Question: Memsat-SVM: error running PSI-BLAST
0
gravatar for Thomas B.
12 weeks ago by
Thomas B.10
Thomas B.10 wrote:

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?

ADD COMMENTlink modified 11 weeks ago • written 12 weeks ago by Thomas B.10

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.

ADD REPLYlink written 11 weeks ago by RamRS19k
0
gravatar for Thomas B.
11 weeks ago by
Thomas B.10
Thomas B.10 wrote:

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
ADD COMMENTlink modified 11 weeks ago by RamRS19k • written 11 weeks ago by Thomas B.10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1833 users visited in the last hour