$ deltablast -query rhodopsin_proteins.fasta
-subject four_human_proteins.fasta -evalue 1e-08 -outfmt "6 qseqid
sseqid score" -rpsdb /data/blastdb/cdd_delta
BLAST engine error: /data/blastdb/cdd_delta contains no frequency ratios needed for composition-based statistics.
Please disable composition-based statistics when searching against /data/blastdb/ncbi/cdd/cdd_delta.
BLAST engine error: /data/blastdb/cdd_delta contains no frequency ratios needed for composition-based statistics.
Please disable composition-based statistics when searching against /data/blastdb/ncbi/cdd/cdd_delta.
To cut a long story short, to fix this you need to download and unpack a newer cdd_delta.tar.gz which now includes another file cdd_delta.freq containing frequency ratio information which the newer deltablast tool requires.
The same applies to the rpsblast tool, although here you just get a warning rather than an error:
$ rpsblast -query four_human_proteins.fasta -db /data/blastdb/cdd_delta -evalue 1e-08 -outfmt "6 qseqid sseqid score"
Warning: /data/blastdb/cdd_delta contain(s) no freq ratios needed for composition-based statistics.
RPSBLAST will be run without composition-based statistics.
sp|Q9BS26|ERP44_HUMAN gnl|CDD|222416 401
...
sp|P06213|INSR_HUMAN gnl|CDD|238021 137
sp|P08100|OPSD_HUMAN gnl|CDD|215646 411
Warning: /data/blastdb/cdd_delta contain(s) no freq ratios needed for composition-based statistics.
RPSBLAST will be run without composition-based statistics.
sp|Q9BS26|ERP44_HUMAN gnl|CDD|222416 401
...
sp|P06213|INSR_HUMAN gnl|CDD|238021 137
sp|P08100|OPSD_HUMAN gnl|CDD|215646 411