# AttributeError: ‘Clade’ object has no attribute ‘country\_exposure\_confidence’ **URL:** \ **Category:** Help and Getting Started\ **Created:** [September 3, 2021, 12:22pm UTC](https://nextstrain.discourse.group/t/attributeerror-clade-object-has-no-attribute-country-exposure-confidence/699 "2021-09-03T12:22:19Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![b.rad](https://avatars.discourse-cdn.com/v4/letter/b/b782af/32.png) [@b.rad](https://nextstrain.discourse.group/u/b.rad)\ **Post date:** [September 3, 2021, 12:22pm UTC](https://nextstrain.discourse.group/t/attributeerror-clade-object-has-no-attribute-country-exposure-confidence/699/1 "2021-09-03T12:22:20Z")
I am hoping someone can help me get past an error I’m having when trying to run a local dataset in the context of a global dataset. My _aim_ is to use a curated dataset of GISAID IDs stored in a text file to produce metadata.tsv and sequence.fasta files. Then, I’d like to create a random sample of global data and output their metadata and fasta files. Finally, I’d like to build a tree of auspice using the two datasets. However, I’m getting the following error when running the build: > augur traits is using TreeTime version 0.8.4 > WARNING: no states found for discrete state reconstruction. > Traceback (most recent call last): > File “ncov/ncov-8/.snakemake/conda/8ec83933e66c3abe39927a0c6a3f5220/bin/augur”, line 10, in > sys.exit(main()) > File “ncov/ncov-8/.snakemake/conda/8ec83933e66c3abe39927a0c6a3f5220/lib/python3.8/site-packages/augur/ **main**.py”, line 10, in main > return augur.run( argv[1:] ) > File “ncov/ncov-8/.snakemake/conda/8ec83933e66c3abe39927a0c6a3f5220/lib/python3.8/site-packages/augur/ **init**.py”, line 75, in run > return args. **command**.run(args) > File “ncov/ncov-8/.snakemake/conda/8ec83933e66c3abe39927a0c6a3f5220/lib/python3.8/site-packages/augur/traits.py”, line 179, in run > mugration\_states[node.name][column+‘\_confidence’] = node. **getattribute** (column+‘\_confidence’) > AttributeError: ‘Clade’ object has no attribute ‘country\_exposure\_confidence’ # My Steps ## 1. Installed the program Ran the getting\_started build and everything worked ## 2. Prepared the Data Used [Method 3](https://docs.nextstrain.org/projects/ncov/en/latest/analysis/data-prep.html#curate-data-from-the-full-gisaid-database) from Preparring your Data 1. Downloaded the FASTA and metadata tar.xz files 2. Sanitized the FASTA file by ```auto python3 scripts/sanitize_sequences.py \ --sequences data/sequences_fasta.tar.xz \ --strip-prefixes "hCoV-19/" \ --output data/sequences_gisaid.fasta.gz ``` 1. Indexed the sequences ```auto augur index \ --sequences data/sequences_gisaid.fasta.gz \ --output data/sequence_index_gisaid.tsv.gz ``` 1. Prepared the metadata ```auto python3 scripts/sanitize_metadata.py \ --metadata data/metadata_tsv.tar.xz \ --parse-location-field Location \ --rename-fields 'Virus name=strain' 'Accession ID=gisaid_epi_isl' 'Collection date=date' \ --strip-prefixes "hCoV-19/" \ --output data/metadata_gisaid.tsv.gz ``` 1. Created a txt file with GISAID ids to be included (“hCoV-19/” already removed) 2. Used the txt file to output subsampled metadata and sequences ```auto augur filter \ --metadata data/metadata_gisaid.tsv.gz \ --sequence-index data/sequence_index_gisaid.tsv.gz \ --sequences data/sequences_gisaid.fasta.gz \ --exclude-all \ --include focal_gisaid_ids.txt \ --output-metadata data/focal_metadata_gisaid.tsv.gz \ --output-sequences data/focal_sequences_gisaid.fasta.gz ``` 1. Filtered GISAID database to create a sample global dataset ```auto augur filter \ --metadata data/metadata_gisaid.tsv.gz \ --exclude-ambiguous-dates-by any \ --subsample-max-sequences 1000 \ --group-by region year month \ --output-strains strains_global.txt ``` ```auto augur filter \ --metadata data/metadata_gisaid.tsv.gz \ --sequence-index data/sequence_index_gisaid.tsv.gz \ --sequences data/sequences_gisaid.fasta.gz \ --exclude-all \ --include strains_global.txt \ --output-metadata data/context_metadata_gisaid.tsv.gz \ --output-sequences data/context_sequences_gisaid.fasta.gz ``` ## Created and Ran the build 1. Copied the example\_global\_context profile and edited the build to ```auto inputs: - name: focal metadata: "data/focal_metadata_gisaid.tsv.gz" sequences: "data/focal_sequences_gisaid.fasta.gz" - name: contextual metadata: "data/contextual_metadata_gisaid.tsv.gz" filtered: "data/contextual_sequences_gisaid.fasta.gz" builds: global: subsampling_scheme: custom-scheme use_nextalign: true filter: focal: skip_diagnostics: True subsampling: custom-scheme: focal: query: --query "focal == 'yes'" contextual: query: --query "contextual == 'yes'" skip_travel_history_adjustment: True ``` 1. Run the build `snakemake --cores 2 --profie ./my_profiles/custom_build -p` ---
**Author:** ![james](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/james/32/11_2.png) [@james](https://nextstrain.discourse.group/u/james)\ **Post date:** [September 7, 2021, 12:17am UTC](https://nextstrain.discourse.group/t/attributeerror-clade-object-has-no-attribute-country-exposure-confidence/699/2 "2021-09-07T00:17:21Z")
Hmm, the error `WARNING: no states found for discrete state reconstruction` makes me wonder what traits we are trying to reconstruct. By [default](https://github.com/nextstrain/ncov/blob/master/defaults/parameters.yaml#L153-L159) this is on “country\_exposure” which may not appear in your metadata? You can change this by adding the following to your `builds.yaml`: ```auto traits: global: # use the name of your build sampling_bias_correction: 2.5 columns: ["country"] # or "region", or an empty array, as appropriate. ``` P.S. In your `custom-scheme` it looks like you are not actually subsampling, instead taking all of the focal and all of the contextual sequences. If so, you can change to `subsampling_scheme: all` which will speed things up a bit. P.P.S. a common gotcha is not updating the `./my_profiles/custom_build/config.yaml` so that it indeed refers to `./my_profiles/custom_build/builds.yaml` - could you double check this?