<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title></title>
</head>
<body>
<p>
Hi Amine,<br />
<br />
That's good to know. Thank you!<br />
<br />
Ning<br />
<br />
Quoting chebbi mohamed amine <mohamed.amine.chebbi@univ-poitiers.fr>:<br />
<br />
> Hi J iangn !<br />
><br />
> I did some modifications in the script<br />
> ProtExcluder1.2/mspesl-sfetch.pl by replacing :<br />
><br />
> "esl-sfetch --index $ARGV[0] " by "samtools faidx $ARGV[0]"<br />
> and<br />
> "esl-sfetch -c $from..$to $ARGV[0] $line[7] >> $ARGV[3]" by "samtools<br />
> faidx $ARGV[0] $line[7]:$from-$to >> $ARGV[3]"<br />
><br />
> it works fine know and the script can extract the subsequences correctly.<br />
><br />
> Best regard,<br />
> Amine<br />
><br />
><br />
> De: "chebbi mohamed amine" <mohamed.amine.chebbi@univ-poitiers.fr><br />
> À: "jiangn" <jiangn@msu.edu><br />
> Envoyé: Vendredi 4 Novembre 2016 01:03:40<br />
> Objet: Re: [maker-devel] ProtExcluder1.2 Error<br />
><br />
> Hi J iangn<br />
><br />
> In fact, this sequence has a size of 19031 bases.<br />
> When I try the command<br />
> /hmmer-3.1b2-linux-intel-x86_64/binaries/esl-sfetch -c 1242..19031<br />
> all-te.lib rnd-4_family-1731#DNA I get the error , however by testing<br />
> with coordiantes inferior to 19031 it works fine. I think that it's a<br />
> related problem to hmmer. I will try to add manualy the subsequence<br />
> to the file .fnolowm50seq.<br />
><br />
> Thank you<br />
> Amine<br />
><br />
> De: "jiangn" <jiangn@msu.edu><br />
> À: "chebbi mohamed amine" <mohamed.amine.chebbi@univ-poitiers.fr><br />
> Cc: "Prashant S Hosmani" <psh65@cornell.edu>, "Michael Campbell"<br />
> <michael.s.campbell1@gmail.com><br />
> Envoyé: Vendredi 4 Novembre 2016 00:54:09<br />
> Objet: Re: [maker-devel] ProtExcluder1.2 Error<br />
><br />
><br />
><br />
> Hi Amine,<br />
><br />
> I don't have this kind of experience. If only one sequence failed, I<br />
> would suspect there might be some format issue for that specific<br />
> sequence.<br />
><br />
> Regards,<br />
><br />
> Ning<br />
><br />
> Quoting chebbi mohamed amine <mohamed.amine.chebbi@univ-poitiers.fr>:<br />
><br />
>><br />
>> Hi !<br />
>><br />
>> Thank you Prashant for sharing your experience. Indeed using the same<br />
>> blast version 2.2.29 for makeblastdb seems to resolve the problem. It<br />
>> is looking to work fine for all the sequences except one as I have<br />
>> the message above:<br />
>><br />
>> Fatal exception (source file ../../easel/esl_sqio_ascii.c, line 2001):<br />
>> Failed to fetch subsequence residues -- corrupt coords?<br />
>> sh: line 1: 46520 Aborted (core dumped)<br />
>> /hmmer-3.1b2-linux-intel-x86_64/binaries/esl-sfetch -c 1242..19031<br />
>> all-te.lib rnd-4_family-1731#DNA >><br />
>> blastx_results-all-te.txt.fnolowm50seq<br />
>><br />
>> Did you encounter this problem before?<br />
>><br />
>> Thank you for your help.<br />
>><br />
>> Amine<br />
>><br />
>><br />
>> De: jiangn@msu.edu<br />
>> À: "Prashant S Hosmani" <psh65@cornell.edu><br />
>> Cc: "Michael Campbell" <michael.s.campbell1@gmail.com>, "Mohamed<br />
>> Amine Chebbi" <mohamed.amine.chebbi@univ-poitiers.fr><br />
>> Envoyé: Jeudi 3 Novembre 2016 23:54:05<br />
>> Objet: Re: [maker-devel] ProtExcluder1.2 Error<br />
>><br />
>><br />
>><br />
>> Hi Prashant,<br />
>><br />
>> Thank you so much for sharing your experience. It is important to<br />
>> keep everything in the same version. I will remind users about this<br />
>> when we update it and I may need to bother you then.<br />
>><br />
>> Best regards,<br />
>><br />
>> Ning<br />
>><br />
>> Quoting Prashant S Hosmani <psh65@cornell.edu>:<br />
>><br />
>>> Hi Amine,<br />
>>><br />
>>> I was getting similar error. You need to be careful with the blast<br />
>>> versions. Try using the same blast version for makeblastdb. I was<br />
>>> using BLAST 2.2.29+. After recreating new blast database with same<br />
>>> version, it worked for me.<br />
>>><br />
>>> Hope this helps.<br />
>>> Prashant<br />
>>><br />
>>><br />
>>> Prashant Hosmani<br />
>>> Sol Genomics Network<br />
>>> Boyce Thompson Institute, Ithaca, NY, USA<br />
>>><br />
>>><br />
>>><br />
>>> On Nov 3, 2016, at 1:57 PM, Michael Campbell<br />
>>> <michael.s.campbell1@gmail.com<mailto:michael.s.campbell1@gmail.com>><br />
>>> wrote:<br />
>>><br />
>>> Hi Amine,<br />
>>><br />
>>> That script is maintained by Ning Jiang and Kevin Childs. They know<br />
>>> best what this script is expecting. I?ve ccd them on this email in<br />
>>> the hope that they can provide some direction.<br />
>>><br />
>>> Thanks,<br />
>>> Mike<br />
>>> On Nov 2, 2016, at 2:09 PM, Mohamed Amine Chebbi<br />
>>> <mohamed.amine.chebbi@univ-poitiers.fr<mailto:mohamed.amine.chebbi@univ-poitiers.fr>><br />
>>> wrote:<br />
>>><br />
>>> Hi!<br />
>>><br />
>>> I am working on creating a custom repeat library and I want to use<br />
>>> ProtExcluder1.2 to trim potential genes from my repeat sequences.<br />
>>> My blast version is BLAST 2.2.30+<br />
>>><br />
>>> I get this message error :<br />
>>><br />
>>> Can not open the seqfile test.lib_blast_results.txt.fnolowm50seq<br />
>>> mergeunmatchedregion.pl seqfile<br />
>>> Illegal division by zero at ProtExcluder1.2/GCcontent.pl line 122.<br />
>>><br />
>>> I wonder if you can help me to fix this.<br />
>>><br />
>>> Thank you.<br />
>>><br />
>>> Amine<br />
>>> _______________________________________________<br />
>>> maker-devel mailing list<br />
>>> maker-devel@box290.bluehost.com<mailto:maker-devel@box290.bluehost.com><br />
>>> <a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br />
>>><br />
>>> _______________________________________________<br />
>>> maker-devel mailing list<br />
>>> maker-devel@box290.bluehost.com<mailto:maker-devel@box290.bluehost.com><br />
>>> <a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br />
>>><br />
>>><br />
>><br />
>><br />
><br />
><br />
><br />
</p>
</body>
</html>