Need to specify input filenames!
Usage: krakenuniq --report-file FILENAME [options] <filename(s)>
Options:
--db NAME Name for Kraken DB (default: none)
--threads NUM Number of threads (default: 1)
--fasta-input Input is FASTA format
--fastq-input Input is FASTQ format
--gzip-compressed Input is gzip compressed
--bzip2-compressed Input is bzip2 compressed
--hll-precision INT Precision for HyperLogLog k-mer cardinality estimation, between 10 and 18 (default: 12)
--exact Compute exact cardinality instead of estimate (slower, requires memory proportional to cardinality!)
--quick Quick operation (use first hit or hits)
--min-hits NUM In quick op., number of hits req''d for classification
NOTE: this is ignored if --quick is not specified
--unclassified-out FILENAME
Print unclassified sequences to filename
--classified-out FILENAME
Print classified sequences to filename
--output FILENAME Print output to filename (default: stdout); "off" will
suppress normal output
--only-classified-output
Print no Kraken output for unclassified sequences
--preload Loads DB into memory before classification
--paired The two filenames provided are paired-end reads
--check-names Ensure each pair of reads have names that agree
with each other; ignored if --paired is not specified
--help Print this message
--version Print version information
Experimental:
--uid-mapping Map using UID database
If none of the *-input or *-compressed flags are specified, and the
file is a regular file, automatic format detection is attempted.