Errors and warnings

When processing of a sequence fails for various reasons, not all output files will contain the corresponding entry (due to limitations of file formats):

Output file CLI arg Failed entries?
Nucleotide alignment --output-fasta no
Translations --output-translations no
Tree - Auspice v2 JSON --output-tree no
Tree - Newick --output-tree no
Analysis results CSV --output-csv yes
Analysis results TSV --output-tsv yes
Analysis results NDJSON --output-ndjson yes
Analysis results JSON --output-json yes

You can find the reason for a particular failure by reading:

  • errors and warnings column in tabular outputs (TSV, CSV)

  • errors array in JSON output

  • error field in each entry in NDJSON output