From carsonhh at gmail.com  Wed Oct  2 09:14:44 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 02 Oct 2013 10:14:44 -0400
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
Message-ID: <CE709D72.EF15%carsonhh@gmail.com>

It still works, but it will be reduced.  Without ESTs you won't get any
UTR prediction, also you will be limited by how well the protein set
matches to the genes.  If you use the protein set of a close relative you
will capture most things.  You will probably capture 80-95% of what you
would by also including ESTs.  It all depending on how different the
species in the proteins evidence file are compared to the the species
being annotated.

--Carson

On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for your message and your kind help. Now conversion from
>match/match_part to gene/mRNA/exons/CDS works well after blanking out
>some options in control file.
>
>I have one more question about maker2. In case we don't have EST evidence
>(set of ESTs or assembled mRNA-seq in fasta format) for a genome, does
>maker2 function? If it does function, could you please let me know the
>performance of maker2 without providing EST evidence compared to the one
>with EST evidence?
>
>Thank you  again and I look forward to hearing from you.
>
>Best,
>Xia
>
>
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Wednesday, September 25, 2013 10:36 AM
>To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>If it is launching predictors then you have snap hmm or augustus_species
>set.  You ned to blank out all other options in the control files
>(including repeat masking options, proteins, ESTs, etc.) when trying to
>convert mathc/match_part to gene/mRNA/exons/CDS, or else those other
>programs will run.
>
>--Carson
>
>
>On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>
>>Hi Carson,
>>
>>Thank you for the message and your kind help. We tested maker2 by
>>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>But it seemed maker2 started to launch all predictors again and it took
>>long time to finish. I wonder if there is any way that we can directly
>>get gene/mRNA/exons/CDS gff file without re-running maker2 to convert
>>match/match_part features into gene/mRNA/exons/CDS.
>>
>>Thanks,
>>Xia
>>
>>-----Original Message-----
>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>Sent: Thursday, September 19, 2013 5:58 PM
>>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY;
>>maker-devel at yandell-lab.org
>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>
>>Hello Corban & Xia,
>>
>>Some scripts like gff3_preds2models are deprecated.  To get the same
>>result as was offered by gff3_preds2models, just give your
>>match/match_part features to pref_gff= in the maker_opts.ctl file, set
>>keep_preds=1, and run with all other options and predictors turned off.
>>The final MAKER result will be your match/match_part features converted
>>into gene/mRNA/exons/CDS.
>>
>>For functional annotation, you can use Interproscan, BLASTP against
>>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO
>>terms and proteins domains via the ipr_update_gff and iprscan2gff3
>>scripts.  Then add putative gene functions via BLASTP to UniProt and
>>maker_functional_fasta and maker_functional_gff scripts.
>>
>>Go ahead and take a look and that those tools and let me know if you
>>have any questions or need help you configuring them.
>>
>>Thanks,
>>Carson
>>
>>
>>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>
>>>Hi  Corban & Xia,
>>>
>>>
>>>I've forwarded your question along to the MAKER_dev list, were you can
>>>get speedy answers to your maker related questions. Thanks for using
>>>MAKER.
>>>
>>>--mark
>>>
>>>
>>>Mark Yandell
>>>Professor of Human Genetics
>>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of
>>>Human Genetics University of Utah
>>>15 North 2030 East, Room 2100
>>>Salt Lake City, UT 84112-5330
>>>ph:801-587-7707
>>>
>>>________________________________________
>>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>Sent: Thursday, September 19, 2013 11:49 AM
>>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>Subject: maker2 scripts for functional annotation
>>>
>>>Dr. Yandell,
>>>
>>>We were recently evaluating maker2 for annotation and going through
>>>the maker tutorial from 2012.
>>>
>>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>>
>>>The tutorial makes references to some scripts that we couldn?t find in
>>>the current release.  We were looking for scripts like
>>>gff3_preds2models to convert match/match_part format into annotations
>>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did
>>>not have the most up to date version.
>>>
>>>In addition to getting accurate gene annotations, I was looking for a
>>>solution to get functional assignments.  I see that there are some
>>>scripts like maker_functional_fasta that may help, but I was wondering
>>>what you would recommend.
>>>
>>>Thanks,
>>>
>>>Corban & Xia
>>>
>>>This communication is for use by the intended recipient and contains
>>>information that may be Privileged, confidential or copyrighted under
>>>applicable law. If you are not the intended recipient, you are hereby
>>>formally notified that any use, copying or distribution of this
>>>e-mail, in whole or in part, is strictly prohibited. Please notify the
>>>sender by return e-mail and delete this e-mail from your system.
>>>Unless explicitly and conspicuously designated as "E-Contract
>>>Intended", this e-mail does not constitute a contract offer, a
>>>contract amendment, or an acceptance of a contract offer. This e-mail
>>>does not constitute a consent to the use of sender's contact
>>>information for direct marketing purposes or for transfers of data to
>>>third parties.
>>>
>>>The dupont.com web address will continue in use for a transitional
>>>period for communications sent or received on behalf of DuPont
>>>Performance Coatings., which is not affiliated in any way with the
>>>DuPont Company.
>>>
>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>>Korean
>>>
>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>g
>>
>>
>>
>>This communication is for use by the intended recipient and contains
>>information that may be Privileged, confidential or copyrighted under
>>applicable law. If you are not the intended recipient, you are hereby
>>formally notified that any use, copying or distribution of this e-mail,
>>in whole or in part, is strictly prohibited. Please notify the sender
>>by return e-mail and delete this e-mail from your system. Unless
>>explicitly and conspicuously designated as "E-Contract Intended", this
>>e-mail does not constitute a contract offer, a contract amendment, or
>>an acceptance of a contract offer. This e-mail does not constitute a
>>consent to the use of sender's contact information for direct marketing
>>purposes or for transfers of data to third parties.
>>
>>The dupont.com<http://dupont.com/> web address will continue in use for
>>a transitional period for communications sent or received on behalf of
>>DuPont Performance Coatings., which is not affiliated in any way with
>>the DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>Korean
>>
>>           http://www.DuPont.com/corp/email_disclaimer.html
>>
>
>
>
>This communication is for use by the intended recipient and contains
>information that may be Privileged, confidential or copyrighted under
>applicable law. If you are not the intended recipient, you are hereby
>formally notified that any use, copying or distribution of this e-mail,
>in whole or in part, is strictly prohibited. Please notify the sender by
>return e-mail and delete this e-mail from your system. Unless explicitly
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>not constitute a contract offer, a contract amendment, or an acceptance
>of a contract offer. This e-mail does not constitute a consent to the
>use of sender's contact information for direct marketing purposes or for
>transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for a
>transitional period for communications sent or received on behalf of
>DuPont
>Performance Coatings., which is not affiliated in any way with the DuPont
>Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>





From Xia.Cao at dupont.com  Tue Oct  1 14:00:42 2013
From: Xia.Cao at dupont.com (Xia.Cao at dupont.com)
Date: Tue, 1 Oct 2013 19:00:42 +0000
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <CE686C71.ECAC%carsonhh@gmail.com>
References: <AAF36CDE29C45F45AE125A1D13F5D675ACE4B8@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE686C71.ECAC%carsonhh@gmail.com>
Message-ID: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>

Hi Carson,

Thank you for your message and your kind help. Now conversion from match/match_part to gene/mRNA/exons/CDS works well after blanking out some options in control file.  

I have one more question about maker2. In case we don't have EST evidence (set of ESTs or assembled mRNA-seq in fasta format) for a genome, does maker2 function? If it does function, could you please let me know the performance of maker2 without providing EST evidence compared to the one with EST evidence?

Thank you  again and I look forward to hearing from you.

Best,
Xia




-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Wednesday, September 25, 2013 10:36 AM
To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] maker2 scripts for functional annotation

If it is launching predictors then you have snap hmm or augustus_species set.  You ned to blank out all other options in the control files (including repeat masking options, proteins, ESTs, etc.) when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else those other programs will run.

--Carson


On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for the message and your kind help. We tested maker2 by 
>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun . 
>But it seemed maker2 started to launch all predictors again and it took 
>long time to finish. I wonder if there is any way that we can directly 
>get gene/mRNA/exons/CDS gff file without re-running maker2 to convert 
>match/match_part features into gene/mRNA/exons/CDS.
>
>Thanks,
>Xia
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Thursday, September 19, 2013 5:58 PM
>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; 
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>Hello Corban & Xia,
>
>Some scripts like gff3_preds2models are deprecated.  To get the same 
>result as was offered by gff3_preds2models, just give your 
>match/match_part features to pref_gff= in the maker_opts.ctl file, set 
>keep_preds=1, and run with all other options and predictors turned off.
>The final MAKER result will be your match/match_part features converted 
>into gene/mRNA/exons/CDS.
>
>For functional annotation, you can use Interproscan, BLASTP against 
>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO 
>terms and proteins domains via the ipr_update_gff and iprscan2gff3 
>scripts.  Then add putative gene functions via BLASTP to UniProt and 
>maker_functional_fasta and maker_functional_gff scripts.
>
>Go ahead and take a look and that those tools and let me know if you 
>have any questions or need help you configuring them.
>
>Thanks,
>Carson
>
>
>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>
>>Hi  Corban & Xia,
>>
>>
>>I've forwarded your question along to the MAKER_dev list, were you can 
>>get speedy answers to your maker related questions. Thanks for using 
>>MAKER.
>>
>>--mark
>>
>>
>>Mark Yandell
>>Professor of Human Genetics
>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of 
>>Human Genetics University of Utah
>>15 North 2030 East, Room 2100
>>Salt Lake City, UT 84112-5330
>>ph:801-587-7707
>>
>>________________________________________
>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>Sent: Thursday, September 19, 2013 11:49 AM
>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>Subject: maker2 scripts for functional annotation
>>
>>Dr. Yandell,
>>
>>We were recently evaluating maker2 for annotation and going through 
>>the maker tutorial from 2012.
>>
>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>
>>The tutorial makes references to some scripts that we couldn?t find in 
>>the current release.  We were looking for scripts like 
>>gff3_preds2models to convert match/match_part format into annotations 
>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did 
>>not have the most up to date version.
>>
>>In addition to getting accurate gene annotations, I was looking for a 
>>solution to get functional assignments.  I see that there are some 
>>scripts like maker_functional_fasta that may help, but I was wondering 
>>what you would recommend.
>>
>>Thanks,
>>
>>Corban & Xia
>>
>>This communication is for use by the intended recipient and contains 
>>information that may be Privileged, confidential or copyrighted under 
>>applicable law. If you are not the intended recipient, you are hereby 
>>formally notified that any use, copying or distribution of this 
>>e-mail, in whole or in part, is strictly prohibited. Please notify the 
>>sender by return e-mail and delete this e-mail from your system. 
>>Unless explicitly and conspicuously designated as "E-Contract 
>>Intended", this e-mail does not constitute a contract offer, a 
>>contract amendment, or an acceptance of a contract offer. This e-mail 
>>does not constitute a consent to the use of sender's contact 
>>information for direct marketing purposes or for transfers of data to third parties.
>>
>>The dupont.com web address will continue in use for a transitional 
>>period for communications sent or received on behalf of DuPont 
>>Performance Coatings., which is not affiliated in any way with the 
>>DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>Korean
>>
>>          http://www.DuPont.com/corp/email_disclaimer.html
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>g
>
>
>
>This communication is for use by the intended recipient and contains 
>information that may be Privileged, confidential or copyrighted under 
>applicable law. If you are not the intended recipient, you are hereby 
>formally notified that any use, copying or distribution of this e-mail, 
>in whole or in part, is strictly prohibited. Please notify the sender 
>by return e-mail and delete this e-mail from your system. Unless 
>explicitly and conspicuously designated as "E-Contract Intended", this 
>e-mail does not constitute a contract offer, a contract amendment, or 
>an acceptance of a contract offer. This e-mail does not constitute a 
>consent to the use of sender's contact information for direct marketing 
>purposes or for transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for 
>a transitional period for communications sent or received on behalf of 
>DuPont Performance Coatings., which is not affiliated in any way with 
>the DuPont Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  
>Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>



This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
applicable law. If you are not the intended recipient, you are hereby
formally notified that any use, copying or distribution of this e-mail,
in whole or in part, is strictly prohibited. Please notify the sender by
return e-mail and delete this e-mail from your system. Unless explicitly
and conspicuously designated as "E-Contract Intended", this e-mail does
not constitute a contract offer, a contract amendment, or an acceptance
of a contract offer. This e-mail does not constitute a consent to the
use of sender's contact information for direct marketing purposes or for
transfers of data to third parties.

The dupont.com<http://dupont.com/> web address will continue in use for a
transitional period for communications sent or received on behalf of DuPont
Performance Coatings., which is not affiliated in any way with the DuPont Company.

Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean

           http://www.DuPont.com/corp/email_disclaimer.html




From carsonhh at gmail.com  Wed Oct  2 09:43:29 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 02 Oct 2013 10:43:29 -0400
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
Message-ID: <CE71A8D4.F2AD%carsonhh@gmail.com>

That's ok.  If it is very closely related, provide it directly to the est=
option, otherwise provide it to the altest= option.  The difference
between the two options is how they are aligned.  The altest= alignments
takes about 10x longer than the est= alignments.

