Currently im working on a project where I need to use a metagenomic identifier. I chose to use kraken2. Im encountering some problems using kraken2 and making a custom database.
When I try to make a custom database with the following line:
kraken2-build --build --db custom_database /home/database/arb-silva.de_2024-03-06_id1308990_tax_silva_trunc.fasta
But I get the following error, no matter what I try:
Extra arguments on command line.Usage: kraken2-build [task option] [options]Task options (exactly one must be selected): --download-taxonomy Download NCBI taxonomic information --download-library TYPE Download partial library (TYPE = one of "archaea", "bacteria", "plasmid","viral", "human", "fungi", "plant", "protozoa","nr", "nt", "UniVec", "UniVec_Core") --special TYPE Download and build a special database (TYPE = one of "greengenes", "silva", "rdp") --add-to-library FILE Add FILE to library --build Create DB from library (requires taxonomy d/l'ed and at least one file in library) --clean Remove unneeded files from a built database --standard Download and build default database --help Print this message --version Print version informationOptions: --db NAME Kraken 2 DB name (mandatory except for --help/--version) --threads # Number of threads (def: 1) --kmer-len NUM K-mer length in bp/aa (build task only; def: 35 nt, 15 aa) --minimizer-len NUM Minimizer length in bp/aa (build task only; def: 31 nt, 12 aa) --minimizer-spaces NUM Number of characters in minimizer that are ignored in comparisons (build task only; def: 7 nt, 0 aa) --protein Build a protein database for translated search --no-masking Used with --standard/--download-library/ --add-to-library to avoid masking low-complexity sequences prior to building; masking requires dustmasker or segmasker to be installed in PATH, which some users might not have. --max-db-size NUM Maximum number of bytes for Kraken 2 hash table; if the estimator determines more would normally be needed, the reference library will be downsampled to fit. (Used with --build/--standard/--special) --use-ftp Use FTP for downloading instead of RSYNC; used with --download-library/--download-taxonomy/--standard. --skip-maps Avoids downloading accession number to taxid maps, used with --download-taxonomy. --load-factor FRAC Proportion of the hash table to be populated (build task only; def: 0.7, must be between 0 and 1). --fast-build Do not require database to be deterministically built when using multiple threads. This is faster, but does introduce variability in minimizer/LCA pairs. Used with --build and --standard options.
Does anybody have any idea about this?I also tried it with a NCBI .fasta file, but still didn't work.
Thanks in advance!
Kind regards!