Hello,
I have installed the BSpred standalone software on our server and submitted a sequence as specified in the README file. However I am getting some errors when I run the program and hence getting an empty prediction.txt file.
First I get the following information:
running psipred for secondary structure prediction...
Running solvent accessibility prediction...
running Psi-blast .....
running interface prediction...
BSpred output file prediction.txt has been generated. Quitting...
And also I am getting some warnings related to blastpgd like the following:
[blastpgp] WARNING: [000.000] Failed to retrieve sequence gi|194382826
[blastpgp] WARNING: [000.000] Failed to retrieve sequence gi|213424171
[blastpgp] WARNING: [000.000] Failed to retrieve sequence gi|290560013
[blastpgp] WARNING: [000.000] Failed to retrieve sequence gi|197725116
And then in the end I am getting the following errors:
cat: protein1.mtx: No such file or directory
rm: cannot remove 'input.txt': No such file or directory
rm: cannot remove 'nninp.txt': No such file or directory
rm: cannot remove 'example.seq': No such file or directory
rm: cannot remove 'output1': No such file or directory
And these errors result with an empty prediction.txt file.
Could you possibly help me fix this problem please? I saw in previous posts that other people also ran into similar problems but I couldn't find a solution in the posts. I would be very grateful for any help.
Thank you very much for your time!