--Carson


On 10/2/13 10:40 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for your quick and kind reply. One more question here. If we
>don't have EST evidence for the strain we sequenced/assembled, will it be
>ok to provide some EST evidence that is from some other strains which are
>close to the one we are trying to annotate? Could you please let us know
>how this will affect performance of maker2?
>
>Thank you again.
>
>Best,
>Xia
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Wednesday, October 02, 2013 10:15 AM
>To: CAO, XIA
>Cc: myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>It still works, but it will be reduced.  Without ESTs you won't get any
>UTR prediction, also you will be limited by how well the protein set
>matches to the genes.  If you use the protein set of a close relative you
>will capture most things.  You will probably capture 80-95% of what you
>would by also including ESTs.  It all depending on how different the
>species in the proteins evidence file are compared to the the species
>being annotated.
>
>--Carson
>
>On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>
>>Hi Carson,
>>
>>Thank you for your message and your kind help. Now conversion from
>>match/match_part to gene/mRNA/exons/CDS works well after blanking out
>>some options in control file.
>>
>>I have one more question about maker2. In case we don't have EST
>>evidence (set of ESTs or assembled mRNA-seq in fasta format) for a
>>genome, does
>>maker2 function? If it does function, could you please let me know the
>>performance of maker2 without providing EST evidence compared to the
>>one with EST evidence?
>>
>>Thank you  again and I look forward to hearing from you.
>>
>>Best,
>>Xia
>>
>>
>>
>>
>>-----Original Message-----
>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>Sent: Wednesday, September 25, 2013 10:36 AM
>>To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>>maker-devel at yandell-lab.org
>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>
>>If it is launching predictors then you have snap hmm or
>>augustus_species set.  You ned to blank out all other options in the
>>control files (including repeat masking options, proteins, ESTs, etc.)
>>when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else
>>those other programs will run.
>>
>>--Carson
>>
>>
>>On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>>
>>>Hi Carson,
>>>
>>>Thank you for the message and your kind help. We tested maker2 by
>>>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>>But it seemed maker2 started to launch all predictors again and it
>>>took long time to finish. I wonder if there is any way that we can
>>>directly get gene/mRNA/exons/CDS gff file without re-running maker2 to
>>>convert match/match_part features into gene/mRNA/exons/CDS.
>>>
>>>Thanks,
>>>Xia
>>>
>>>-----Original Message-----
>>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>>Sent: Thursday, September 19, 2013 5:58 PM
>>>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY;
>>>maker-devel at yandell-lab.org
>>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>>
>>>Hello Corban & Xia,
>>>
>>>Some scripts like gff3_preds2models are deprecated.  To get the same
>>>result as was offered by gff3_preds2models, just give your
>>>match/match_part features to pref_gff= in the maker_opts.ctl file, set
>>>keep_preds=1, and run with all other options and predictors turned off.
>>>The final MAKER result will be your match/match_part features
>>>converted into gene/mRNA/exons/CDS.
>>>
>>>For functional annotation, you can use Interproscan, BLASTP against
>>>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO
>>>terms and proteins domains via the ipr_update_gff and iprscan2gff3
>>>scripts.  Then add putative gene functions via BLASTP to UniProt and
>>>maker_functional_fasta and maker_functional_gff scripts.
>>>
>>>Go ahead and take a look and that those tools and let me know if you
>>>have any questions or need help you configuring them.
>>>
>>>Thanks,
>>>Carson
>>>
>>>
>>>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>>
>>>>Hi  Corban & Xia,
>>>>
>>>>
>>>>I've forwarded your question along to the MAKER_dev list, were you
>>>>can get speedy answers to your maker related questions. Thanks for
>>>>using MAKER.
>>>>
>>>>--mark
>>>>
>>>>
>>>>Mark Yandell
>>>>Professor of Human Genetics
>>>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of
>>>>Human Genetics University of Utah
>>>>15 North 2030 East, Room 2100
>>>>Salt Lake City, UT 84112-5330
>>>>ph:801-587-7707
>>>>
>>>>________________________________________
>>>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>>Sent: Thursday, September 19, 2013 11:49 AM
>>>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>>Subject: maker2 scripts for functional annotation
>>>>
>>>>Dr. Yandell,
>>>>
>>>>We were recently evaluating maker2 for annotation and going through
>>>>the maker tutorial from 2012.
>>>>
>>>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>>>
>>>>The tutorial makes references to some scripts that we couldn?t find
>>>>in the current release.  We were looking for scripts like
>>>>gff3_preds2models to convert match/match_part format into annotations
>>>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did
>>>>not have the most up to date version.
>>>>
>>>>In addition to getting accurate gene annotations, I was looking for a
>>>>solution to get functional assignments.  I see that there are some
>>>>scripts like maker_functional_fasta that may help, but I was
>>>>wondering what you would recommend.
>>>>
>>>>Thanks,
>>>>
>>>>Corban & Xia
>>>>
>>>>This communication is for use by the intended recipient and contains
>>>>information that may be Privileged, confidential or copyrighted under
>>>>applicable law. If you are not the intended recipient, you are hereby
>>>>formally notified that any use, copying or distribution of this
>>>>e-mail, in whole or in part, is strictly prohibited. Please notify
>>>>the sender by return e-mail and delete this e-mail from your system.
>>>>Unless explicitly and conspicuously designated as "E-Contract
>>>>Intended", this e-mail does not constitute a contract offer, a
>>>>contract amendment, or an acceptance of a contract offer. This e-mail
>>>>does not constitute a consent to the use of sender's contact
>>>>information for direct marketing purposes or for transfers of data to
>>>>third parties.
>>>>
>>>>The dupont.com web address will continue in use for a transitional
>>>>period for communications sent or received on behalf of DuPont
>>>>Performance Coatings., which is not affiliated in any way with the
>>>>DuPont Company.
>>>>
>>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>>>Korean
>>>>
>>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>>>
>>>>_______________________________________________
>>>>maker-devel mailing list
>>>>maker-devel at box290.bluehost.com
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>>r
>>>>g
>>>
>>>
>>>
>>>This communication is for use by the intended recipient and contains
>>>information that may be Privileged, confidential or copyrighted under
>>>applicable law. If you are not the intended recipient, you are hereby
>>>formally notified that any use, copying or distribution of this
>>>e-mail, in whole or in part, is strictly prohibited. Please notify the
>>>sender by return e-mail and delete this e-mail from your system.
>>>Unless explicitly and conspicuously designated as "E-Contract
>>>Intended", this e-mail does not constitute a contract offer, a
>>>contract amendment, or an acceptance of a contract offer. This e-mail
>>>does not constitute a consent to the use of sender's contact
>>>information for direct marketing purposes or for transfers of data to
>>>third parties.
>>>
>>>The dupont.com<http://dupont.com/> web address will continue in use
>>>for a transitional period for communications sent or received on
>>>behalf of DuPont Performance Coatings., which is not affiliated in any
>>>way with the DuPont Company.
>>>
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>>>Korean
>>>
>>>           http://www.DuPont.com/corp/email_disclaimer.html
>>>
>>
>>
>>
>>This communication is for use by the intended recipient and contains
>>information that may be Privileged, confidential or copyrighted under
>>applicable law. If you are not the intended recipient, you are hereby
>>formally notified that any use, copying or distribution of this e-mail,
>>in whole or in part, is strictly prohibited. Please notify the sender
>>by return e-mail and delete this e-mail from your system. Unless
>>explicitly and conspicuously designated as "E-Contract Intended", this
>>e-mail does not constitute a contract offer, a contract amendment, or
>>an acceptance of a contract offer. This e-mail does not constitute a
>>consent to the use of sender's contact information for direct marketing
>>purposes or for transfers of data to third parties.
>>
>>The dupont.com<http://dupont.com/> web address will continue in use for
>>a transitional period for communications sent or received on behalf of
>>DuPont Performance Coatings., which is not affiliated in any way with
>>the DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>Korean
>>
>>           http://www.DuPont.com/corp/email_disclaimer.html
>>
>
>
>
>This communication is for use by the intended recipient and contains
>information that may be Privileged, confidential or copyrighted under
>applicable law. If you are not the intended recipient, you are hereby
>formally notified that any use, copying or distribution of this e-mail,
>in whole or in part, is strictly prohibited. Please notify the sender by
>return e-mail and delete this e-mail from your system. Unless explicitly
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>not constitute a contract offer, a contract amendment, or an acceptance
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>use of sender's contact information for direct marketing purposes or for
>transfers of data to third parties.
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>transitional period for communications sent or received on behalf of
>DuPont
>Performance Coatings., which is not affiliated in any way with the DuPont
>Company.
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From Carson.Holt at oicr.on.ca  Wed Oct  2 10:24:42 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Wed, 2 Oct 2013 15:24:42 +0000
Subject: [maker-devel] Incorrect gene model, antisense transcripts
In-Reply-To: <A21F03FBB429334EB4D450CC75E8CBF37F0454C6@CH1PRD0210MB384.namprd02.prod.outlook.com>
Message-ID: <CE71B238.F2B7%carson.holt@oicr.on.ca>

SNAP appears to be making small ab initio calls all over the place.  You may need to retrain it, or just drop it completely from your analysis and just use augustus.

Try running with protein2genome and then training SNAP off of those results.  Also make sure your repeat masking is sufficient.  You may be getting too many SANP predictions if that is the case.

Thanks,
Carson



From: Sivaranjani Namasivayam <ranjani at uga.edu<mailto:ranjani at uga.edu>>
Date: Tuesday, October 1, 2013 5:01 PM
To: "maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>" <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>>
Subject: Incorrect gene model, antisense transcripts

Hello,

I am working on annotating a genome. I have RNAseq data assembled with Cufflinks and Trinity. I am using to predict gene models. Below is the procedure I used

- For the first round of prediction I provided the following : EST evidence: assembled RNAseq, Protein evidence: proteins from related organism, Gene predictor: augustus trained on a related organism.
- The number of genes I got was much less than expected (Expect atleast 10K genes, got ~4K genes)
- Used the gene models from the first round of annotations to train SNAP (default parameters) and provided the HMM for the second round of annotation (used augustus also). All other data I passed as such in the gff3, except the gene models.I also included the some manually curated genes in the EST evidence.

- The number of genes were much higher, ~11k, but many seemed incorrect and appear to have been generated from the SNAP models. I am attaching a screen shot from Apollo showing this.

Would you have any suggestions on why this might be happening and how I can fix?
I am essentially looking for gene models for my assembled RNAseq, can I achieve this by setting est2genome to 1? Would I be losing/misrepresenting any data if I do this.

Also, I recently noticed my RNAseq data has assembled antisense transcripts. MAKER seems to be predicting a coding region for these antisense transcripts in some cases, (although the coding region predicted is much smaller than that of the sense gene model.) Is there a way to tell MAKER not to predict gene models on both strands at the same loci.

Appreciate your help.

Thanks,
Ranjani





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From Xia.Cao at dupont.com  Wed Oct  2 09:40:12 2013
From: Xia.Cao at dupont.com (Xia.Cao at dupont.com)
Date: Wed, 2 Oct 2013 14:40:12 +0000
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <CE709D72.EF15%carsonhh@gmail.com>
References: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE709D72.EF15%carsonhh@gmail.com>
Message-ID: <AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>

Hi Carson,

Thank you for your quick and kind reply. One more question here. If we don't have EST evidence for the strain we sequenced/assembled, will it be ok to provide some EST evidence that is from some other strains which are close to the one we are trying to annotate? Could you please let us know how this will affect performance of maker2?

Thank you again.

Best,
Xia

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Wednesday, October 02, 2013 10:15 AM
To: CAO, XIA
Cc: myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] maker2 scripts for functional annotation

It still works, but it will be reduced.  Without ESTs you won't get any UTR prediction, also you will be limited by how well the protein set matches to the genes.  If you use the protein set of a close relative you will capture most things.  You will probably capture 80-95% of what you would by also including ESTs.  It all depending on how different the species in the proteins evidence file are compared to the the species being annotated.

--Carson

On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for your message and your kind help. Now conversion from 
>match/match_part to gene/mRNA/exons/CDS works well after blanking out 
>some options in control file.
>
>I have one more question about maker2. In case we don't have EST 
>evidence (set of ESTs or assembled mRNA-seq in fasta format) for a 
>genome, does
>maker2 function? If it does function, could you please let me know the 
>performance of maker2 without providing EST evidence compared to the 
>one with EST evidence?
>
>Thank you  again and I look forward to hearing from you.
>
>Best,
>Xia
>
>
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Wednesday, September 25, 2013 10:36 AM
>To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; 
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>If it is launching predictors then you have snap hmm or 
>augustus_species set.  You ned to blank out all other options in the 
>control files (including repeat masking options, proteins, ESTs, etc.) 
>when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else 
>those other programs will run.
>
>--Carson
>
>
>On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>
>>Hi Carson,
>>
>>Thank you for the message and your kind help. We tested maker2 by 
>>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>But it seemed maker2 started to launch all predictors again and it 
>>took long time to finish. I wonder if there is any way that we can 
>>directly get gene/mRNA/exons/CDS gff file without re-running maker2 to 
>>convert match/match_part features into gene/mRNA/exons/CDS.
>>
>>Thanks,
>>Xia
>>
>>-----Original Message-----
>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>Sent: Thursday, September 19, 2013 5:58 PM
>>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; 
>>maker-devel at yandell-lab.org
>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>
>>Hello Corban & Xia,
>>
>>Some scripts like gff3_preds2models are deprecated.  To get the same 
>>result as was offered by gff3_preds2models, just give your 
>>match/match_part features to pref_gff= in the maker_opts.ctl file, set 
>>keep_preds=1, and run with all other options and predictors turned off.
>>The final MAKER result will be your match/match_part features 
>>converted into gene/mRNA/exons/CDS.
>>
>>For functional annotation, you can use Interproscan, BLASTP against 
>>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO 
>>terms and proteins domains via the ipr_update_gff and iprscan2gff3 
>>scripts.  Then add putative gene functions via BLASTP to UniProt and 
>>maker_functional_fasta and maker_functional_gff scripts.
>>
>>Go ahead and take a look and that those tools and let me know if you 
>>have any questions or need help you configuring them.
>>
>>Thanks,
>>Carson
>>
>>
>>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>
>>>Hi  Corban & Xia,
>>>
>>>
>>>I've forwarded your question along to the MAKER_dev list, were you 
>>>can get speedy answers to your maker related questions. Thanks for 
>>>using MAKER.
>>>
>>>--mark
>>>
>>>
>>>Mark Yandell
>>>Professor of Human Genetics
>>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of 
>>>Human Genetics University of Utah
>>>15 North 2030 East, Room 2100
>>>Salt Lake City, UT 84112-5330
>>>ph:801-587-7707
>>>
>>>________________________________________
>>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>Sent: Thursday, September 19, 2013 11:49 AM
>>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>Subject: maker2 scripts for functional annotation
>>>
>>>Dr. Yandell,
>>>
>>>We were recently evaluating maker2 for annotation and going through 
>>>the maker tutorial from 2012.
>>>
>>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>>
>>>The tutorial makes references to some scripts that we couldn?t find 
>>>in the current release.  We were looking for scripts like 
>>>gff3_preds2models to convert match/match_part format into annotations 
>>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did 
>>>not have the most up to date version.
>>>
>>>In addition to getting accurate gene annotations, I was looking for a 
>>>solution to get functional assignments.  I see that there are some 
>>>scripts like maker_functional_fasta that may help, but I was 
>>>wondering what you would recommend.
>>>
>>>Thanks,
>>>
>>>Corban & Xia
>>>
>>>This communication is for use by the intended recipient and contains 
>>>information that may be Privileged, confidential or copyrighted under 
>>>applicable law. If you are not the intended recipient, you are hereby 
>>>formally notified that any use, copying or distribution of this 
>>>e-mail, in whole or in part, is strictly prohibited. Please notify 
>>>the sender by return e-mail and delete this e-mail from your system.
>>>Unless explicitly and conspicuously designated as "E-Contract 
>>>Intended", this e-mail does not constitute a contract offer, a 
>>>contract amendment, or an acceptance of a contract offer. This e-mail 
>>>does not constitute a consent to the use of sender's contact 
>>>information for direct marketing purposes or for transfers of data to 
>>>third parties.
>>>
>>>The dupont.com web address will continue in use for a transitional 
>>>period for communications sent or received on behalf of DuPont 
>>>Performance Coatings., which is not affiliated in any way with the 
>>>DuPont Company.
>>>
>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>>Korean
>>>
>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>r
>>>g
>>
>>
>>
>>This communication is for use by the intended recipient and contains 
>>information that may be Privileged, confidential or copyrighted under 
>>applicable law. If you are not the intended recipient, you are hereby 
>>formally notified that any use, copying or distribution of this 
>>e-mail, in whole or in part, is strictly prohibited. Please notify the 
>>sender by return e-mail and delete this e-mail from your system. 
>>Unless explicitly and conspicuously designated as "E-Contract 
>>Intended", this e-mail does not constitute a contract offer, a 
>>contract amendment, or an acceptance of a contract offer. This e-mail 
>>does not constitute a consent to the use of sender's contact 
>>information for direct marketing purposes or for transfers of data to third parties.
>>
>>The dupont.com<http://dupont.com/> web address will continue in use 
>>for a transitional period for communications sent or received on 
>>behalf of DuPont Performance Coatings., which is not affiliated in any 
>>way with the DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>Korean
>>
>>           http://www.DuPont.com/corp/email_disclaimer.html
>>
>
>
>
>This communication is for use by the intended recipient and contains 
>information that may be Privileged, confidential or copyrighted under 
>applicable law. If you are not the intended recipient, you are hereby 
>formally notified that any use, copying or distribution of this e-mail, 
>in whole or in part, is strictly prohibited. Please notify the sender 
>by return e-mail and delete this e-mail from your system. Unless 
>explicitly and conspicuously designated as "E-Contract Intended", this 
>e-mail does not constitute a contract offer, a contract amendment, or 
>an acceptance of a contract offer. This e-mail does not constitute a 
>consent to the use of sender's contact information for direct marketing 
>purposes or for transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for 
>a transitional period for communications sent or received on behalf of 
>DuPont Performance Coatings., which is not affiliated in any way with 
>the DuPont Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  
>Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>



