usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta | | | | | | | Command Input filename | Output option with filename Binary filename Parameter option(s)
The command line starts with the binary filename. In this manual, examples are always shown using 'usearch' as the filename. You should use the actual name of your binary file. You can rename your binary file to usearch or use the original name, e.g. usearch11.0.98_i86linux32. Or, you can set an environment variable to the usearch binary path name, e.g. $usearch, you can then type $usearch instead of usearch.
The binary file must be in a directory in your shell's PATH variable, otherwise you must type the full path name, e.g. (Linux or OSX):
/usr/bin/usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta
Under a Windows command shell, use backslashes and drive letters as needed:
C:\binaries\usearch.exe -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta
If the binary is in your current directory, you can use ./ or .\ (dot-slash or dot-backslash) as the path name:
./usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta
The USEARCH command-line must have one command and may have other options. An option is given after a hyphen (-). Command names are options, so must also have a hyphen. Two hyphens are allowed (Linux long option form), so both -id 0.9 and --id 0.9 are allowed. There must be a space between the option name and its value, so -id0.9 is not allowed.
Unused option warning
If a command-line option was not used by the given command, a warning message is issued.