<br>
<div class="gmail_quote">
<div class="gmail_quote">
<div class="gmail_quote">
<div> </div>
<div>
<div></div>
<div>
<div>Dear Members,</div>
<div>Currently I am working on protein secondary structure prediction using neural network. I was using PSIPRED but I am getting error: </div>
<div>[makematrices] FATAL ERROR : unable to open file psitmp68765db92331.chk</div>
<div>I am sending my script for your reference: <br>#!/bin/tcsh<br># This is a simple script which will carry out all of the basic steps<br># required to make a PSIPRED V2 prediction. Note that it assumes that the<br># following programs are in the appropriate directories:<br>
# blastpgp - PSIBLAST executable (from NCBI toolkit)<br># makemat - IMPALA utility (from NCBI toolkit)<br># psipred - PSIPRED V2 program<br># psipass2 - PSIPRED V2 program<br># NOTE: Script modified to be more cluster friendly (DTJ April 2008)<br>
# The name of the BLAST data bank<br>set dbname = nr.fasta<br># set dbname = nr<br># Where the NCBI programs have been installed<br>set ncbidir = ./binblast<br># set ncbidir = C:/cygwin/usr/local/bin<br># Where the PSIPRED V2 programs have been installed<br>
set execdir = ./bin<br># Where the PSIPRED V2 data files have been installed<br>set datadir = ./data<br>set basename = $1:r<br>set rootname = $basename:t<br># Generate a "unique" temporary filename root<br>set hostid = `hostid`<br>
set tmproot = psitmp$$$hostid<br>\cp -f $1 $tmproot.fasta<br>echo "Running PSI-BLAST with sequence" $1 "..."<br>#$ncbidir/blastpgp -b 0 -j 3 -h 0.001 -d $dbname -i $tmproot.fasta -C $tmproot.chk >& $tmproot.blast</div>
<div>$ncbidir/blastpgp -b 0 -j 3 -h 0.001 -d $dbname -i $tmproot.fasta -C $tmproot.chk<br>echo "Predicting secondary structure..."<br>echo $tmproot.chk > $<a href="http://tmproot.pn/" target="_blank">tmproot.pn</a><br>
echo $tmproot.fasta > $<a href="http://tmproot.sn/" target="_blank">tmproot.sn</a><br>$ncbidir/makemat -P $tmproot<br>echo Pass1 ...<br>$execdir/psipred $tmproot.mtx $datadir/weights.dat $datadir/weights.dat2 $datadir/weights.dat3 $datadir/weights.dat4 > $rootname.ss<br>
echo Pass2 ...<br>$execdir/psipass2 $datadir/weights_p2.dat 1 1.0 1.0 $rootname.ss2 $rootname.ss > $rootname.horiz<br># Remove temporary files<br>echo Cleaning up ...<br>#\rm -f $tmproot.* error.log<br>echo "Final output files:" $rootname.ss2 $rootname.horiz<br>
echo "Finished."</div>
<div> </div>
<div>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. </div>
<div>Any help will be greatly thanked. <br>
<div class="im"><br clear="all"><br><br clear="all"><br>-- <br>Thanking You,<br>Yours Truly,<br>Nilanjana G<br>@+40 749527113<br></div></div></div></div></div></div></div>