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:
errorsandwarningscolumn in tabular outputs (TSV, CSV)errorsarray in JSON outputerrorfield in each entry in NDJSON output