Parsing error with Provean : Someone else ?
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8.0 years ago
jsgounot ▴ 170

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] 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.

Thanks!

Provean software-error • 2.2k views
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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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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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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