Metadata validation errors FAQ

Common validation errors and solutions

Metadata validation error messages are intended to be succinct. Below we provide additional context for common error messages and guidance on resolving those issues. If more information is needed, please email [e-mail].

Error

ERROR:<column header>: only alphanumeric characters and underscore allowed in the metadata name

Reason	Solution
Valid characters for metadata names are limited.	Remove all non-alphanumeric characters (except underscore) from the column header.

Error

ERROR:Numeric annotation, <column header>, contains non-numeric data (or unidentified NA 
values)

Reason	Solution
Metadata TYPE declared as numeric but column contains strings or empty cells.	Ensure that all values for <metadata> are numeric.

Error

Unexpected exit status 137 while running "python ingest_pipeline.py "

Reason	Solution
Cloud instance used for ingest errored due to memory issue.	Contact [e-mail] for assistance with requesting more memory.

Error

ERROR:<column header>: Could not parse provided ontology id, "PATO_0000461, PATO_0000461, 
PATO_0000461"

Reason	Solution
Arrays of metadata information must be delimited by the pipe (|) symbol.	Replace with pipe(|) delimiter.

Error

ERROR:<column header>: '<text>' does not match '^[-A-Za-z0-9]+[_:][-A-Za-z0-9]+'

Reason	Solution
Metadata validation expected ontology IDs as values for the specified column header.	Browse the ontology listed in required conventional metadata and select terms that best describe your data. Note that an ontology_label column with the natural language name is also required.

Error

ERROR:'<column header>' is a required property

Reason	Solution
Required metadata is missing from the metadata file.	Add missing metadata as a new column in the metadata file.

Error

ValueError: Unable to parse file - Duplicate annotation header names are not allowed. 

Reason	Solution
Metadata headers must all be unique	Remove any duplicate columns or rename a column where the same column name is accidentally used twice for different purposes.
(AnnData) NAME data is provided by adata.obs_names	Remove any column in adata.obs called "NAME"