Parsing error with Provean : Someone else ?

Hi,

I'm trying to use the software PROVEAN to predict the effect of non synonymous substitutions, 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 available in the ensembl website 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

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updated 4.0 years ago by tony •

• written 11.8 years ago by jsgounot

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

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written 7.7 years ago by 820021668 •

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

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written 7.7 years ago by jsgounot

I am getting the same error as you, any luck resolving this?

here is my command line:

antho@x005:~/provean-1.1.5/examples$ provean.sh -q P04637.fasta -v P04637.var --save_supporting_set P04637.sss

>## PROVEAN v1.1 output ## 
># Query sequence file:  P04637.fasta
># Variation file:       P04637.var
># Protein database:     /home/antho/BLASTDB/data
>[11:43:05] searching related sequences... 
>[12:35:19] Parsing Error

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written 4.0 years ago by tony •

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