This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
applicable law. If you are not the intended recipient, you are hereby
formally notified that any use, copying or distribution of this e-mail,
in whole or in part, is strictly prohibited. Please notify the sender by
return e-mail and delete this e-mail from your system. Unless explicitly
and conspicuously designated as "E-Contract Intended", this e-mail does
not constitute a contract offer, a contract amendment, or an acceptance
of a contract offer. This e-mail does not constitute a consent to the
use of sender's contact information for direct marketing purposes or for
transfers of data to third parties.

The dupont.com<http://dupont.com/> web address will continue in use for a
transitional period for communications sent or received on behalf of DuPont
Performance Coatings., which is not affiliated in any way with the DuPont Company.

Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean

           http://www.DuPont.com/corp/email_disclaimer.html




From markwiz at us.ibm.com  Wed Oct  2 11:52:55 2013
From: markwiz at us.ibm.com (Mark Wisner)
Date: Wed, 2 Oct 2013 12:52:55 -0400
Subject: [maker-devel] Maker2 on IBM PowerLinux?
Message-ID: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>

IBMs PowerLinux is tuned for Big Data workloads. We have had queries for 
Maker2 on PowerLinux.
How do we work with Maker2 development to create a PowerLinux port.
Thanks,

Mark K. Wisner
Linux On Power ISV PM
IBM
3039 Cornwallis Rd
RTP, NC 27709
Cell 919-649-5813
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From barry.moore at genetics.utah.edu  Wed Oct  2 12:29:36 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Wed, 2 Oct 2013 11:29:36 -0600
Subject: [maker-devel] Maker2 on IBM PowerLinux?
In-Reply-To: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>
References: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>
Message-ID: <E59BC7E8-B562-4AD6-B4CF-C793329B688B@genetics.utah.edu>

Hi Mark,

Carson Holt is the primary Maker developer, but others of us may be able to help as well.  I've added e-mails for Carson, Michael Campbell, Mark Yandell and myself who are currently developers on the project.   You can feel free to contact this mailing list - or if the conversation is getting too far afield for general interest you can contact us off list and we will do whatever we can to help.  If you feel like you need to do some modification of MAKER code to optimize it for PowerLinux I'm happy to give you a branch on the subversion repo to work with and then we can work with you to merge these changes back to the trunk when you feel like you have some improvements that benefit PowerLinux (and all other) users.

Thanks very much for your interest in MAKER - your participation in the community is most welcome!

Barry

On Oct 2, 2013, at 10:52 AM, Mark Wisner wrote:

> IBMs PowerLinux is tuned for Big Data workloads. We have had queries for Maker2 on PowerLinux. 
> How do we work with Maker2 development to create a PowerLinux port. 
> Thanks,
> 
> Mark K. Wisner
> Linux On Power ISV PM
> IBM
> 3039 Cornwallis Rd
> RTP, NC 27709
> Cell 919-649-5813
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From carsonhh at gmail.com  Wed Oct  2 12:29:50 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 02 Oct 2013 13:29:50 -0400
Subject: [maker-devel] Maker2 on IBM PowerLinux?
In-Reply-To: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>
Message-ID: <CE71CD2E.F2D8%carsonhh@gmail.com>

MAKER is written in perl, so it can work pretty much anywhere you have perl.
It is more an issue of the tools MAKER uses.  If you can get SNAP, BLAST,
exonerate, etc. to run then MAKER should be no problem.

You can let MAKER try and install and configure any missing perl libraries
as well as external tools for you (this is by far the easiest way).  You
will need an internet connection.

cd ?/maker/src/
perl Build.PL               #say 'Y' to local installation of libraries and
'N' to MPI for now
./Build installdeps     #grabs missing perl libraries from the ether, and
installs them in  the .../maker/perl/ directory
./Build installers        #grabs missing tools from the ether, installs, and
configures them in the .../maker/exe/ directory
./Build install              #just installs maker


If you want to run via MPI, I'd recommend OpenMPI, and you will need to
rerun the 'perl Build.PL' and './Build install' steps (say yes to MPI this
time around).

Here are some variables you will likly have to add to your .bash_profile to
get openmpi to run with MAKER (you must add these and source the profile
before attempting to install with OpenMPI), otherwise compilation will not
work correctly (OpenMPI shared library issue).

#you need to set $OMPIHOME to OpenMPI's location here -->
export LD_PRELOAD=$OMPIHOME/lib/libmpi.so:$LD_PRELOAD


#this one just suppresses a warning -->
export OMPI_MCA_mpi_warn_on_fork=0


And on some systems you have to add this  ' -mca btl ^openib' to the mpiexec
command when I run maker.
Example-->
mpiexec -mca btl ^openib -n 20 maker

Thanks,
Carson


From:  Mark Wisner <markwiz at us.ibm.com>
Date:  Wednesday, October 2, 2013 12:52 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker2 on IBM PowerLinux?

IBMs PowerLinux is tuned for Big Data workloads. We have had queries for
Maker2 on PowerLinux.
How do we work with Maker2 development to create a PowerLinux port.
Thanks,

Mark K. Wisner
Linux On Power ISV PM
IBM
3039 Cornwallis Rd
RTP, NC 27709
Cell 919-649-5813
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From barry.moore at genetics.utah.edu  Wed Oct  2 12:21:29 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Wed, 2 Oct 2013 11:21:29 -0600
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
References: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE709D72.EF15%carsonhh@gmail.com>
	<AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
Message-ID: <E9DC8DC1-8E1F-42E7-94CC-5D58EF0A1F21@genetics.utah.edu>

Hi Xia,

You can use EST evidence from other strains/species.  The considerations are as follows:  When you pass EST (or mRNASeq based transcripts) evidence MAKER uses blastn to align those with alignment parameters that assume they sequences will align easily with almost perfect identity - this is fast.  If you use EST/mRNA evidence from another species MAKER uses tblastx to compare the RNA evidence to the assembly, both translated into protein space - this works fine, but it is slow and often doesn't get you much more evidence than you could have gotten from proteins as evidence.  If you believe that you're other strain should have very little divergence in sequence at the nt level then you could experiment with passing EST/mRNA evidence as est in the control file.  Consider this an experiment, do it on a few contigs and examine the results carefully and skeptically.  If it works well, that would be the way to go because you've get better UTRs, but if it doesn't you'll see that you get little support for models because sequence divergence was too much for good alignment.  In that case you'll need to use alt_est and this will be slower and you'll likely get little in the way of support for UTRs - in this case as well, do a few contigs and examine the output carefully to see if the additional alignment time with tblastx is worth it in your case.

Barry


On Oct 2, 2013, at 8:40 AM, <Xia.Cao at dupont.com>
 wrote:

> Hi Carson,
> 
> Thank you for your quick and kind reply. One more question here. If we don't have EST evidence for the strain we sequenced/assembled, will it be ok to provide some EST evidence that is from some other strains which are close to the one we are trying to annotate? Could you please let us know how this will affect performance of maker2?
> 
> Thank you again.
> 
> Best,
> Xia
> 
> -----Original Message-----
> From: Carson Holt [mailto:carsonhh at gmail.com] 
> Sent: Wednesday, October 02, 2013 10:15 AM
> To: CAO, XIA
> Cc: myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org
> Subject: Re: [maker-devel] maker2 scripts for functional annotation
> 
> It still works, but it will be reduced.  Without ESTs you won't get any UTR prediction, also you will be limited by how well the protein set matches to the genes.  If you use the protein set of a close relative you will capture most things.  You will probably capture 80-95% of what you would by also including ESTs.  It all depending on how different the species in the proteins evidence file are compared to the the species being annotated.
> 
> --Carson
> 
> On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
> 
>> Hi Carson,
>> 
>> Thank you for your message and your kind help. Now conversion from 
>> match/match_part to gene/mRNA/exons/CDS works well after blanking out 
>> some options in control file.
>> 
>> I have one more question about maker2. In case we don't have EST 
>> evidence (set of ESTs or assembled mRNA-seq in fasta format) for a 
>> genome, does
>> maker2 function? If it does function, could you please let me know the 
>> performance of maker2 without providing EST evidence compared to the 
>> one with EST evidence?
>> 
>> Thank you  again and I look forward to hearing from you.
>> 
>> Best,
>> Xia
>> 
>> 
>> 
>> 
>> -----Original Message-----
>> From: Carson Holt [mailto:carsonhh at gmail.com]
>> Sent: Wednesday, September 25, 2013 10:36 AM
>> To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; 
>> maker-devel at yandell-lab.org
>> Subject: Re: [maker-devel] maker2 scripts for functional annotation
>> 
>> If it is launching predictors then you have snap hmm or 
>> augustus_species set.  You ned to blank out all other options in the 
>> control files (including repeat masking options, proteins, ESTs, etc.) 
>> when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else 
>> those other programs will run.
>> 
>> --Carson
>> 
>> 
>> On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>> 
>>> Hi Carson,
>>> 
>>> Thank you for the message and your kind help. We tested maker2 by 
>>> setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>> But it seemed maker2 started to launch all predictors again and it 
>>> took long time to finish. I wonder if there is any way that we can 
>>> directly get gene/mRNA/exons/CDS gff file without re-running maker2 to 
>>> convert match/match_part features into gene/mRNA/exons/CDS.
>>> 
>>> Thanks,
>>> Xia
>>> 
>>> -----Original Message-----
>>> From: Carson Holt [mailto:carsonhh at gmail.com]
>>> Sent: Thursday, September 19, 2013 5:58 PM
>>> To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; 
>>> maker-devel at yandell-lab.org
>>> Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>> 
>>> Hello Corban & Xia,
>>> 
>>> Some scripts like gff3_preds2models are deprecated.  To get the same 
>>> result as was offered by gff3_preds2models, just give your 
>>> match/match_part features to pref_gff= in the maker_opts.ctl file, set 
>>> keep_preds=1, and run with all other options and predictors turned off.
>>> The final MAKER result will be your match/match_part features 
>>> converted into gene/mRNA/exons/CDS.
>>> 
>>> For functional annotation, you can use Interproscan, BLASTP against 
>>> UniProt, or BALST2GO.  My preference is to use InterProScan to add GO 
>>> terms and proteins domains via the ipr_update_gff and iprscan2gff3 
>>> scripts.  Then add putative gene functions via BLASTP to UniProt and 
>>> maker_functional_fasta and maker_functional_gff scripts.
>>> 
>>> Go ahead and take a look and that those tools and let me know if you 
>>> have any questions or need help you configuring them.
>>> 
>>> Thanks,
>>> Carson
>>> 
>>> 
>>> On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>> 
>>>> Hi  Corban & Xia,
>>>> 
>>>> 
>>>> I've forwarded your question along to the MAKER_dev list, were you 
>>>> can get speedy answers to your maker related questions. Thanks for 
>>>> using MAKER.
>>>> 
>>>> --mark
>>>> 
>>>> 
>>>> Mark Yandell
>>>> Professor of Human Genetics
>>>> H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of 
>>>> Human Genetics University of Utah
>>>> 15 North 2030 East, Room 2100
>>>> Salt Lake City, UT 84112-5330
>>>> ph:801-587-7707
>>>> 
>>>> ________________________________________
>>>> From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>> Sent: Thursday, September 19, 2013 11:49 AM
>>>> To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>> Subject: maker2 scripts for functional annotation
>>>> 
>>>> Dr. Yandell,
>>>> 
>>>> We were recently evaluating maker2 for annotation and going through 
>>>> the maker tutorial from 2012.
>>>> 
>>>> http://gmod.org/wiki/MAKER_Tutorial_2012
>>>> 
>>>> The tutorial makes references to some scripts that we couldn?t find 
>>>> in the current release.  We were looking for scripts like 
>>>> gff3_preds2models to convert match/match_part format into annotations 
>>>> with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did 
>>>> not have the most up to date version.
>>>> 
>>>> In addition to getting accurate gene annotations, I was looking for a 
>>>> solution to get functional assignments.  I see that there are some 
>>>> scripts like maker_functional_fasta that may help, but I was 
>>>> wondering what you would recommend.
>>>> 
>>>> Thanks,
>>>> 
>>>> Corban & Xia
>>>> 
>>>> This communication is for use by the intended recipient and contains 
>>>> information that may be Privileged, confidential or copyrighted under 
>>>> applicable law. If you are not the intended recipient, you are hereby 
>>>> formally notified that any use, copying or distribution of this 
>>>> e-mail, in whole or in part, is strictly prohibited. Please notify 
>>>> the sender by return e-mail and delete this e-mail from your system.
>>>> Unless explicitly and conspicuously designated as "E-Contract 
>>>> Intended", this e-mail does not constitute a contract offer, a 
>>>> contract amendment, or an acceptance of a contract offer. This e-mail 
>>>> does not constitute a consent to the use of sender's contact 
>>>> information for direct marketing purposes or for transfers of data to 
>>>> third parties.
>>>> 
>>>> The dupont.com web address will continue in use for a transitional 
>>>> period for communications sent or received on behalf of DuPont 
>>>> Performance Coatings., which is not affiliated in any way with the 
>>>> DuPont Company.
>>>> 
>>>> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>>> Korean
>>>> 
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>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
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>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>> r
>>>> g
>>> 
>>> 
>>> 
>>> This communication is for use by the intended recipient and contains 
>>> information that may be Privileged, confidential or copyrighted under 
>>> applicable law. If you are not the intended recipient, you are hereby 
>>> formally notified that any use, copying or distribution of this 
>>> e-mail, in whole or in part, is strictly prohibited. Please notify the 
>>> sender by return e-mail and delete this e-mail from your system. 
>>> Unless explicitly and conspicuously designated as "E-Contract 
>>> Intended", this e-mail does not constitute a contract offer, a 
>>> contract amendment, or an acceptance of a contract offer. This e-mail 
>>> does not constitute a consent to the use of sender's contact 
>>> information for direct marketing purposes or for transfers of data to third parties.
>>> 
>>> The dupont.com<http://dupont.com/> web address will continue in use 
>>> for a transitional period for communications sent or received on 
>>> behalf of DuPont Performance Coatings., which is not affiliated in any 
>>> way with the DuPont Company.
>>> 
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>>> Korean
>>> 
>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>> 
>> 
>> 
>> 
>> This communication is for use by the intended recipient and contains 
>> information that may be Privileged, confidential or copyrighted under 
>> applicable law. If you are not the intended recipient, you are hereby 
>> formally notified that any use, copying or distribution of this e-mail, 
>> in whole or in part, is strictly prohibited. Please notify the sender 
>> by return e-mail and delete this e-mail from your system. Unless 
>> explicitly and conspicuously designated as "E-Contract Intended", this 
>> e-mail does not constitute a contract offer, a contract amendment, or 
>> an acceptance of a contract offer. This e-mail does not constitute a 
>> consent to the use of sender's contact information for direct marketing 
>> purposes or for transfers of data to third parties.
>> 
>> The dupont.com<http://dupont.com/> web address will continue in use for 
>> a transitional period for communications sent or received on behalf of 
>> DuPont Performance Coatings., which is not affiliated in any way with 
>> the DuPont Company.
>> 
>> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  
>> Korean
>> 
>>          http://www.DuPont.com/corp/email_disclaimer.html
>> 
> 
> 
> 
> This communication is for use by the intended recipient and contains
> information that may be Privileged, confidential or copyrighted under
> applicable law. If you are not the intended recipient, you are hereby
> formally notified that any use, copying or distribution of this e-mail,
> in whole or in part, is strictly prohibited. Please notify the sender by
> return e-mail and delete this e-mail from your system. Unless explicitly
> and conspicuously designated as "E-Contract Intended", this e-mail does
> not constitute a contract offer, a contract amendment, or an acceptance
> of a contract offer. This e-mail does not constitute a consent to the
> use of sender's contact information for direct marketing purposes or for
> transfers of data to third parties.
> 
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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From Xia.Cao at dupont.com  Wed Oct  2 12:51:26 2013
From: Xia.Cao at dupont.com (Xia.Cao at dupont.com)
Date: Wed, 2 Oct 2013 17:51:26 +0000
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <E9DC8DC1-8E1F-42E7-94CC-5D58EF0A1F21@genetics.utah.edu>
References: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE709D72.EF15%carsonhh@gmail.com>
	<AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
	<E9DC8DC1-8E1F-42E7-94CC-5D58EF0A1F21@genetics.utah.edu>
Message-ID: <AAF36CDE29C45F45AE125A1D13F5D675AE2175@033-CH1MPN2-063.033d.mgd.msft.net>

