Maker questions

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Maker questions

Dave Clements
Hi Yeching,

I'm forwarding this to the MAKER list, which is the best place to post MAKER questions.

The [hidden email] address can be dropped from future correspondence.

Dave C

Forwarded conversation
Subject: [Gmod-help] Maker questions
------------------------

From: Yecheng Huang <[hidden email]>
Date: Wed, Nov 10, 2010 at 12:48 AM
To: "[hidden email]" <[hidden email]>
Cc: "[hidden email]" <[hidden email]>


 Hi,
We have installed Maker at our linux 64 bit with gcc compiler.
We have installed all required packages except FGENESH, we are working on get the license.

The install process is smooth. There is no complain/errors during installation.

When we follow the steps at testing samples (http://gmod.org/wiki/MAKER_Tutorial#RUNNING_MAKER_WITH_EXAMPLE_DATA ),
we got errors as:
WARNING: Cannot find> dpp-CDS-1, trying to re-index the fasta.
stop here:dpp-CDS-1
ERROR: Fasta index error

FATAL ERROR
ERROR: Failed while doing exonerate of proteins!!

ERROR: Chunk failed at level 14
!!
FAILED CONTIG:contig-dpp-500-500

------------

I have attached the control files and running log"maker.log" at the email.

Any advise would be greatly appreciated.


sincerely,
Yecheng Huang

Research Computing Center
University of Georgia

http://www.rcc.uga.edu
706-542-9071


----------
From: Yecheng Huang <[hidden email]>
Date: Wed, Nov 10, 2010 at 12:52 AM
To: "[hidden email]" <[hidden email]>
Cc: "[hidden email]" <[hidden email]>


 Here are the attached control files and log file.
Thanks,


From: Yecheng Huang
Sent: Wednesday, November 10, 2010 12:48 AM
To: [hidden email]
Cc: [hidden email]
Subject: Maker questions





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Re: Maker questions

Carson Hinton Holt
Re: [maker-devel] Maker questions The place and way it failed suggests that you are using the wrong version of Bio Perl.  This is identical to a failure that happens when using Bio Perl 1.5x with MAKER.  You need at least version 1.6.

I also would suggest installing the current MAKER 2.04 beta ( http://malachite.genetics.utah.edu/cgi-bin/yandell-lab/register.cgi ) as it has more features and tests the version of dependencies during installation and offers to install the correct ones for you.

Thanks,
Carson



On 11/10/10 9:09 AM, "Dave Clements" <clements@...> wrote:

Hi Yeching,

I'm forwarding this to the MAKER list, which is the best place to post MAKER questions.

The help@... address can be dropped from future correspondence.

Dave C

Forwarded conversation
Subject: [Gmod-help] Maker questions
------------------------

From: Yecheng Huang <yhuang@...>
Date: Wed, Nov 10, 2010 at 12:48 AM
To: "help@..." <help@...>
Cc: "joshbridgers@..." <joshbridgers@...>


 Hi,
We have installed Maker at our linux 64 bit with gcc compiler.
We have installed all required packages except FGENESH, we are working on get the license.

The install process is smooth. There is no complain/errors during installation.

When we follow the steps at testing samples (http://gmod.org/wiki/MAKER_Tutorial#RUNNING_MAKER_WITH_EXAMPLE_DATA ),
we got errors as:
WARNING: Cannot find> dpp-CDS-1, trying to re-index the fasta.
stop here:dpp-CDS-1
ERROR: Fasta index error

FATAL ERROR
ERROR: Failed while doing exonerate of proteins!!

ERROR: Chunk failed at level 14
!!
FAILED CONTIG:contig-dpp-500-500

------------

I have attached the control files and running log"maker.log" at the email.

Any advise would be greatly appreciated.


sincerely,
Yecheng Huang

Research Computing Center
University of Georgia

http://www.rcc.uga.edu
706-542-9071


----------
From: Yecheng Huang <yhuang@...>
Date: Wed, Nov 10, 2010 at 12:52 AM
To: "help@..." <help@...>
Cc: "joshbridgers@..." <joshbridgers@...>


 Here are the attached control files and log file.
Thanks,


From: Yecheng Huang
Sent: Wednesday, November 10, 2010 12:48 AM
To: help@...
Cc: joshbridgers@...
Subject: Maker questions





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Re: Maker questions

Yecheng Huang
Carson,
you are right.
After carefully check on our system, there was a path of bioperl 1.15 present before 1.16 in the environment variable PATH.
 
After remove this 1.15, maker 2.0.3 runs fines with bioperl 1.16
Maker 2.0.4 beta runs like a charm as well.
We greatly appreciate your prompt response and help,
best


Yecheng Huang

Research Computing Center
University of Georgia

http://www.rcc.uga.edu
706-542-9071


From: Carson Holt [[hidden email]]
Sent: Wednesday, November 10, 2010 1:25 PM
To: MAKER Developers List; Yecheng Huang; [hidden email]
Subject: Re: [maker-devel] Maker questions

The place and way it failed suggests that you are using the wrong version of Bio Perl.  This is identical to a failure that happens when using Bio Perl 1.5x with MAKER.  You need at least version 1.6.

I also would suggest installing the current MAKER 2.04 beta ( http://malachite.genetics.utah.edu/cgi-bin/yandell-lab/register.cgi ) as it has more features and tests the version of dependencies during installation and offers to install the correct ones for you.

Thanks,
Carson



On 11/10/10 9:09 AM, "Dave Clements" <clements@...> wrote:

Hi Yeching,

I'm forwarding this to the MAKER list, which is the best place to post MAKER questions.

The help@... address can be dropped from future correspondence.

Dave C

Forwarded conversation
Subject: [Gmod-help] Maker questions
------------------------

From: Yecheng Huang <yhuang@...>
Date: Wed, Nov 10, 2010 at 12:48 AM
To: "help@..." <help@...>
Cc: "joshbridgers@..." <joshbridgers@...>


 Hi,
We have installed Maker at our linux 64 bit with gcc compiler.
We have installed all required packages except FGENESH, we are working on get the license.

The install process is smooth. There is no complain/errors during installation.

When we follow the steps at testing samples (http://gmod.org/wiki/MAKER_Tutorial#RUNNING_MAKER_WITH_EXAMPLE_DATA ),
we got errors as:
WARNING: Cannot find> dpp-CDS-1, trying to re-index the fasta.
stop here:dpp-CDS-1
ERROR: Fasta index error

FATAL ERROR
ERROR: Failed while doing exonerate of proteins!!

ERROR: Chunk failed at level 14
!!
FAILED CONTIG:contig-dpp-500-500

------------

I have attached the control files and running log"maker.log" at the email.

Any advise would be greatly appreciated.


sincerely,
Yecheng Huang

Research Computing Center
University of Georgia

http://www.rcc.uga.edu
706-542-9071


----------
From: Yecheng Huang <yhuang@...>
Date: Wed, Nov 10, 2010 at 12:52 AM
To: "help@..." <help@...>
Cc: "joshbridgers@..." <joshbridgers@...>


 Here are the attached control files and log file.
Thanks,


From: Yecheng Huang
Sent: Wednesday, November 10, 2010 12:48 AM
To: help@...
Cc: joshbridgers@...
Subject: Maker questions





_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org