[maker-devel] ProtExcluder1.2 Error

231 views
Skip to first unread message

Mohamed Amine Chebbi

unread,
Nov 2, 2016, 2:16:53 PM11/2/16
to Maker Mailing List

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

Michael Campbell

unread,
Nov 3, 2016, 1:57:54 PM11/3/16
to Mohamed Amine Chebbi, Maker Mailing List, Ning Jiang
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
_______________________________________________
maker-devel mailing list
maker...@box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Prashant S Hosmani

unread,
Nov 3, 2016, 2:16:32 PM11/3/16
to Michael Campbell, Maker Mailing List, Ning Jiang, Mohamed Amine Chebbi
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


chebbi mohamed amine

unread,
Nov 9, 2016, 1:07:58 PM11/9/16
to jiangn, Maker Mailing List
Hi Jiangn !

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.am...@univ-poitiers.fr>
À: "jiangn" <jia...@msu.edu>
Envoyé: Vendredi 4 Novembre 2016 01:03:40
Objet: Re: [maker-devel] ProtExcluder1.2 Error

Hi Jiangn

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" <jia...@msu.edu>
À: "chebbi mohamed amine" <mohamed.am...@univ-poitiers.fr>
Cc: "Prashant S Hosmani" <ps...@cornell.edu>, "Michael Campbell" <michael.s...@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.am...@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: jia...@msu.edu
> À: "Prashant S Hosmani" <ps...@cornell.edu>
> Cc: "Michael Campbell" <michael.s...@gmail.com>, "Mohamed
> Amine Chebbi" <mohamed.am...@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 <ps...@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


>> 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


>> 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


>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>> _______________________________________________
>> maker-devel mailing list

chebbi mohamed amine

unread,
Nov 9, 2016, 1:08:00 PM11/9/16
to jia...@msu.edu, Maker Mailing List

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: jia...@msu.edu
À: "Prashant S Hosmani" <ps...@cornell.edu>
Cc: "Michael Campbell" <michael.s...@gmail.com>, "Mohamed Amine Chebbi" <mohamed.am...@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 <ps...@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


> 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


> 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


> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> _______________________________________________
> maker-devel mailing list

jia...@msu.edu

unread,
Nov 9, 2016, 1:56:28 PM11/9/16
to chebbi mohamed amine, Maker Mailing List

Hi Amine,

That's good to know. Thank you!



Ning

Quoting chebbi mohamed amine <mohamed.am...@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.am...@univ-poitiers.fr>
> À: "jiangn" <jia...@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
>

Reply all
Reply to author
Forward
0 new messages