Error running ncov-tutorial after fresh install

Help and Getting Started
1

Hello everyone,

Just did a fresh install of Nextstrain components. Conda runtime as default.

After running the ‘nextstrain setup --set-default conda’ command in my environment and getting the all good, I went through the process of running the example data and received the error below (appears to be related to generation of the ‘rbd_levels.json’ file). Any help troubleshooting will be greatly appreciated. Thanks.

ERROR: results/default-build/rbd_levels.json did not contain either `nodes` or `branches`. Please check the formatting of this JSON!
Validating schema of 'results/default-build/nt_muts.json'...
Validating schema of 'results/default-build/aa_muts.json'...
[Wed May 10 11:32:07 2023]
Error in rule export:
    jobid: 4
    input: results/default-build/tree.nwk, results/default-build/metadata_adjusted.tsv.xz, results/default-build/branch_lengths.json, results/default-build/nt_muts.json, results/default-build/aa_muts.json, results/default-build/emerging_lineages.json, results/default-build/clades.json, results/default-build/recency.json, results/default-build/traits.json, results/default-build/logistic_growth.json, results/default-build/mutational_fitness.json, results/default-build/distances.json, results/default-build/epiweeks.json, results/default-build/rbd_levels.json, defaults/auspice_config.json, results/default-build/colors.tsv, defaults/lat_longs.tsv, results/default-build/description.md
    output: results/default-build/ncov_with_accessions.json, results/default-build/ncov_with_accessions_root-sequence.json
    log: logs/export_default-build.txt (check log file(s) for error details)
    conda-env: /data/nextstrain/hawaii_2023/.snakemake/conda/6d8107c87e6d133fe50e00ac4282e48f_
    shell:

        augur export v2             --tree results/default-build/tree.nwk             --metadata results/default-build/metadata_adjusted.tsv.xz             --node-data results/default-build/branch_lengths.json results/default-build/nt_muts.json results/default-build/aa_muts.json results/default-build/emerging_lineages.json results/default-build/clades.json results/default-build/recency.json results/default-build/traits.json results/default-build/logistic_growth.json results/default-build/mutational_fitness.json results/default-build/distances.json results/default-build/epiweeks.json results/default-build/rbd_levels.json             --auspice-config defaults/auspice_config.json             --include-root-sequence             --colors results/default-build/colors.tsv             --lat-longs defaults/lat_longs.tsv             --title 'Genomic epidemiology of novel coronavirus - Default Build-focused subsampling'             --description results/default-build/description.md             --output results/default-build/ncov_with_accessions.json 2>&1 | tee logs/export_default-build.txt

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-05-10T113203.662797.snakemake.log

Contents of rbd_levels.json file (opened in Notepad):

{
  "nodes": {},
  "rbd_level_details": {}
}
2

Hi @dstrange,

Sorry to hear you are running issues! Good thinking, your rbd_levels.json files looks empty which is unexpected.

I just ran through the same process myself and was unable to reproduce your error. I’ll need more logs to troubleshoot. Can you re-run the workflow then upload all the logs as a compressed archive file? Here are the commands to do so:

# Go to the ncov directory if you haven't already
cd ncov

# Remove files from previous runs
git clean -fdx .

# Run the build command from the tutorial
nextstrain build . --configfile ncov-tutorial/example-data.yaml

# Create a compressed archive file
tar -cJf ncov-tutorial-log.tar.xz logs/

You can upload the file ncov-tutorial-log.tar.xz in a reply to this post using the upload icon in the reply editor toolbar.

– Victor

3

Actually, we are seeing this error elsewhere. It looks to be a problem with the Conda runtime which we will investigate.

In the meantime, the Docker runtime should work without this issue, if you are able to go back to the Nextstrain installation instructions and set that up.

4

Hi @victorlin,

Thanks a lot for looking into it. Will go with the Docker runtime for now.

-Dan