Hi Barry,

Thank you very much for the message and suggestions. It's really helpful to us.  We will do some tests to see how we can take advantage of Maker2  to produce high-quality gene models from our assembled genome.

Thank you again,
Xia


From: Barry Moore [mailto:barry.moore at genetics.utah.edu]
Sent: Wednesday, October 02, 2013 1:21 PM
To: CAO, XIA
Cc: carsonhh at gmail.com; maker-devel at yandell-lab.org; RIVERA, CORBAN GREGORY
Subject: Re: [maker-devel] maker2 scripts for functional annotation

Hi Xia,

You can use EST evidence from other strains/species.  The considerations are as follows:  When you pass EST (or mRNASeq based transcripts) evidence MAKER uses blastn to align those with alignment parameters that assume they sequences will align easily with almost perfect identity - this is fast.  If you use EST/mRNA evidence from another species MAKER uses tblastx to compare the RNA evidence to the assembly, both translated into protein space - this works fine, but it is slow and often doesn't get you much more evidence than you could have gotten from proteins as evidence.  If you believe that you're other strain should have very little divergence in sequence at the nt level then you could experiment with passing EST/mRNA evidence as est in the control file.  Consider this an experiment, do it on a few contigs and examine the results carefully and skeptically.  If it works well, that would be the way to go because you've get better UTRs, but if it doesn't you'll see that you get little support for models because sequence divergence was too much for good alignment.  In that case you'll need to use alt_est and this will be slower and you'll likely get little in the way of support for UTRs - in this case as well, do a few contigs and examine the output carefully to see if the additional alignment time with tblastx is worth it in your case.

Barry


On Oct 2, 2013, at 8:40 AM, <Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>>
 wrote:


Hi Carson,

Thank you for your quick and kind reply. One more question here. If we don't have EST evidence for the strain we sequenced/assembled, will it be ok to provide some EST evidence that is from some other strains which are close to the one we are trying to annotate? Could you please let us know how this will affect performance of maker2?

Thank you again.

Best,
Xia

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Wednesday, October 02, 2013 10:15 AM
To: CAO, XIA
Cc: myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker2 scripts for functional annotation

It still works, but it will be reduced.  Without ESTs you won't get any UTR prediction, also you will be limited by how well the protein set matches to the genes.  If you use the protein set of a close relative you will capture most things.  You will probably capture 80-95% of what you would by also including ESTs.  It all depending on how different the species in the proteins evidence file are compared to the the species being annotated.

--Carson

On 10/1/13 3:00 PM, "Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>" <Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>> wrote:


Hi Carson,

Thank you for your message and your kind help. Now conversion from
match/match_part to gene/mRNA/exons/CDS works well after blanking out
some options in control file.

I have one more question about maker2. In case we don't have EST
evidence (set of ESTs or assembled mRNA-seq in fasta format) for a
genome, does
maker2 function? If it does function, could you please let me know the
performance of maker2 without providing EST evidence compared to the
one with EST evidence?

Thank you  again and I look forward to hearing from you.

Best,
Xia




-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Wednesday, September 25, 2013 10:36 AM
To: CAO, XIA; myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>; RIVERA, CORBAN GREGORY;
maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker2 scripts for functional annotation

If it is launching predictors then you have snap hmm or
augustus_species set.  You ned to blank out all other options in the
control files (including repeat masking options, proteins, ESTs, etc.)
when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else
those other programs will run.

--Carson


On 9/25/13 10:31 AM, "Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>" <Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>> wrote:

Hi Carson,

Thank you for the message and your kind help. We tested maker2 by
setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
But it seemed maker2 started to launch all predictors again and it
took long time to finish. I wonder if there is any way that we can
directly get gene/mRNA/exons/CDS gff file without re-running maker2 to
convert match/match_part features into gene/mRNA/exons/CDS.

Thanks,
Xia

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Thursday, September 19, 2013 5:58 PM
To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY;
maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker2 scripts for functional annotation

Hello Corban & Xia,

Some scripts like gff3_preds2models are deprecated.  To get the same
result as was offered by gff3_preds2models, just give your
match/match_part features to pref_gff= in the maker_opts.ctl file, set
keep_preds=1, and run with all other options and predictors turned off.
The final MAKER result will be your match/match_part features
converted into gene/mRNA/exons/CDS.

For functional annotation, you can use Interproscan, BLASTP against
UniProt, or BALST2GO.  My preference is to use InterProScan to add GO
terms and proteins domains via the ipr_update_gff and iprscan2gff3
scripts.  Then add putative gene functions via BLASTP to UniProt and
maker_functional_fasta and maker_functional_gff scripts.

Go ahead and take a look and that those tools and let me know if you
have any questions or need help you configuring them.

Thanks,
Carson


On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>> wrote:

Hi  Corban & Xia,


I've forwarded your question along to the MAKER_dev list, were you
can get speedy answers to your maker related questions. Thanks for
using MAKER.

--mark


Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of
Human Genetics University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com> [Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>]
Sent: Thursday, September 19, 2013 11:49 AM
To: Mark Yandell; Corban-Gregory.Rivera at dupont.com<mailto:Corban-Gregory.Rivera at dupont.com>
Subject: maker2 scripts for functional annotation

Dr. Yandell,

We were recently evaluating maker2 for annotation and going through
the maker tutorial from 2012.

http://gmod.org/wiki/MAKER_Tutorial_2012

The tutorial makes references to some scripts that we couldn?t find
in the current release.  We were looking for scripts like
gff3_preds2models to convert match/match_part format into annotations
with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did
not have the most up to date version.

In addition to getting accurate gene annotations, I was looking for a
solution to get functional assignments.  I see that there are some
scripts like maker_functional_fasta that may help, but I was
wondering what you would recommend.

Thanks,

Corban & Xia

This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
applicable law. If you are not the intended recipient, you are hereby
formally notified that any use, copying or distribution of this
e-mail, in whole or in part, is strictly prohibited. Please notify
the sender by return e-mail and delete this e-mail from your system.
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The dupont.com<http://dupont.com> web address will continue in use for a transitional
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DuPont Company.

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Korean

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r
g



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This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
applicable law. If you are not the intended recipient, you are hereby
formally notified that any use, copying or distribution of this e-mail,
in whole or in part, is strictly prohibited. Please notify the sender by
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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543





This communication is for use by the intended recipient and contains
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From cjfields at illinois.edu  Thu Oct  3 13:44:07 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 3 Oct 2013 18:44:07 +0000
Subject: [maker-devel] NFSLock problem
Message-ID: <B9943BBA-BEFF-4B23-A6B8-7581247F3C95@illinois.edu>

I have a MAKER job running that seems to be stalled on a failed scaffold.  It's running via MPI (MAKER v2.28, openMPI 1.6.3), that appears to have worked successfully for the most part.  This is a run that only uses transcriptome and protein information in order to get a decent dseat of 

The failed scaffold seems to be holding the job from completion.  There does seem to be changes, but mainly they are on the NFSLock files:

./.NFSLock.gi_lock.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.282.start.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.281.end.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.281.end.blastn.holdover.NFSLock.STACK

Everything else seems to have completed.  

I have seen a few issues re: NFS locking problems, would this be related?  Should I stop the job?  

We're running GPFS for our NFS.  Here's 'mount':

-system-specific-4.1$ mount
/dev/sda5 on / type ext4 (rw)
proc on /proc type proc (rw)
sysfs on /sys type sysfs (rw)
devpts on /dev/pts type devpts (rw,gid=5,mode=620)
tmpfs on /dev/shm type tmpfs (rw)
/dev/sda1 on /boot type ext4 (rw)
/dev/sdb1 on /export type ext4 (rw)
/dev/sda2 on /var type ext4 (rw)
tmpfs on /var/lib/ganglia/rrds type tmpfs (rw,size=6180842000,gid=99,uid=99)
none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
nfsd on /proc/fs/nfsd type nfsd (rw)
/dev/IGBHOME0 on /home type gpfs (rw,mtime,dev=IGBHOME0)
128.174.124.79:/shares/group on /archive/group type nfs (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,proto=tcp,mountproto=tcp,addr=128.174.124.79)
128.174.124.79:/shares/CBC on /archive/CBC type nfs (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,proto=tcp,mountproto=tcp,addr=128.174.124.79)

chris


From carsonhh at gmail.com  Thu Oct  3 13:45:37 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 03 Oct 2013 14:45:37 -0400
Subject: [maker-devel] NFSLock problem
In-Reply-To: <B9943BBA-BEFF-4B23-A6B8-7581247F3C95@illinois.edu>
Message-ID: <CE73336F.F347%carsonhh@gmail.com>

Stop the job and restart it.  No need to delete anything.  Just restart it.

