Memsat-SVM: error running PSI-BLAST
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3.2 years ago
Thomas B. ▴ 30

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:

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?

software error memsat-svm psi-blast • 766 views
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Entering edit mode

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.

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Entering edit mode
3.2 years ago
Thomas B. ▴ 30

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
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