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: #!/bin/tcsh # 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 $tmproot.chk 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 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