Thanks,
Carson


On 10/3/13 2:44 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

>I have a MAKER job running that seems to be stalled on a failed scaffold.
> It's running via MPI (MAKER v2.28, openMPI 1.6.3), that appears to have
>worked successfully for the most part.  This is a run that only uses
>transcriptome and protein information in order to get a decent dseat of
>
>The failed scaffold seems to be holding the job from completion.  There
>does seem to be changes, but mainly they are on the NFSLock files:
>
>./.NFSLock.gi_lock.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.282.start.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.end.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.end.blastn.holdover.NFSLock.STACK
>
>Everything else seems to have completed.
>
>I have seen a few issues re: NFS locking problems, would this be related?
> Should I stop the job?
>
>We're running GPFS for our NFS.  Here's 'mount':
>
>-system-specific-4.1$ mount
>/dev/sda5 on / type ext4 (rw)
>proc on /proc type proc (rw)
>sysfs on /sys type sysfs (rw)
>devpts on /dev/pts type devpts (rw,gid=5,mode=620)
>tmpfs on /dev/shm type tmpfs (rw)
>/dev/sda1 on /boot type ext4 (rw)
>/dev/sdb1 on /export type ext4 (rw)
>/dev/sda2 on /var type ext4 (rw)
>tmpfs on /var/lib/ganglia/rrds type tmpfs
>(rw,size=6180842000,gid=99,uid=99)
>none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
>sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
>nfsd on /proc/fs/nfsd type nfsd (rw)
>/dev/IGBHOME0 on /home type gpfs (rw,mtime,dev=IGBHOME0)
>128.174.124.79:/shares/group on /archive/group type nfs
>(rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>roto=tcp,mountproto=tcp,addr=128.174.124.79)
>128.174.124.79:/shares/CBC on /archive/CBC type nfs
>(rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>roto=tcp,mountproto=tcp,addr=128.174.124.79)
>
>chris
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From cjfields at illinois.edu  Thu Oct  3 21:45:29 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 4 Oct 2013 02:45:29 +0000
Subject: [maker-devel] NFSLock problem
In-Reply-To: <CE73336F.F347%carsonhh@gmail.com>
References: <CE73336F.F347%carsonhh@gmail.com>
Message-ID: <EB3895BA-F1EF-4F14-813F-233D1B4269AB@illinois.edu>

Carson,

Took a couple of restarts but finally processed through.  I saw a prior email on the mail list where you mentioned this could be due to failed jobs hanging things up; I may set up my next job to allow one processor for logging into the nodes in case there is a similar problem, maybe try to track this down.

chris

On Oct 3, 2013, at 1:45 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Stop the job and restart it.  No need to delete anything.  Just restart it.
> 
> Thanks,
> Carson
> 
> 
> On 10/3/13 2:44 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> 
>> I have a MAKER job running that seems to be stalled on a failed scaffold.
>> It's running via MPI (MAKER v2.28, openMPI 1.6.3), that appears to have
>> worked successfully for the most part.  This is a run that only uses
>> transcriptome and protein information in order to get a decent dseat of
>> 
>> The failed scaffold seems to be holding the job from completion.  There
>> does seem to be changes, but mainly they are on the NFSLock files:
>> 
>> ./.NFSLock.gi_lock.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.282.start.blastn.holdover.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.281.end.blastn.holdover.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.281.end.blastn.holdover.NFSLock.STACK
>> 
>> Everything else seems to have completed.
>> 
>> I have seen a few issues re: NFS locking problems, would this be related?
>> Should I stop the job?
>> 
>> We're running GPFS for our NFS.  Here's 'mount':
>> 
>> -system-specific-4.1$ mount
>> /dev/sda5 on / type ext4 (rw)
>> proc on /proc type proc (rw)
>> sysfs on /sys type sysfs (rw)
>> devpts on /dev/pts type devpts (rw,gid=5,mode=620)
>> tmpfs on /dev/shm type tmpfs (rw)
>> /dev/sda1 on /boot type ext4 (rw)
>> /dev/sdb1 on /export type ext4 (rw)
>> /dev/sda2 on /var type ext4 (rw)
>> tmpfs on /var/lib/ganglia/rrds type tmpfs
>> (rw,size=6180842000,gid=99,uid=99)
>> none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
>> sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
>> nfsd on /proc/fs/nfsd type nfsd (rw)
>> /dev/IGBHOME0 on /home type gpfs (rw,mtime,dev=IGBHOME0)
>> 128.174.124.79:/shares/group on /archive/group type nfs
>> (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>> roto=tcp,mountproto=tcp,addr=128.174.124.79)
>> 128.174.124.79:/shares/CBC on /archive/CBC type nfs
>> (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>> roto=tcp,mountproto=tcp,addr=128.174.124.79)
>> 
>> chris
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 




From felix.bemm at uni-wuerzburg.de  Fri Oct  4 02:10:08 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Fri, 04 Oct 2013 09:10:08 +0200
Subject: [maker-devel] Contigs failing - could not make datastore directory
Message-ID: <524E69D0.1090905@uni-wuerzburg.de>

Hi,

I have a problem with Contigs failing like this:

examining contents of the fasta file and run log
ERROR: could not make datastore directory
--> rank=11, hostname=r5n04
ERROR: Failed while examining contents of the fasta file and run log
ERROR: Chunk failed at level:0, tier_type:0
FAILED CONTIG:MA_gen_v8.05_c31675

There is enough space available on both the storage device and the tmp 
device that is being used. The datastore log files looks like this:

MA_gen_v8.05_c1149              FAILED
MA_gen_v8.05_c1153              FAILED
MA_gen_v8.05_c1154              FAILED
MA_gen_v8.05_c1155              FAILED
MA_gen_v8.05_c1156              FAILED

Since there is no datastore for this contigs, I can not provide any more 
informationen. Approx. 1/3 of the contigs were annotated, after that 
maker started to fail. It kept running for a while and finishing some of 
the contigs in the second or third try like this:

MA_gen_v8.05_c4443		FAILED
MA_gen_v8.05_c4443		FAILED
MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	STARTED
MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/ 
FINISHED

Any ideas what can cause this problems?

Best regards
Felix

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Fri Oct  4 13:15:35 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 04 Oct 2013 14:15:35 -0400
Subject: [maker-devel] Contigs failing - could not make datastore
 directory
In-Reply-To: <524E69D0.1090905@uni-wuerzburg.de>
Message-ID: <CE747D9A.F599%carsonhh@gmail.com>

Let me know what you find.  With some failures it's hard to identify the
problem especially with long running processes, which is why I made MAKER
restartable, so you can at least get completion by just launching again.

--Carson


On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi,
>
>I have a problem with Contigs failing like this:
>
>examining contents of the fasta file and run log
>ERROR: could not make datastore directory
>--> rank=11, hostname=r5n04
>ERROR: Failed while examining contents of the fasta file and run log
>ERROR: Chunk failed at level:0, tier_type:0
>FAILED CONTIG:MA_gen_v8.05_c31675
>
>There is enough space available on both the storage device and the tmp
>device that is being used. The datastore log files looks like this:
>
>MA_gen_v8.05_c1149              FAILED
>MA_gen_v8.05_c1153              FAILED
>MA_gen_v8.05_c1154              FAILED
>MA_gen_v8.05_c1155              FAILED
>MA_gen_v8.05_c1156              FAILED
>
>Since there is no datastore for this contigs, I can not provide any more
>informationen. Approx. 1/3 of the contigs were annotated, after that
>maker started to fail. It kept running for a while and finishing some of
>the contigs in the second or third try like this:
>
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	START
>ED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>FINISHED
>
>Any ideas what can cause this problems?
>
>Best regards
>Felix
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Fri Oct  4 13:21:42 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 04 Oct 2013 14:21:42 -0400
Subject: [maker-devel] Contigs failing - could not make datastore
 directory
In-Reply-To: <524E69D0.1090905@uni-wuerzburg.de>
Message-ID: <CE743B26.F369%carsonhh@gmail.com>

Hi Felix,

There are other potential issues as well, for example a file quota limit
set by your administrator or full local /tmp which will be unique to each
node and cannot be queried directly from the root node on a cluster.  On a
cluster one node may also not have the NFS location mounted.  Or it could
be system related, for example on ibrix NFS mounted systems you can get a
weird filesystem issue with ghost files and directories when using MAKER
that can neither be created nor deleted.  Try running the failed contigs
in a different directory (even if it's on the same disk).  Also what
version of MAKER are you using?

--Carson



On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi,
>
>I have a problem with Contigs failing like this:
>
>examining contents of the fasta file and run log
>ERROR: could not make datastore directory
>--> rank=11, hostname=r5n04
>ERROR: Failed while examining contents of the fasta file and run log
>ERROR: Chunk failed at level:0, tier_type:0
>FAILED CONTIG:MA_gen_v8.05_c31675
>
>There is enough space available on both the storage device and the tmp
>device that is being used. The datastore log files looks like this:
>
>MA_gen_v8.05_c1149              FAILED
>MA_gen_v8.05_c1153              FAILED
>MA_gen_v8.05_c1154              FAILED
>MA_gen_v8.05_c1155              FAILED
>MA_gen_v8.05_c1156              FAILED
>
>Since there is no datastore for this contigs, I can not provide any more
>informationen. Approx. 1/3 of the contigs were annotated, after that
>maker started to fail. It kept running for a while and finishing some of
>the contigs in the second or third try like this:
>
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	START
>ED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>FINISHED
>
>Any ideas what can cause this problems?
>
>Best regards
>Felix
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From felix.bemm at uni-wuerzburg.de  Sat Oct  5 09:09:15 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Sat, 05 Oct 2013 16:09:15 +0200
Subject: [maker-devel] Contigs failing - could not make datastore
	directory
In-Reply-To: <CE743B26.F369%carsonhh@gmail.com>
References: <CE743B26.F369%carsonhh@gmail.com>
Message-ID: <52501D8B.2060301@uni-wuerzburg.de>

Hi Carson,

there is definitely no quota neither a full local tmp device. I changed 
to another tmp device, which is unfortunately residing on nfs but now it 
seems to work. I am using the latest version of maker (2.28). The 
complete job is running on a single machine with 32 mpi threads.

Bests
Felix

Am 04.10.2013 20:21, schrieb Carson Holt:
> Hi Felix,
>
> There are other potential issues as well, for example a file quota limit
> set by your administrator or full local /tmp which will be unique to each
> node and cannot be queried directly from the root node on a cluster.  On a
> cluster one node may also not have the NFS location mounted.  Or it could
> be system related, for example on ibrix NFS mounted systems you can get a
> weird filesystem issue with ghost files and directories when using MAKER
> that can neither be created nor deleted.  Try running the failed contigs
> in a different directory (even if it's on the same disk).  Also what
> version of MAKER are you using?
>
> --Carson
>
>
>
> On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>> Hi,
>>
>> I have a problem with Contigs failing like this:
>>
>> examining contents of the fasta file and run log
>> ERROR: could not make datastore directory
>> --> rank=11, hostname=r5n04
>> ERROR: Failed while examining contents of the fasta file and run log
>> ERROR: Chunk failed at level:0, tier_type:0
>> FAILED CONTIG:MA_gen_v8.05_c31675
>>
>> There is enough space available on both the storage device and the tmp
>> device that is being used. The datastore log files looks like this:
>>
>> MA_gen_v8.05_c1149              FAILED
>> MA_gen_v8.05_c1153              FAILED
>> MA_gen_v8.05_c1154              FAILED
>> MA_gen_v8.05_c1155              FAILED
>> MA_gen_v8.05_c1156              FAILED
>>
>> Since there is no datastore for this contigs, I can not provide any more
>> informationen. Approx. 1/3 of the contigs were annotated, after that
>> maker started to fail. It kept running for a while and finishing some of
>> the contigs in the second or third try like this:
>>
>> MA_gen_v8.05_c4443		FAILED
>> MA_gen_v8.05_c4443		FAILED
>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	START
>> ED
>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>> FINISHED
>>
>> Any ideas what can cause this problems?
>>
>> Best regards
>> Felix
>>
>> --
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From jfierst at uoregon.edu  Fri Oct  4 12:06:36 2013
From: jfierst at uoregon.edu (Janna Fierst)
Date: Fri, 4 Oct 2013 10:06:36 -0700
Subject: [maker-devel] Fwd:  exon/intron boundaries
In-Reply-To: <CAGoyurYe_c3Cd6KK-z0t0WqYmGGh5VQsSZXo9_=Lt9MGMSz=kA@mail.gmail.com>
References: <CAGoyuraVoRp94vbk_mb1qLzELeXSbeybGwkvgFx-6smEVt_DcQ@mail.gmail.com>
	<CE411E31.998A%carsonhh@gmail.com>
	<CAGoyurYe_c3Cd6KK-z0t0WqYmGGh5VQsSZXo9_=Lt9MGMSz=kA@mail.gmail.com>
Message-ID: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>

Hi,

thanks for your reply- I have been going through our annotations in detail
and trying different parameter sets, and I think I have identified what is
going on but I'm not sure how to set the MAKER2 parameters for our
situation. We are working with a species of Caenorhabditid worm and there
are long gene-dense blocks that are being incorrectly annotated as large
single genes instead of several smaller closely spaced genes. The protein
alignments (tblastx and protein2genome) show very clearly where the
exon/intron boundaries are and in most cases agree with the augustus
predictions. The assembled cufflinks output (through blastn, est2genome and
est_gff:cufflinks) does not agree in some locations; I think this may be
because in some cases the UTR nearly overlaps adjacent genes.

I have included a screenshot of an annotated region viewed in apollo to try
to show this. The large gene in the middle is actually 7 different genes
that are extremely close together and MAKER2 is collapsing them into a
single gene. I tried running without any RNASeq/cufflinks data and MAKER2
annotates the region as two genes instead of one, but I can't get it to
recognize the 7 as different genes. I have retrained SNAP but we have not
been able to successfully train Augustus, we are currently using the
default caenhorhabditis species model. I also included a species specific
repeat library. I tried setting correct_est_fusion=1 and reducing
pred_flank but these changes appear to really alter the annotations and we
end up annotating almost nothing. I also tried setting est2genome=0 to
decrease the influence of the cufflinks assembly but it didn't appear to
help. There are some very large introns in these genes so I haven't tried
yet decreasing the maximum intron size because I'm concerned this may
generate too many split genes instead of our current merged gene problem.
Thanks for your help, any advice is greatly appreciated! -Janna Fierst


On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Are you getting gene fusions or just more exons?  Gene fusions can be
> reduced by setting correct_est_fusion=1, or reducing pred_flank, although
> reducing pred_flank can cause other issues (but those generally only appear
> if setting the value below below 150).  Also if you have the maximum intron
> size set to high (split_hit option), you may also be generating bridging
> alignments that make evidence align across distant paralogous genes as well
> (this can result in gene merging)
>
> You should also look at your results manually in a viewer like Apollo.
>  Then see if the extra exons are supported by something such as protein
> alignments from another species.  If this is the case, you may have a
> poorly annotated protein set that is being used as evidence that is
> carrying over it's erroneous exons into the species you are annotating.  If
> the extra  exons are supported by EST evidence, then perhaps you should try
> and rebuild the EST assembly (for example trinity has an option to use a
> Jarccardian similarity coefficient to avoid fusing transcripts).
>
> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
> produce any of the models itself (it is a pipeline not a predictor).  The
> models are all generated using these other algorithms, MAKER just feeds
> them hints based on protein and transcript alignments, so making sure
> training is sufficient is important for those programs to produce their
> best models.
>
> Finally make sure your repeat database is sufficient, you may need to
> generate a species specific repeat library using something like
> RepeatModeler.  Repeats can end up being included as extra exons in gene
> models because they may contain reading frames the do code for proteins
> (I.e. reverse transcriptases).
>
> If you have any questions on any of the above, just let us know.
>
> Thanks,
> Carson
>
>
> From: Janna Fierst <jfierst at uoregon.edu>
> Date: Monday, August 26, 2013 2:54 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] exon/intron boundaries
>
> Hi,
>
> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
> initial results appear fairly good but we seem to be be annotating too many
> exons for multiple genes. I was wondering which parameters should be tuned
> to change the threshold for exon/intron boundaries? Thanks for your help
> -Janna Fierst
>  _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From jfierst at uoregon.edu  Sat Oct  5 17:18:52 2013
From: jfierst at uoregon.edu (Janna Fierst)
Date: Sat, 5 Oct 2013 15:18:52 -0700
Subject: [maker-devel] Fwd:  exon/intron boundaries
In-Reply-To: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
References: <CAGoyuraVoRp94vbk_mb1qLzELeXSbeybGwkvgFx-6smEVt_DcQ@mail.gmail.com>
	<CE411E31.998A%carsonhh@gmail.com>
	<CAGoyurYe_c3Cd6KK-z0t0WqYmGGh5VQsSZXo9_=Lt9MGMSz=kA@mail.gmail.com>
	<CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
Message-ID: <CAGoyurYHu9ir90T2-xhBxDyv_xVY5=AGFHJJL3Fu0o2fxtvqOg@mail.gmail.com>

Hi,

thanks for your reply- I have been going through our annotations in detail
and trying different parameter sets, and I think I have identified what is
going on but I'm not sure how to set the MAKER2 parameters for our
situation. We are working with a species of Caenorhabditid worm and there
are long gene-dense blocks that are being incorrectly annotated as large
single genes instead of several smaller closely spaced genes. The protein
alignments (tblastx and protein2genome) show very clearly where the
exon/intron boundaries are and in most cases agree with the augustus
predictions. The assembled cufflinks output (through blastn, est2genome and
est_gff:cufflinks) does not agree in some locations; I think this may be
because in some cases the UTR nearly overlaps adjacent genes.

