Validation of results/default-build/ncov_with_accessions.json failed

Help and Getting Started
1

Hello Everyone,

I have been getting this error:

Error in rule export:
    jobid: 4
    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 message)
    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/aa_muts_explicit.json results/default-build/distances.json results/default-build/epiweeks.json             --auspice-config defaults/auspice_config.json             --include-root-sequence             --colors my_profiles/PHL_default/colors.tsv             --lat-longs defaults/lat_longs.tsv             --title 'Genomic epidemiology of novel coronavirus - Default Build-focused subsampling'             --description my_profiles/PHL_GISAID_tracing/012020-122021-testCountries/description.md             --output results/default-build/ncov_with_accessions.json 2>&1 | tee logs/export_default-build.txt

        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
        ERROR: 'https:__www.gisaid.org_' does not match '^https?://.+$'. Trace: ... - properties - node_attrs - properties - url - pattern
Validating schema of 'results/default-build/aa_muts.json'...
Validating config file defaults/auspice_config.json against the JSON schema
Validating schema of 'defaults/auspice_config.json'...
Validating produced JSON
Validating schema of 'results/default-build/ncov_with_accessions.json'...
Validation of 'results/default-build/ncov_with_accessions.json' failed.

------------------------
Validation of results/default-build/ncov_with_accessions.json failed. Please check this in a local instance of `auspice`, as it is not expected to display correctly.
------------------------


Removing output files of failed job export since they might be corrupted:
results/default-build/ncov_with_accessions.json, results/default-build/ncov_with_accessions_root-sequence.json
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

I appreciate your help,

Thank you

2

Hey @AroobAlhumaidy - in your metadata it seems you have URLs starting with https:__www.gisaid.org where they should be https://www.gisaid.org. Fixing these should allow the workflow to complete :crossed_fingers:

1 Like
3

Many Thanks, it worked