For convenience, you can obtain all output files listed in the followup sections at once.
In Nextclade Web: download
Nextclade CLI arguments:
<OUTPUT_DIR>- set output directory where the files will be written
--output-selectionallows to select which files are written
--output-basenameallows to customize base name of the output files
⚠️ For CLI users: Note that due to technical limitations of the JSON format, it cannot be streamed entry-by entry, i.e. before writing the output to the file, all entries need to be accumulated in memory. If the JSON results output or tree output is requested (through
--output-allarguments), for large input data, it can cause very high memory consumption, disk swapping, decreased performance and crashes. Consider removing these outputs for large input data, running on a machine with more RAM, or processing data in smaller chunks.