib/python3.6/site-packages/augur/main.py", line 10, in main
return augur.run( argv[1:] )
File "/home/vs/anaconda3/envs/nextstrain/lib/python3.6/site-packages/augur/init.py", line 74, in run
return args.command.run(args)
File "/home/vs/anaconda3/envs/nextstrain/lib/python3.6/site-packages/augur/traits.py", line 175, in run
mugration_states[node.name][column+'_confidence'] = node.getattribute(column+'_confidence')
AttributeError: 'Clade' object has no attribute 'country_exposure_confidence'
[Sun Jun 7 17:35:21 2020]
Error in rule traits:
jobid: 14
output: results/global/traits.json
log: logs/traits_global.txt (check log file(s) for error message)
shell:

    augur traits             --tree results/global/tree.nwk             --metadata data/metadata.tsv             --output results/global/traits.json             --columns country_exposure             --confidence             --sampling-bias-correction 2.5 2>&1 | tee logs/traits_global.txt
    
    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

How can I fix this?

[rneher]

this is something that we will need to fix in augur. there is no immediate solution to this other disabling trait reconstruction (or including a sequence that is not from China)

[XPHenry]

What do we do to disable trait reconstruction?

[jameshadfield]

You can disable trait reconstruction by not running the augur traits step. It should be enough to remove / comment out this line which will remove the step from the snakemake graph of jobs needed to run.

[XPHenry]

oh ok cool thanks for the quick reply!

[rneher]

I opened in issue in augur (see above) and will close here. thanks for raising this.

[livia-wllr]

You can disable trait reconstruction by not running the augur traits step. It should be enough to remove / comment out this line which will remove the step from the snakemake graph of jobs needed to run.

Is it possible that you link that again ? Because the link you mentioned is broken