createquerydb 'shuffle database cannot be combined with ‐‐createdb‐mode 0'

When running createquerydb, one can get the following message:

Shuffle database cannot be combined with --createdb-mode 0

We recompute with --shuffle 0

Converting sequences

Multiline fasta can not be combined with --createdb-mode 0

We recompute with --createdb-mode 1

This message comes from the underlying MMseqs tool. By default, it shuffles sequences (--shuffle 0) for indexing which is compatible only with –createdb-mode 1 (see user guide). If a user provides a multi-lined FASTA file, MMseqs will automatically convert the input into single-lined (linearized) FASTA sequences to be compatible with the –createdb-mode 1 setup (i.e., –createdb-mode 1 requires that the sequences not be text wrapped/non-linearized). This message is not a cause for concern for the user.