I have included a screenshot of an annotated region viewed in apollo to try
to show this. The large gene in the middle is actually 7 different genes
that are extremely close together and MAKER2 is collapsing them into a
single gene. I tried running without any RNASeq/cufflinks data and MAKER2
annotates the region as two genes instead of one, but I can't get it to
recognize the 7 as different genes. I have retrained SNAP but we have not
been able to successfully train Augustus, we are currently using the
default caenhorhabditis species model. I also included a species specific
repeat library. I tried setting correct_est_fusion=1 and reducing
pred_flank but these changes appear to really alter the annotations and we
end up annotating almost nothing. I also tried setting est2genome=0 to
decrease the influence of the cufflinks assembly but it didn't appear to
help. There are some very large introns in these genes so I haven't tried
yet decreasing the maximum intron size because I'm concerned this may
generate too many split genes instead of our current merged gene problem.
Thanks for your help, any advice is greatly appreciated! -Janna Fierst


On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Are you getting gene fusions or just more exons?  Gene fusions can be
> reduced by setting correct_est_fusion=1, or reducing pred_flank, although
> reducing pred_flank can cause other issues (but those generally only appear
> if setting the value below below 150).  Also if you have the maximum intron
> size set to high (split_hit option), you may also be generating bridging
> alignments that make evidence align across distant paralogous genes as well
> (this can result in gene merging)
>
> You should also look at your results manually in a viewer like Apollo.
>  Then see if the extra exons are supported by something such as protein
> alignments from another species.  If this is the case, you may have a
> poorly annotated protein set that is being used as evidence that is
> carrying over it's erroneous exons into the species you are annotating.  If
> the extra  exons are supported by EST evidence, then perhaps you should try
> and rebuild the EST assembly (for example trinity has an option to use a
> Jarccardian similarity coefficient to avoid fusing transcripts).
>
> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
> produce any of the models itself (it is a pipeline not a predictor).  The
> models are all generated using these other algorithms, MAKER just feeds
> them hints based on protein and transcript alignments, so making sure
> training is sufficient is important for those programs to produce their
> best models.
>
> Finally make sure your repeat database is sufficient, you may need to
> generate a species specific repeat library using something like
> RepeatModeler.  Repeats can end up being included as extra exons in gene
> models because they may contain reading frames the do code for proteins
> (I.e. reverse transcriptases).
>
> If you have any questions on any of the above, just let us know.
>
> Thanks,
> Carson
>
>
> From: Janna Fierst <jfierst at uoregon.edu>
> Date: Monday, August 26, 2013 2:54 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] exon/intron boundaries
>
> Hi,
>
> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
> initial results appear fairly good but we seem to be be annotating too many
> exons for multiple genes. I was wondering which parameters should be tuned
> to change the threshold for exon/intron boundaries? Thanks for your help
> -Janna Fierst
>  _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From myandell at genetics.utah.edu  Mon Oct  7 06:36:53 2013
From: myandell at genetics.utah.edu (Mark Yandell)
Date: Mon, 7 Oct 2013 11:36:53 +0000
Subject: [maker-devel] maker apollo error
In-Reply-To: <8687323557146056ef885dd8a1bf2ea4@buzonweb.us.es>
References: <8687323557146056ef885dd8a1bf2ea4@buzonweb.us.es>
Message-ID: <7A60AB257EFF2B48B1F4C814817EA05365E66B3C@mxb2.hg.genetics.utah.edu>


Hi Gabriel,

I've forwarded your request on to the MAKER email list...

cheers,

--mark

Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: ggpozo at us.es [ggpozo at us.es]
Sent: Monday, October 07, 2013 2:49 AM
To: Mark Yandell
Subject: maker apollo error

Dear Dr. Yandell,

First, thank you very much for provide us such a great tool as MAKER. I am traying to install it in my Linux system, everything is ok, however when I try to instal Apollo with ./Build apollo...

Downloading apollo...
--2013-10-07 10:45:37--  http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 302 Found
Localizaci?n: http://sourceforge.net/p/gmod/svn/ [siguiendo]
--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/
Resolviendo sourceforge.net... 216.34.181.60
Connecting to sourceforge.net|216.34.181.60|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 302 Found
Localizaci?n: http://sourceforge.net/p/gmod/svn/HEAD/tree/ [siguiendo]
--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/HEAD/tree/
Connecting to sourceforge.net|216.34.181.60|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 200 OK
Longitud: 37730 (37K) [text/html]
Saving to: `/home/maker/src/../exe/apollo.tar.gz'

100%[==================================================================================================================================>] 37.730      92,1K/s   in 0,4s

2013-10-07 10:45:40 (92,1 KB/s) - `/home/maker/src/../exe/apollo.tar.gz' saved [37730/37730]

Unpacking apollo tarball...

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now


ERROR: Failed installing apollo, now cleaning installation path...
You may need to install apollo manually.



It seems that the http direction  in locations file is wrong, Apollo has changed its version and now Apollo is integrated in Apolloweb, may be this the problem.



I would greatly appreciate any help you can give me.

Thank you very much.



Dr. Gabriel Gutierrez

Department of Genetcis

University of Seville

Spain




From carsonhh at gmail.com  Mon Oct  7 08:20:17 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 09:20:17 -0400
Subject: [maker-devel] Fwd:  exon/intron boundaries
In-Reply-To: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
Message-ID: <CE782A71.F621%carsonhh@gmail.com>

Hi Janna,

There are a couple of things to do.  Download the maker-2.29p-beta from the
lab website.  This includes some changes made to improve the performance of
correct_est_fusion.  Whenever using the correct_est_fusion option, this also
reduces the influence of ESTs on annotation.  So normally you would need to
increase your protein dataset, but given that you have supplied 3 nematode
species and all of UniProt already you should probably be fine. But there is
one last thing you can do.  Instead of using cufflinks, try using trinity to
assemble the ESTs.  There is a Jaccard clip option that reducing merging
caused by overlapping UTR.  Between the trinity and correct_est_fusion you
should be able to really reduce the effect of those ESTs.

If those changes don't work there is one last option.  If you take the MAKER
results and filter them for SNAP and Augustus ab initio results
(match/match_part in the GFF3), then you can pass those in to the pred_gff
options.  Then turn snaphmm and augustus_species off in the control files.
Basically what this will do is turn MAKER's hint based prediction off and
force it to filter the ab intio results and select directly models from
there.  Since the merging is being caused by bad hints (merged transcripts
from mRNAseq) this would reduce that effect.  You will still need
correct_est_fusion=1 though to trim UTR coming from the merged transcripts,
because even though MAEKR can't process hints to rerun SNAP and Augustus
this way, it will try and add UTR using the EST evidence.

--Carson


From:  Janna Fierst <jfierst at uoregon.edu>
Date:  Friday, October 4, 2013 1:06 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Fwd:  exon/intron boundaries

Hi,

thanks for your reply- I have been going through our annotations in detail
and trying different parameter sets, and I think I have identified what is
going on but I'm not sure how to set the MAKER2 parameters for our
situation. We are working with a species of Caenorhabditid worm and there
are long gene-dense blocks that are being incorrectly annotated as large
single genes instead of several smaller closely spaced genes. The protein
alignments (tblastx and protein2genome) show very clearly where the
exon/intron boundaries are and in most cases agree with the augustus
predictions. The assembled cufflinks output (through blastn, est2genome and
est_gff:cufflinks) does not agree in some locations; I think this may be
because in some cases the UTR nearly overlaps adjacent genes.

I have included a screenshot of an annotated region viewed in apollo to try
to show this. The large gene in the middle is actually 7 different genes
that are extremely close together and MAKER2 is collapsing them into a
single gene. I tried running without any RNASeq/cufflinks data and MAKER2
annotates the region as two genes instead of one, but I can't get it to
recognize the 7 as different genes. I have retrained SNAP but we have not
been able to successfully train Augustus, we are currently using the default
caenhorhabditis species model. I also included a species specific repeat
library. I tried setting correct_est_fusion=1 and reducing pred_flank but
these changes appear to really alter the annotations and we end up
annotating almost nothing. I also tried setting est2genome=0 to decrease the
influence of the cufflinks assembly but it didn't appear to help. There are
some very large introns in these genes so I haven't tried yet decreasing the
maximum intron size because I'm concerned this may generate too many split
genes instead of our current merged gene problem. Thanks for your help, any
advice is greatly appreciated! -Janna Fierst


On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:
> Are you getting gene fusions or just more exons?  Gene fusions can be reduced
> by setting correct_est_fusion=1, or reducing pred_flank, although reducing
> pred_flank can cause other issues (but those generally only appear if setting
> the value below below 150).  Also if you have the maximum intron size set to
> high (split_hit option), you may also be generating bridging alignments that
> make evidence align across distant paralogous genes as well (this can result
> in gene merging)
> 
> You should also look at your results manually in a viewer like Apollo.  Then
> see if the extra exons are supported by something such as protein alignments
> from another species.  If this is the case, you may have a poorly annotated
> protein set that is being used as evidence that is carrying over it's
> erroneous exons into the species you are annotating.  If the extra  exons are
> supported by EST evidence, then perhaps you should try and rebuild the EST
> assembly (for example trinity has an option to use a Jarccardian similarity
> coefficient to avoid fusing transcripts).
> 
> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
> produce any of the models itself (it is a pipeline not a predictor).  The
> models are all generated using these other algorithms, MAKER just feeds them
> hints based on protein and transcript alignments, so making sure training is
> sufficient is important for those programs to produce their best models.
> 
> Finally make sure your repeat database is sufficient, you may need to generate
> a species specific repeat library using something like RepeatModeler.  Repeats
> can end up being included as extra exons in gene models because they may
> contain reading frames the do code for proteins (I.e. reverse transcriptases).
> 
> If you have any questions on any of the above, just let us know.
> 
> Thanks,
> Carson
> 
> 
> From:  Janna Fierst <jfierst at uoregon.edu>
> Date:  Monday, August 26, 2013 2:54 PM
> To:  <maker-devel at yandell-lab.org>
> Subject:  [maker-devel] exon/intron boundaries
> 
> Hi,
> 
> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
> initial results appear fairly good but we seem to be be annotating too many
> exons for multiple genes. I was wondering which parameters should be tuned to
> change the threshold for exon/intron boundaries? Thanks for your help -Janna
> Fierst
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak
> er-devel_yandell-lab.org


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

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From carsonhh at gmail.com  Mon Oct  7 09:12:24 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 10:12:24 -0400
Subject: [maker-devel] maker apollo error
In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05365E66B3C@mxb2.hg.genetics.utah.edu>
Message-ID: <CE783792.F640%carsonhh@gmail.com>

This was a location from GMOD for the older Apollo.  It looks like they've
dropped it, so it now points to nothing. Perhaps there is another location
that still has the old code I can get from Ed.

--Carson



On 10/7/13 7:36 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:

>
>Hi Gabriel,
>
>I've forwarded your request on to the MAKER email list...
>
>cheers,
>
>--mark
>
>Mark Yandell
>Professor of Human Genetics
>H.A. & Edna Benning Presidential Endowed Chair
>Eccles Institute of Human Genetics
>University of Utah
>15 North 2030 East, Room 2100
>Salt Lake City, UT 84112-5330
>ph:801-587-7707
>
>________________________________________
>From: ggpozo at us.es [ggpozo at us.es]
>Sent: Monday, October 07, 2013 2:49 AM
>To: Mark Yandell
>Subject: maker apollo error
>
>Dear Dr. Yandell,
>
>First, thank you very much for provide us such a great tool as MAKER. I
>am traying to install it in my Linux system, everything is ok, however
>when I try to instal Apollo with ./Build apollo...
>
>Downloading apollo...
>--2013-10-07 10:45:37--
>http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
>Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
>Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
>Petici?n HTTP enviada, esperando respuesta... 302 Found
>Localizaci?n: http://sourceforge.net/p/gmod/svn/ [siguiendo]
>--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/
>Resolviendo sourceforge.net... 216.34.181.60
>Connecting to sourceforge.net|216.34.181.60|:80... conectado.
>Petici?n HTTP enviada, esperando respuesta... 302 Found
>Localizaci?n: http://sourceforge.net/p/gmod/svn/HEAD/tree/ [siguiendo]
>--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/HEAD/tree/
>Connecting to sourceforge.net|216.34.181.60|:80... conectado.
>Petici?n HTTP enviada, esperando respuesta... 200 OK
>Longitud: 37730 (37K) [text/html]
>Saving to: `/home/maker/src/../exe/apollo.tar.gz'
>
>100%[=====================================================================
>=============================================================>] 37.730
>  92,1K/s   in 0,4s
>
>2013-10-07 10:45:40 (92,1 KB/s) - `/home/maker/src/../exe/apollo.tar.gz'
>saved [37730/37730]
>
>Unpacking apollo tarball...
>
>gzip: stdin: not in gzip format
>tar: Child returned status 1
>tar: Error is not recoverable: exiting now
>
>
>ERROR: Failed installing apollo, now cleaning installation path...
>You may need to install apollo manually.
>
>
>
>It seems that the http direction  in locations file is wrong, Apollo has
>changed its version and now Apollo is integrated in Apolloweb, may be
>this the problem.
>
>
>
>I would greatly appreciate any help you can give me.
>
>Thank you very much.
>
>
>
>Dr. Gabriel Gutierrez
>
>Department of Genetcis
>
>University of Seville
>
>Spain
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Mon Oct  7 09:33:44 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 10:33:44 -0400
Subject: [maker-devel] Contigs failing - could not make datastore
 directory
In-Reply-To: <52501D8B.2060301@uni-wuerzburg.de>
Message-ID: <CE783CF2.F65A%carsonhh@gmail.com>

You can also try the 2.29 beta if you want (on the website).  Also when
MAKER exits, it tries to delete anything left behind in temporary folders,
so is it possible that it is creating space on exit after filling up /tmp?

