[maker-devel] ProtExcluder1.2 Error

[jiangn at msu.edu]

Hi Amine,

That's good to know. Thank you!

Ning

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

> 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
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>
>>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20161104/d1b2b900/attachment-0001.html>