[maker-devel] ProtExcluder1.2 Error

[chebbi mohamed amine]

Hi J iangn ! 

I did some modifications in the script ProtExcluder1.2/mspesl-sfetch.pl by replacing : 

"esl-sfetch --index $ARGV[0] " by "samtools faidx $ARGV[0]" 
and 
"esl-sfetch -c $from..$to $ARGV[0] $line[7] >> $ARGV[3]" by "samtools faidx $ARGV[0] $line[7]:$from-$to >> $ARGV[3]" 

it works fine know and the script can extract the subsequences correctly. 

Best regard, 
Amine 


De: "chebbi mohamed amine" <mohamed.amine.chebbi at univ-poitiers.fr> 
À: "jiangn" <jiangn at msu.edu> 
Envoyé: Vendredi 4 Novembre 2016 01:03:40 
Objet: Re: [maker-devel] ProtExcluder1.2 Error 

Hi J iangn 

In fact, this sequence has a size of 19031 bases. 
When I try the command /hmmer-3.1b2-linux-intel-x86_64/binaries/esl-sfetch -c 1242..19031 all-te.lib rnd-4_family-1731#DNA I get the error , however by testing with coordiantes inferior to 19031 it works fine. I think that it's a related problem to hmmer. I will try to add manualy the subsequence to the file .fnolowm50seq. 

Thank you 
Amine 

De: "jiangn" <jiangn at msu.edu> 
À: "chebbi mohamed amine" <mohamed.amine.chebbi at univ-poitiers.fr> 
Cc: "Prashant S Hosmani" <psh65 at cornell.edu>, "Michael Campbell" <michael.s.campbell1 at gmail.com> 
Envoyé: Vendredi 4 Novembre 2016 00:54:09 
Objet: Re: [maker-devel] ProtExcluder1.2 Error 



Hi Amine, 

I don't have this kind of experience. If only one sequence failed, I would suspect there might be some format issue for that specific sequence. 

Regards, 

Ning 

Quoting chebbi mohamed amine <mohamed.amine.chebbi at univ-poitiers.fr>: 

> 
> 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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>> 
> 
> 


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