Given that the issue seems to go away when you switch to another
directory, it suggests that this might be the kind of thing that is
specific to something about the current state of your your system.

Thanks,
Carson


On 10/5/13 10:09 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi Carson,
>
>there is definitely no quota neither a full local tmp device. I changed
>to another tmp device, which is unfortunately residing on nfs but now it
>seems to work. I am using the latest version of maker (2.28). The
>complete job is running on a single machine with 32 mpi threads.
>
>Bests
>Felix
>
>Am 04.10.2013 20:21, schrieb Carson Holt:
>> Hi Felix,
>>
>> There are other potential issues as well, for example a file quota limit
>> set by your administrator or full local /tmp which will be unique to
>>each
>> node and cannot be queried directly from the root node on a cluster.
>>On a
>> cluster one node may also not have the NFS location mounted.  Or it
>>could
>> be system related, for example on ibrix NFS mounted systems you can get
>>a
>> weird filesystem issue with ghost files and directories when using MAKER
>> that can neither be created nor deleted.  Try running the failed contigs
>> in a different directory (even if it's on the same disk).  Also what
>> version of MAKER are you using?
>>
>> --Carson
>>
>>
>>
>> On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Hi,
>>>
>>> I have a problem with Contigs failing like this:
>>>
>>> examining contents of the fasta file and run log
>>> ERROR: could not make datastore directory
>>> --> rank=11, hostname=r5n04
>>> ERROR: Failed while examining contents of the fasta file and run log
>>> ERROR: Chunk failed at level:0, tier_type:0
>>> FAILED CONTIG:MA_gen_v8.05_c31675
>>>
>>> There is enough space available on both the storage device and the tmp
>>> device that is being used. The datastore log files looks like this:
>>>
>>> MA_gen_v8.05_c1149              FAILED
>>> MA_gen_v8.05_c1153              FAILED
>>> MA_gen_v8.05_c1154              FAILED
>>> MA_gen_v8.05_c1155              FAILED
>>> MA_gen_v8.05_c1156              FAILED
>>>
>>> Since there is no datastore for this contigs, I can not provide any
>>>more
>>> informationen. Approx. 1/3 of the contigs were annotated, after that
>>> maker started to fail. It kept running for a while and finishing some
>>>of
>>> the contigs in the second or third try like this:
>>>
>>> MA_gen_v8.05_c4443		FAILED
>>> MA_gen_v8.05_c4443		FAILED
>>> 
>>>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	STA
>>>RT
>>> ED
>>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>>> FINISHED
>>>
>>> Any ideas what can cause this problems?
>>>
>>> Best regards
>>> Felix
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de





From felix.bemm at uni-wuerzburg.de  Mon Oct  7 11:40:12 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Mon, 07 Oct 2013 18:40:12 +0200
Subject: [maker-devel] Contigs failing - could not make datastore
	directory
In-Reply-To: <CE783CF2.F65A%carsonhh@gmail.com>
References: <CE783CF2.F65A%carsonhh@gmail.com>
Message-ID: <5252E3EC.6050908@uni-wuerzburg.de>

Do you have a changelog for 2.29b?

On 07.10.2013 16:33, Carson Holt wrote:
> You can also try the 2.29 beta if you want (on the website).  Also when
> MAKER exits, it tries to delete anything left behind in temporary folders,
> so is it possible that it is creating space on exit after filling up /tmp?

I will try to monitor that!

> Given that the issue seems to go away when you switch to another
> directory, it suggests that this might be the kind of thing that is
> specific to something about the current state of your your system.

I agree with that. Interestingly it happens with the only directory 
where I would not expect that.

> Thanks,
> Carson
>
>
> On 10/5/13 10:09 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>> Hi Carson,
>>
>> there is definitely no quota neither a full local tmp device. I changed
>> to another tmp device, which is unfortunately residing on nfs but now it
>> seems to work. I am using the latest version of maker (2.28). The
>> complete job is running on a single machine with 32 mpi threads.
>>
>> Bests
>> Felix
>>
>> Am 04.10.2013 20:21, schrieb Carson Holt:
>>> Hi Felix,
>>>
>>> There are other potential issues as well, for example a file quota limit
>>> set by your administrator or full local /tmp which will be unique to
>>> each
>>> node and cannot be queried directly from the root node on a cluster.
>>> On a
>>> cluster one node may also not have the NFS location mounted.  Or it
>>> could
>>> be system related, for example on ibrix NFS mounted systems you can get
>>> a
>>> weird filesystem issue with ghost files and directories when using MAKER
>>> that can neither be created nor deleted.  Try running the failed contigs
>>> in a different directory (even if it's on the same disk).  Also what
>>> version of MAKER are you using?
>>>
>>> --Carson
>>>
>>>
>>>
>>> On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a problem with Contigs failing like this:
>>>>
>>>> examining contents of the fasta file and run log
>>>> ERROR: could not make datastore directory
>>>> --> rank=11, hostname=r5n04
>>>> ERROR: Failed while examining contents of the fasta file and run log
>>>> ERROR: Chunk failed at level:0, tier_type:0
>>>> FAILED CONTIG:MA_gen_v8.05_c31675
>>>>
>>>> There is enough space available on both the storage device and the tmp
>>>> device that is being used. The datastore log files looks like this:
>>>>
>>>> MA_gen_v8.05_c1149              FAILED
>>>> MA_gen_v8.05_c1153              FAILED
>>>> MA_gen_v8.05_c1154              FAILED
>>>> MA_gen_v8.05_c1155              FAILED
>>>> MA_gen_v8.05_c1156              FAILED
>>>>
>>>> Since there is no datastore for this contigs, I can not provide any
>>>> more
>>>> informationen. Approx. 1/3 of the contigs were annotated, after that
>>>> maker started to fail. It kept running for a while and finishing some
>>>> of
>>>> the contigs in the second or third try like this:
>>>>
>>>> MA_gen_v8.05_c4443		FAILED
>>>> MA_gen_v8.05_c4443		FAILED
>>>>
>>>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	STA
>>>> RT
>>>> ED
>>>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>>>> FINISHED
>>>>
>>>> Any ideas what can cause this problems?
>>>>
>>>> Best regards
>>>> Felix
>>>>
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> --
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Mon Oct  7 12:25:34 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 13:25:34 -0400
Subject: [maker-devel] maker apollo error
In-Reply-To: <14a642f3dc9cb615f048b70228bad3be@buzonweb.us.es>
Message-ID: <CE78668C.F68A%carsonhh@gmail.com>

Here is a new location for the source -->
http://sourceforge.net/code-snapshots/svn/g/gm/gmod/svn/gmod-svn-25291-apoll
o-trunk.zip

--Carson


From:  <ggpozo at us.es>
Date:  Monday, October 7, 2013 12:47 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Mark Yandell <myandell at genetics.utah.edu>,
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] maker apollo error

Thanks, I have modified the locations file pointing to a personal server
where I downloaded an old version of Apollo but it did not work, but if you
can get a new one I would try it again.

Thanks

Gabriel

 
El 07/10/2013 16:12, Carson Holt escribi?:
> This was a location from GMOD for the older Apollo.  It looks like they've
> dropped it, so it now points to nothing. Perhaps there is another location
> that still has the old code I can get from Ed.
> 
> --Carson
> 
> 
> 
> On 10/7/13 7:36 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>> Hi Gabriel, I've forwarded your request on to the MAKER email list... cheers,
>> --mark Mark Yandell Professor of Human Genetics H.A. & Edna Benning
>> Presidential Endowed Chair Eccles Institute of Human Genetics University of
>> Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330
>> ph:801-587-7707 ________________________________________ From: ggpozo at us.es
>> [ggpozo at us.es] Sent: Monday, October 07, 2013 2:49 AM To: Mark Yandell
>> Subject: maker apollo error Dear Dr. Yandell, First, thank you very much for
>> provide us such a great tool as MAKER. I am traying to install it in my Linux
>> system, everything is ok, however when I try to instal Apollo with ./Build
>> apollo... Downloading apollo... --2013-10-07 10:45:37--
>> http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
>> Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
>> Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
>> Petici?n HTTP enviada, esperando respuesta... 302 Found Localizaci?n:
>> http://sourceforge.net/p/gmod/svn/ [siguiendo] --2013-10-07 10:45:38--
>> http://sourceforge.net/p/gmod/svn/ Resolviendo sourceforge.net...
>> 216.34.181.60 Connecting to sourceforge.net|216.34.181.60|:80... conectado.
>> Petici?n HTTP enviada, esperando respuesta... 302 Found Localizaci?n:
>> http://sourceforge.net/p/gmod/svn/HEAD/tree/ [siguiendo] --2013-10-07
>> 10:45:38-- http://sourceforge.net/p/gmod/svn/HEAD/tree/ Connecting to
>> sourceforge.net|216.34.181.60|:80... conectado. Petici?n HTTP enviada,
>> esperando respuesta... 200 OK Longitud: 37730 (37K) [text/html] Saving to:
>> `/home/maker/src/../exe/apollo.tar.gz'
>> 100%[=====================================================================
>> =============================================================>] 37.730
>> 92,1K/s in 0,4s 2013-10-07 10:45:40 (92,1 KB/s) -
>> `/home/maker/src/../exe/apollo.tar.gz' saved [37730/37730] Unpacking apollo
>> tarball... gzip: stdin: not in gzip format tar: Child returned status 1 tar:
>> Error is not recoverable: exiting now ERROR: Failed installing apollo, now
>> cleaning installation path... You may need to install apollo manually. It
>> seems that the http direction in locations file is wrong, Apollo has changed
>> its version and now Apollo is integrated in Apolloweb, may be this the
>> problem. I would greatly appreciate any help you can give me. Thank you very
>> much. Dr. Gabriel Gutierrez Department of Genetcis University of Seville
>> Spain _______________________________________________ maker-devel mailing
>> list maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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From ggpozo at us.es  Mon Oct  7 11:47:13 2013
From: ggpozo at us.es (ggpozo at us.es)
Date: Mon, 07 Oct 2013 18:47:13 +0200
Subject: [maker-devel] maker apollo error
In-Reply-To: <CE783792.F640%carsonhh@gmail.com>
References: <CE783792.F640%carsonhh@gmail.com>
Message-ID: <14a642f3dc9cb615f048b70228bad3be@buzonweb.us.es>

 

Thanks, I have modified the locations file pointing to a personal
server where I downloaded an old version of Apollo but it did not work,
but if you can get a new one I would try it again. 

Thanks 

Gabriel


El 07/10/2013 16:12, Carson Holt escribi?: 

> This was a location
from GMOD for the older Apollo. It looks like they've
> dropped it, so
it now points to nothing. Perhaps there is another location
> that still
has the old code I can get from Ed.
> 
> --Carson
> 
> On 10/7/13 7:36
AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
> 
>> Hi Gabriel,
I've forwarded your request on to the MAKER email list... cheers, --mark
Mark Yandell Professor of Human Genetics H.A. & Edna Benning
Presidential Endowed Chair Eccles Institute of Human Genetics University
of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330
ph:801-587-7707 ________________________________________ From:
ggpozo at us.es [1] [ggpozo at us.es [2]] Sent: Monday, October 07, 2013 2:49
AM To: Mark Yandell Subject: maker apollo error Dear Dr. Yandell, First,
thank you very much for provide us such a great tool as MAKER. I am
traying to install it in my Linux system, everything is ok, however when
I try to instal Apollo with ./Build apollo... Downloading apollo...
--2013-10-07 10:45:37--
http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar [3]
Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 302 Found Localizaci?n:
http://sourceforge.net/p/gmod/svn/ [4] [siguiendo] --2013-10-07
10:45:38-- http://sourceforge.net/p/gmod/svn/ [5] Resolviendo
sourceforge.net... 216.34.181.60 Connecting to
sourceforge.net|216.34.181.60|:80... conectado. Petici?n HTTP enviada,
esperando respuesta... 302 Found Localizaci?n:
http://sourceforge.net/p/gmod/svn/HEAD/tree/ [6] [siguiendo]
--2013-10-07 10:45:38-- http://sourceforge.net/p/gmod/svn/HEAD/tree/ [7]
Connecting to sourceforge.net|216.34.181.60|:80... conectado. Petici?n
HTTP enviada, esperando respuesta... 200 OK Longitud: 37730 (37K)
[text/html] Saving to: `/home/maker/src/../exe/apollo.tar.gz'
100%[=====================================================================
=============================================================>] 37.730
92,1K/s in 0,4s 2013-10-07 10:45:40 (92,1 KB/s) -
`/home/maker/src/../exe/apollo.tar.gz' saved [37730/37730] Unpacking
apollo tarball... gzip: stdin: not in gzip format tar: Child returned
status 1 tar: Error is not recoverable: exiting now ERROR: Failed
installing apollo, now cleaning installation path... You may need to
install apollo manually. It seems that the http direction in locations
file is wrong, Apollo has changed its version and now Apollo is
integrated in Apolloweb, may be this the problem. I would greatly
appreciate any help you can give me. Thank you very much. Dr. Gabriel
Gutierrez Department of Genetcis University of Seville Spain
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com [8]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
[9]
 

Links:
------
[1] mailto:ggpozo at us.es
[2] mailto:ggpozo at us.es
[3]
http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
[4]
http://sourceforge.net/p/gmod/svn/
[5]
http://sourceforge.net/p/gmod/svn/
[6]
http://sourceforge.net/p/gmod/svn/HEAD/tree/
[7]
http://sourceforge.net/p/gmod/svn/HEAD/tree/
[8]
mailto:maker-devel at box290.bluehost.com
[9]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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From felix.bemm at uni-wuerzburg.de  Sat Oct 12 10:06:52 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Sat, 12 Oct 2013 17:06:52 +0200
Subject: [maker-devel] Serious Start Codon Problem
Message-ID: <5259658C.4000102@uni-wuerzburg.de>

Hi,

I have a serious problems with maker annotations especially the start 
codon placement. It started happening with maker version 2.27! About 1/3 
of my genes are missing a proper start codon. When reviewing the GFF 
files gene predictors and est evidence standalone would predict the 
right gene structure including the start codon. I was thinking that this 
problem was somehow linked to my gene models but looking at their 
standalone prediction I discarded that theory. Just some stats about 
proteins with proper start codon (first column) and missing start codon 
(second column).

