I'm using psi-blast (blast version 2.2.30+),this is my command:
psiblast -query seq.fasta -db db -num_threads 15 -out outfile.txt -outfmt 6
I'm not sure than if I have got the right result.It seems that it only run one iteration. But if I add the parameter:
-num_interations 2, warnings appear:
Frequency ratios for PSSM are all zeros, frequency ratios for BLOSUM62 will be used during traceback in composition based statistics
I don't know where is the mistake and how can PSSM are all zeros. any help will be appreciated!