Hi guys, I'm new in bio and I'm trying to make pssm matrix with psi-blast. This is the code I use:
blastdb$ ../ncbi-blast-2.9.0+/bin/psiblast -query /home/sepehr/blastdb/Butyrylation/Butyrylation/P02294.seq -db nr -out $P02294.out -num_iterations 3 -out_ascii_pssm $Pxxx.pssm -inclusion_ethresh 0.001 -num_threads 4;
I get this warning: Warning: [psiblast] Query_1 P02294: Composition-based score adjustment conditioned on sequence properties and unconditional composition-based score adjustment is not supported with PSSMs, resetting to default value of standard composition-based statistics
I have changed the mode for all blast apps like psi-blast, blastp ... every thing in bin folder to 777 but app's result just create .out file that is empty and no .pssm matrix can any one tell me how to fix it? I really appreciate any help...