The command to generate a he query and frequency count ratio matrix using nr might look as follows:

blastpgp -i test1.fa -d nr -h 0.0001 -j 4 -C $id$chain.nr.chk -Q test1.matrix -a2

I need the $id$chain.nr.chk， But I can't find the options in psiblast of blast+.

Now, my command to generat a PSSM using blast+ might look as follows:

psiblast -out_pssm my_protein.ckp -evalue 0.01 -out_ascii_pssm ascii_mtx_file -out output_file -num_iterations 3 -query protein.fasta -db nr

However, I also need the $id$chain.nr.chk file as generated by blastpgp -C. How to gain it with blast+.

Any help is appreciated, Thank you very much.