Zhanglab forum

I need to use PSSPRED for my research work on proteins. I have downloaded and extracted the nr database from ncbi(https://ftp.ncbi.nlm.nih.gov/blast/db/) which I am using in PSSPRED.
But when I run the command "PSSpred.pl seq.txt" I get the following error.

running Psi-blast .....
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.00.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.01.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.02.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.03.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.04.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.05.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.06.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.07.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.08.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.09.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.10.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.11.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.12.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.13.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.14.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.15.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.16.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.17.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.18.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.19.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.20.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.21.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.22.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.23.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.24.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.25.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.26.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.27.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.28.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.29.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.30.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.31.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.32.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.33.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.34.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.35.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.36.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.37.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.38.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.39.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.40.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.41.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.42.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.43.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.44.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.45.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.46.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.47.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.48.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.49.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.50.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.51.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.52.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.53.
[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /home/sourav/BLAST_DB/nr.54.
[makemat] FATAL ERROR: Unable to open file psitmp.chk

cp: cannot stat 'psitmp.mtx': No such file or directory
Running PSSpred1 ...
cannot open file pssm.txt
cannot open file mtx
Running PSSpred2 ...
cannot open file pssm.txt
cannot open file mtx
Running PSSpred3 ...
cannot open file pssm.txt
cannot open file mtx
Running PSSpred4 ...
cannot open file pssm.txt
cannot open file mtx
Running PSSpred5 ...
cannot open file pssm.txt
cannot open file mtx
Running PSSpred6 ...
cannot open file pssm.txt
cannot open file mtx
Running PSSpred7 ...
cannot open file pssm.txt
cannot open file mtx

Based on my knowledge, the newest NR database in NCBI is design for most recent version blast, so it is not suitable for the blast we including in the PSSpred package, I suggest you download the raw NR fasta file and format it as blast database format by "fomatdb" commands in blast package or download a very very old version NR from our lab

wget -o log -c http://zhanglab.ccmb.med.umich.edu/library/nr.tar.gz

Thank you. This database worked.