[maker-devel] ProtExcluder1.2 Error

[chebbi mohamed amine]

Hi ! 

Thank you Prashant for sharing your experience. Indeed using the same blast version 2.2.29 for makeblastdb seems to resolve the problem. It is looking to work fine for all the sequences except one as I have the message above: 

Fatal exception (source file ../../easel/esl_sqio_ascii.c, line 2001): 
Failed to fetch subsequence residues -- corrupt coords? 
sh: line 1: 46520 Aborted (core dumped) /hmmer-3.1b2-linux-intel-x86_64/binaries/esl-sfetch -c 1242..19031 all-te.lib rnd-4_family-1731#DNA >> blastx_results-all-te.txt.fnolowm50seq 

Did you encounter this problem before? 

Thank you for your help. 

Amine 


De: jiangn at msu.edu 
À: "Prashant S Hosmani" <psh65 at cornell.edu> 
Cc: "Michael Campbell" <michael.s.campbell1 at gmail.com>, "Mohamed Amine Chebbi" <mohamed.amine.chebbi at univ-poitiers.fr> 
Envoyé: Jeudi 3 Novembre 2016 23:54:05 
Objet: Re: [maker-devel] ProtExcluder1.2 Error 



Hi Prashant, 

Thank you so much for sharing your experience. It is important to keep everything in the same version. I will remind users about this when we update it and I may need to bother you then. 

Best regards, 

Ning 

Quoting Prashant S Hosmani <psh65 at cornell.edu>: 

> Hi Amine, 
> 
> I was getting similar error. You need to be careful with the blast 
> versions. Try using the same blast version for makeblastdb. I was 
> using BLAST 2.2.29+. After recreating new blast database with same 
> version, it worked for me. 
> 
> Hope this helps. 
> Prashant 
> 
> 
> Prashant Hosmani 
> Sol Genomics Network 
> Boyce Thompson Institute, Ithaca, NY, USA 
> 
> 
> 
> On Nov 3, 2016, at 1:57 PM, Michael Campbell 
> <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> 
> wrote: 
> 
> Hi Amine, 
> 
> That script is maintained by Ning Jiang and Kevin Childs. They know 
> best what this script is expecting. I?ve ccd them on this email in 
> the hope that they can provide some direction. 
> 
> Thanks, 
> Mike 
> On Nov 2, 2016, at 2:09 PM, Mohamed Amine Chebbi 
> <mohamed.amine.chebbi at univ-poitiers.fr<mailto:mohamed.amine.chebbi at univ-poitiers.fr>> 
> wrote: 
> 
> Hi! 
> 
> I am working on creating a custom repeat library and I want to use 
> ProtExcluder1.2 to trim potential genes from my repeat sequences. 
> My blast version is BLAST 2.2.30+ 
> 
> I get this message error : 
> 
> Can not open the seqfile test.lib_blast_results.txt.fnolowm50seq 
> mergeunmatchedregion.pl seqfile 
> Illegal division by zero at ProtExcluder1.2/GCcontent.pl line 122. 
> 
> I wonder if you can help me to fix this. 
> 
> Thank you. 
> 
> Amine 
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