Memsat-SVM: error running PSI-BLAST

Question

[Thomas B.]

Hi,

I try to install Memsat-SVM on my computer but face an issue that I am not able to fix.

Here is what I did:

• Compile Memsat-svm

  tar -zxvf memsat-svm1.3.tar.gz

  cd memsat-svm

  make

• Build database

  mkdir database

  cd database

  Download at
  ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz

  gunzip uniprot_sprot.fasta.gz

  formatdb -i uniprot_sprot.fasta -p T -o T

  cd ..

• Edit Perl script (i.e. set absolute paths)

  gedit run_memsat-svm.pl

• Run Perl script

  ./run_memsat-svm.pl -p 1 examples/1M57_H.fa

The error message I get is:

MEMSAT-SVM: Alpha-helical transmembrane protein topology prediction using Support Vector Machines

Running PSI-BLAST: examples/1M57_H.fa /home/thomas/miniconda3/bin/blastpgp -a 1 -j 2 -h 1e-3 -e 1e-3 -b 0 -d /home/thomas/Softwares/memsat-svm/database/uniprot_sprot.fasta -i /home/thomas/Softwares/memsat-svm/output/memsat-svm_tmp.fasta -C /home/thomas/Softwares/memsat-svm/output/memsat-svm_tmp.chk >& /home/thomas/Softwares/memsat-svm/output/memsat-svm_tmp.out

sh: 1: Syntax error: Bad fd number There was an error running PSI-BLAST. Did you set the database path correctly?

readline() on closed filehandle ERROR at ./run_memsat-svm.pl line 398.

I am running under Ubuntu 18.04. Does anyone knows that I did wrong?

[Ram]

Tags you could have used:

• memsat
• psi-blast
• ubuntu

The only tag you used: software error.

Relevant tags are important for your question's visibility. You're not helping your case, Thomas B.

Answer 1

[Thomas B.]

I added the following lines to my .ncbirc file and it solved the problem.

[BLAST]
BLASTDB=/home/thomas/Softwares/memsat-svm/database/uniprot_sprot.fasta