I am using uniref100 database for running the psipred script (runpsipred) on macOS. On running the runpsipred script :
#!/bin/tcsh
# This is a simple script which will carry out all of the basic steps
# required to make a PSIPRED prediction. Note that it assumes that the
# following programs are in the appropriate directories:
# blastpgp - PSIBLAST executable (from NCBI toolkit)
# makemat - IMPALA utility (from NCBI toolkit)
# psipred - PSIPRED V4 program
# psipass2 - PSIPRED V4 program
# NOTE: Script modified to be more cluster friendly (DTJ April 2008)
# The name of the BLAST data bank
set dbname = /Users/shalini/Desktop/pgen_github/uniref100/uniref100.fasta
# Where the NCBI programs have been installed
set ncbidir = /Users/shalini/Desktop/pgen_github/ncbi-blast-2.10.0+/bin
# Where the PSIPRED V4 programs have been installed
set execdir = /Users/shalini/Desktop/pgen_github/pGenTHREADER-master/psipred/bin
# Where the PSIPRED V4 data files have been installed
set datadir = /Users/shalini/Desktop/pgen_github/pGenTHREADER-master/psipred/data
set basename = $1:r
set rootname = $basename:t
# Generate a "unique" temporary filename root
set hostid = `hostid`
set tmproot = psitmp$$$hostid
\cp -f $1 $tmproot.fasta
echo "Running PSI-BLAST with sequence" $1 "..."
$ncbidir/blastpgp -b 0 -v 5000 -j 3 -h 0.001 -d $dbname -i $tmproot.fasta -C $tmproot.chk >& $tmproot.blast
if ($status != 0) then
tail $tmproot.blast
echo "FATAL: Error whilst running blastpgp - script terminated!"
exit $status
endif
echo "Predicting secondary structure..."
echo $tmproot.chk > $tmproot.pn
echo $tmproot.fasta > $tmproot.sn
$ncbidir/makemat -P $tmproot
if ($status != 0) then
echo "FATAL: Error whilst running makemat - script terminated!"
exit $status
endif
echo Pass1 ...
$execdir/psipred $tmproot.mtx $datadir/weights.dat $datadir/weights.dat2 $datadir/weights.dat3 > $rootname.ss
if ($status != 0) then
echo "FATAL: Error whilst running psipred - script terminated!"
exit $status
endif
echo Pass2 ...
$execdir/psipass2 $datadir/weights_p2.dat 1 1.0 1.0 $rootname.ss2 $rootname.ss > $rootname.horiz
if ($status != 0) then
echo "FATAL: Error whilst running psipass2 - script terminated!"
exit $status
endif
# Remove temporary files
echo Cleaning up ...
\rm -f $tmproot.* error.log
echo "Final output files:" $rootname.ss2 $rootname.horiz
echo "Finished."
The error is
Running PSI-BLAST with sequence /Users/shalini/Desktop/pgen_github/unmodelled_fasta/NP_999840.fasta ...
[NULL_Caption] WARNING: readdb: wrong version of formatdb was used to make database //Users/shalini/Desktop/pgen_github/uniref100/uniref100.fasta.65.
[NULL_Caption] WARNING: readdb: wrong version of formatdb was used to make database //Users/shalini/Desktop/pgen_github/uniref100/uniref100.fasta.66.
[NULL_Caption] WARNING: readdb: wrong version of formatdb was used to make database //Users/shalini/Desktop/pgen_github/uniref100/uniref100.fasta.67.
[NULL_Caption] WARNING: readdb: wrong version of formatdb was used to make database //Users/shalini/Desktop/pgen_github/uniref100/uniref100.fasta.68.
[NULL_Caption] WARNING: readdb: wrong version of formatdb was used to make database //Users/shalini/Desktop/pgen_github/uniref100/uniref100.fasta.69.
[NULL_Caption] WARNING: readdb: wrong version of formatdb was used to make database //Users/shalini/Desktop/pgen_github/uniref100/uniref100.fasta.70.
[NULL_Caption] WARNING: readdb: wrong version of formatdb was used to make database //Users/shalini/Desktop/pgen_github/uniref100/uniref100.fasta.71.
[NULL_Caption] WARNING: readdb: wrong version of formatdb was used to make database //Users/shalini/Desktop/pgen_github/uniref100/uniref100.fasta.72.
[NULL_Caption] WARNING: readdb: wrong version of formatdb was used to make database //Users/shalini/Desktop/pgen_github/uniref100/uniref100.fasta.73.
[NULL_Caption] WARNING: Unable to open uniref100.fasta.pin
FATAL: Error whilst running blastpgp - script terminated!
I have made the database using
makeblastdb -in /Users/shalini/Desktop/pgen_github/uniref100/uniref100.fasta -parse_seqids -blastdb_version 5 -title "Unirefdb" -dbtype prot
results in :
Building a new DB, current time: 01/14/2020 15:45:24
New DB name: /Users/shalini/Desktop/pgen_github/uniref100/uniref100.fasta
New DB title: Unirefdb
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 199397329 sequences in 7009.84 seconds.
There are total 73 .psq, .pin, .pog and .phr files
generated
where did you get the blastpgp executable from? ( as far as I know it's not part of the default blast package) and consequently which version are you using?
perhaps try formatting your DB using the older
-blastdb_version 4
. In any case when formatting large DB you should also get one.pal
(or.nal
for nucleotides) files which 'groups' all the subparts.