[BiO BB] Problem in MAKEMAT in PSIPRED

Nilanjana Gangopadhyay nilanjanag08 at gmail.com
Sat Mar 13 14:30:15 EST 2010

  Dear Members,
Currently I am working on protein secondary structure prediction using
neural network. I was using PSIPRED but I am getting error:
[makematrices] FATAL ERROR : unable to open file psitmp68765db92331.chk
I am sending my script for your reference:
# This is a simple script which will carry out all of the basic steps
# required to make a PSIPRED V2 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 V2 program
# psipass2 - PSIPRED V2 program
# NOTE: Script modified to be more cluster friendly (DTJ April 2008)
# The name of the BLAST data bank
set dbname = nr.fasta
# set dbname = nr
# Where the NCBI programs have been installed
set ncbidir = ./binblast
# set ncbidir = C:/cygwin/usr/local/bin
# Where the PSIPRED V2 programs have been installed
set execdir = ./bin
# Where the PSIPRED V2 data files have been installed
set datadir = ./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 -j 3 -h 0.001 -d $dbname -i $tmproot.fasta -C
$tmproot.chk >& $tmproot.blast
$ncbidir/blastpgp -b 0 -j 3 -h 0.001 -d $dbname -i $tmproot.fasta -C
echo "Predicting secondary structure..."
echo $tmproot.chk > $tmproot.pn
echo $tmproot.fasta > $tmproot.sn
$ncbidir/makemat -P $tmproot
echo Pass1 ...
$execdir/psipred $tmproot.mtx $datadir/weights.dat $datadir/weights.dat2
$datadir/weights.dat3 $datadir/weights.dat4 > $rootname.ss
echo Pass2 ...
$execdir/psipass2 $datadir/weights_p2.dat 1 1.0 1.0 $rootname.ss2
$rootname.ss > $rootname.horiz
# Remove temporary files
echo Cleaning up ...
#\rm -f $tmproot.* error.log
echo "Final output files:" $rootname.ss2 $rootname.horiz
echo "Finished."

I am running the script using Putty. Though that makemat -P test.chk command
is running fine in command prompt.  .mtx file is also generated. and .chk
files are also generated when I am running blastpgp and makemat separately.
Any help will be greatly thanked.

Thanking You,
Yours Truly,
Nilanjana G
@+40 749527113

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