Question: Parsing error with Provean : Someone else ?
0
gravatar for jsgounot
4.5 years ago by
jsgounot130
European Union
jsgounot130 wrote:

Hi,

I'm trying to use the software PROVEAN to predict the effect of non synonymous subtitutions, but I've got a bug when using my own databases (created with makeblastdb). No errors are printed out when I create the database, but when i launch provean with my substitution and fasta file, i've got a parsing error like this :

 

[10:15:48] loading query sequence from a FASTA file...
[10:15:48] loading variations...
[10:15:48] searching related sequences...
[10:15:48] retrieving subject sequence information...
[10:15:48] Parsing Error

 

In order to understand what's wrong, I try to use other dataset. This way, I took all the fungal protein files avaible in the ensembl website ((http://fungi.ensembl.org/info/website/ftp/index.html) and surprisingly, just half of them make the same error.

 

I'm wondering if someone else already had the same problem, and/or if someone can give me an advice about this.

Thanks !

provean software error • 1.2k views
ADD COMMENTlink modified 4 months ago by 8200216680 • written 4.5 years ago by jsgounot130

Did you resolve it? I have the same problem as you. I changed my database, use different Linux systems and different versions of Provean software, but still not solved.

my command like this:

/naslx/projects/pn69xe/di52piv/apps/provean-1.1.5/bin/provean.sh -q 02.peu.fasta/CCG010218.1.fasta -v 02.new.subst.dir/CCG010218.1 --save_supporting_set 02.provean.out/CCG010218.1.sss

> ## PROVEAN v1.1 output ##
> # Query sequence file:  02.peu.fasta/CCG010218.1.fasta
> # Variation file:       02.new.subst.dir/CCG010218.1
> # Protein database:     /naslx/projects/pn69xe/di52piv/db/uniref90/unirf90 
  [21:27:07]  searching related sequences... 
  [21:45:51] Parsing Error
ADD REPLYlink written 4 months ago by 8200216680

Sorry, really old topic and when I look at what I wrote at that time about this, I think I just gave up.

ADD REPLYlink written 4 months ago by jsgounot130
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