Maker		9268	4215
SNAP		16577	896
Genemark	18764	290

Numbers look the same when Augustus is used (currently retraining). 
Manually using EST's in Apollo often fixes the problems but I don't want 
to check > 4000 genes for this.

Do you have any idea what could cause such a problem? If you need some 
example gff files I can send you.

Best regards
Felix

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Sat Oct 12 10:48:29 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Sat, 12 Oct 2013 11:48:29 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <5259658C.4000102@uni-wuerzburg.de>
Message-ID: <CE7EE411.10C24%carsonhh@gmail.com>

This issue just came up this week on another e-mail as well.

One way to fix it, is to edit the Bio::Tools::CodonTable module from
BioPerl (use maker --debug to have maker print out the locations of all
modules it uses).  Such a hack should only be done as a temporary work
around.

You change line 256 from -->
---M---------------M---------------M----------------------------

To-->
-----------------------------------M----------------------------


Maker uses the BioPerl is_start_codon function to determine if the codon
used in a result it receives is acceptable or if it should look upstream
or downstream for a different one. Apparently there are actually 3
acceptable start codons in the standard codon table (2 rare ones and one
common), so making the edit removes the two rare ones from the list.

I'm also preparing a 2.30 release that exports a "strict" codon table to
the BioPerl module, that will be used by default and should fix the issue.

Thanks,
Carson



On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi,
>
>I have a serious problems with maker annotations especially the start
>codon placement. It started happening with maker version 2.27! About 1/3
>of my genes are missing a proper start codon. When reviewing the GFF
>files gene predictors and est evidence standalone would predict the
>right gene structure including the start codon. I was thinking that this
>problem was somehow linked to my gene models but looking at their
>standalone prediction I discarded that theory. Just some stats about
>proteins with proper start codon (first column) and missing start codon
>(second column).
>
>Maker		9268	4215
>SNAP		16577	896
>Genemark	18764	290
>
>Numbers look the same when Augustus is used (currently retraining).
>Manually using EST's in Apollo often fixes the problems but I don't want
>to check > 4000 genes for this.
>
>Do you have any idea what could cause such a problem? If you need some
>example gff files I can send you.
>
>Best regards
>Felix
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From felix.bemm at uni-wuerzburg.de  Sat Oct 12 11:16:06 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Sat, 12 Oct 2013 18:16:06 +0200
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE7EE411.10C24%carsonhh@gmail.com>
References: <CE7EE411.10C24%carsonhh@gmail.com>
Message-ID: <525975C6.4020403@uni-wuerzburg.de>

Thx Carson! Do you now when 2.30 will be available? Bests

On 12.10.2013 17:48, Carson Holt wrote:
> This issue just came up this week on another e-mail as well.
>
> One way to fix it, is to edit the Bio::Tools::CodonTable module from
> BioPerl (use maker --debug to have maker print out the locations of all
> modules it uses).  Such a hack should only be done as a temporary work
> around.
>
> You change line 256 from -->
> ---M---------------M---------------M----------------------------
>
> To-->
> -----------------------------------M----------------------------
>
>
> Maker uses the BioPerl is_start_codon function to determine if the codon
> used in a result it receives is acceptable or if it should look upstream
> or downstream for a different one. Apparently there are actually 3
> acceptable start codons in the standard codon table (2 rare ones and one
> common), so making the edit removes the two rare ones from the list.
>
> I'm also preparing a 2.30 release that exports a "strict" codon table to
> the BioPerl module, that will be used by default and should fix the issue.
>
> Thanks,
> Carson
>
>
>
> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>> Hi,
>>
>> I have a serious problems with maker annotations especially the start
>> codon placement. It started happening with maker version 2.27! About 1/3
>> of my genes are missing a proper start codon. When reviewing the GFF
>> files gene predictors and est evidence standalone would predict the
>> right gene structure including the start codon. I was thinking that this
>> problem was somehow linked to my gene models but looking at their
>> standalone prediction I discarded that theory. Just some stats about
>> proteins with proper start codon (first column) and missing start codon
>> (second column).
>>
>> Maker		9268	4215
>> SNAP		16577	896
>> Genemark	18764	290
>>
>> Numbers look the same when Augustus is used (currently retraining).
>> Manually using EST's in Apollo often fixes the problems but I don't want
>> to check > 4000 genes for this.
>>
>> Do you have any idea what could cause such a problem? If you need some
>> example gff files I can send you.
>>
>> Best regards
>> Felix
>>
>> --
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Sun Oct 13 00:26:17 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 13 Oct 2013 01:26:17 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <525975C6.4020403@uni-wuerzburg.de>
Message-ID: <CE7FA55D.10C4B%carsonhh@gmail.com>

Before Wednesday, because after that I'm on a 6 day road trip, so I have
to have it wrapped up before I leave.

--Carson




On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Thx Carson! Do you now when 2.30 will be available? Bests
>
>On 12.10.2013 17:48, Carson Holt wrote:
>> This issue just came up this week on another e-mail as well.
>>
>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>> BioPerl (use maker --debug to have maker print out the locations of all
>> modules it uses).  Such a hack should only be done as a temporary work
>> around.
>>
>> You change line 256 from -->
>> ---M---------------M---------------M----------------------------
>>
>> To-->
>> -----------------------------------M----------------------------
>>
>>
>> Maker uses the BioPerl is_start_codon function to determine if the codon
>> used in a result it receives is acceptable or if it should look upstream
>> or downstream for a different one. Apparently there are actually 3
>> acceptable start codons in the standard codon table (2 rare ones and one
>> common), so making the edit removes the two rare ones from the list.
>>
>> I'm also preparing a 2.30 release that exports a "strict" codon table to
>> the BioPerl module, that will be used by default and should fix the
>>issue.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Hi,
>>>
>>> I have a serious problems with maker annotations especially the start
>>> codon placement. It started happening with maker version 2.27! About
>>>1/3
>>> of my genes are missing a proper start codon. When reviewing the GFF
>>> files gene predictors and est evidence standalone would predict the
>>> right gene structure including the start codon. I was thinking that
>>>this
>>> problem was somehow linked to my gene models but looking at their
>>> standalone prediction I discarded that theory. Just some stats about
>>> proteins with proper start codon (first column) and missing start codon
>>> (second column).
>>>
>>> Maker		9268	4215
>>> SNAP		16577	896
>>> Genemark	18764	290
>>>
>>> Numbers look the same when Augustus is used (currently retraining).
>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>want
>>> to check > 4000 genes for this.
>>>
>>> Do you have any idea what could cause such a problem? If you need some
>>> example gff files I can send you.
>>>
>>> Best regards
>>> Felix
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de





From carsonhh at gmail.com  Mon Oct 14 09:45:25 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 14 Oct 2013 10:45:25 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <525975C6.4020403@uni-wuerzburg.de>
Message-ID: <CE817BB6.10C72%carsonhh@gmail.com>

Probably Tuesday or Wednesday.

--Carson


On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Thx Carson! Do you now when 2.30 will be available? Bests
>
>On 12.10.2013 17:48, Carson Holt wrote:
>> This issue just came up this week on another e-mail as well.
>>
>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>> BioPerl (use maker --debug to have maker print out the locations of all
>> modules it uses).  Such a hack should only be done as a temporary work
>> around.
>>
>> You change line 256 from -->
>> ---M---------------M---------------M----------------------------
>>
>> To-->
>> -----------------------------------M----------------------------
>>
>>
>> Maker uses the BioPerl is_start_codon function to determine if the codon
>> used in a result it receives is acceptable or if it should look upstream
>> or downstream for a different one. Apparently there are actually 3
>> acceptable start codons in the standard codon table (2 rare ones and one
>> common), so making the edit removes the two rare ones from the list.
>>
>> I'm also preparing a 2.30 release that exports a "strict" codon table to
>> the BioPerl module, that will be used by default and should fix the
>>issue.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Hi,
>>>
>>> I have a serious problems with maker annotations especially the start
>>> codon placement. It started happening with maker version 2.27! About
>>>1/3
>>> of my genes are missing a proper start codon. When reviewing the GFF
>>> files gene predictors and est evidence standalone would predict the
>>> right gene structure including the start codon. I was thinking that
>>>this
>>> problem was somehow linked to my gene models but looking at their
>>> standalone prediction I discarded that theory. Just some stats about
>>> proteins with proper start codon (first column) and missing start codon
>>> (second column).
>>>
>>> Maker		9268	4215
>>> SNAP		16577	896
>>> Genemark	18764	290
>>>
>>> Numbers look the same when Augustus is used (currently retraining).
>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>want
>>> to check > 4000 genes for this.
>>>
>>> Do you have any idea what could cause such a problem? If you need some
>>> example gff files I can send you.
>>>
>>> Best regards
>>> Felix
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de





From cjfields at illinois.edu  Mon Oct 14 10:07:43 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 14 Oct 2013 15:07:43 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE817BB6.10C72%carsonhh@gmail.com>
References: <CE817BB6.10C72%carsonhh@gmail.com>
Message-ID: <D51543B5-DCFB-4F2C-9BE5-3099B96E3317@illinois.edu>

Carson,

Regarding the CodonTable change below, should this be something that needs to be fixed, or made more flexible, in bioperl?  I could see this being a problem if using MAKER for bacterial annotation (where the alternative start codons are actually more common).

chris

On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Probably Tuesday or Wednesday.
> 
> --Carson
> 
> 
> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
> 
>> Thx Carson! Do you now when 2.30 will be available? Bests
>> 
>> On 12.10.2013 17:48, Carson Holt wrote:
>>> This issue just came up this week on another e-mail as well.
>>> 
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>> BioPerl (use maker --debug to have maker print out the locations of all
>>> modules it uses).  Such a hack should only be done as a temporary work
>>> around.
>>> 
>>> You change line 256 from -->
>>> ---M---------------M---------------M----------------------------
>>> 
>>> To-->
>>> -----------------------------------M----------------------------
>>> 
>>> 
>>> Maker uses the BioPerl is_start_codon function to determine if the codon
>>> used in a result it receives is acceptable or if it should look upstream
>>> or downstream for a different one. Apparently there are actually 3
>>> acceptable start codons in the standard codon table (2 rare ones and one
>>> common), so making the edit removes the two rare ones from the list.
>>> 
>>> I'm also preparing a 2.30 release that exports a "strict" codon table to
>>> the BioPerl module, that will be used by default and should fix the
>>> issue.
>>> 
>>> Thanks,
>>> Carson
>>> 
>>> 
>>> 
>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I have a serious problems with maker annotations especially the start
>>>> codon placement. It started happening with maker version 2.27! About
>>>> 1/3
>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>> files gene predictors and est evidence standalone would predict the
>>>> right gene structure including the start codon. I was thinking that
>>>> this
>>>> problem was somehow linked to my gene models but looking at their
>>>> standalone prediction I discarded that theory. Just some stats about
>>>> proteins with proper start codon (first column) and missing start codon
>>>> (second column).
>>>> 
>>>> Maker		9268	4215
>>>> SNAP		16577	896
>>>> Genemark	18764	290
>>>> 
>>>> Numbers look the same when Augustus is used (currently retraining).
>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>> want
>>>> to check > 4000 genes for this.
>>>> 
>>>> Do you have any idea what could cause such a problem? If you need some
>>>> example gff files I can send you.
>>>> 
>>>> Best regards
>>>> Felix
>>>> 
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> -- 
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Mon Oct 14 12:58:24 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 14 Oct 2013 13:58:24 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <D51543B5-DCFB-4F2C-9BE5-3099B96E3317@illinois.edu>
Message-ID: <CE81A824.10C7B%carsonhh@gmail.com>

I think adding one more codon table to the set of available tables would
be sufficient.  Call it the 'Strict' table or 'Canonical' table.  It
doesn't need to be the default, but should be a selectable option just as
the other codon tables are.  There is a way to export codon tables to the
module, which is what I've now added to MAKER, but I'm sure other BoiPerl
users would find a strictly canonical codon table useful as well.

Thanks,
Carson


On 10/14/13 11:07 AM, "Fields, Christopher J" <cjfields at illinois.edu>
wrote:

>Carson,
>
>Regarding the CodonTable change below, should this be something that
>needs to be fixed, or made more flexible, in bioperl?  I could see this
>being a problem if using MAKER for bacterial annotation (where the
>alternative start codons are actually more common).
>
>chris
>
>On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Probably Tuesday or Wednesday.
>> 
>> --Carson
>> 
>> 
>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>> 
>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>> 
>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>> This issue just came up this week on another e-mail as well.
>>>> 
>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>> BioPerl (use maker --debug to have maker print out the locations of
>>>>all
>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>> around.
>>>> 
>>>> You change line 256 from -->
>>>> ---M---------------M---------------M----------------------------
>>>> 
>>>> To-->
>>>> -----------------------------------M----------------------------
>>>> 
>>>> 
>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>codon
>>>> used in a result it receives is acceptable or if it should look
>>>>upstream
>>>> or downstream for a different one. Apparently there are actually 3
>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>one
>>>> common), so making the edit removes the two rare ones from the list.
>>>> 
>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>to
>>>> the BioPerl module, that will be used by default and should fix the
>>>> issue.
>>>> 
>>>> Thanks,
>>>> Carson
>>>> 
>>>> 
>>>> 
>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> I have a serious problems with maker annotations especially the start
>>>>> codon placement. It started happening with maker version 2.27! About
>>>>> 1/3
>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>> files gene predictors and est evidence standalone would predict the
>>>>> right gene structure including the start codon. I was thinking that
>>>>> this
>>>>> problem was somehow linked to my gene models but looking at their
>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>> proteins with proper start codon (first column) and missing start
>>>>>codon
>>>>> (second column).
>>>>> 
>>>>> Maker		9268	4215
>>>>> SNAP		16577	896
>>>>> Genemark	18764	290
>>>>> 
>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>> want
>>>>> to check > 4000 genes for this.
>>>>> 
>>>>> Do you have any idea what could cause such a problem? If you need
>>>>>some
>>>>> example gff files I can send you.
>>>>> 
>>>>> Best regards
>>>>> Felix
>>>>> 
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>> 
>>> -- 
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>> 
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>





From cjfields at illinois.edu  Mon Oct 14 13:51:28 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 14 Oct 2013 18:51:28 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE81A824.10C7B%carsonhh@gmail.com>
References: <CE81A824.10C7B%carsonhh@gmail.com>
Message-ID: <160BC401-0471-4285-8712-21440628A5DA@illinois.edu>

Done, with some added tests.  I labeled it 'Strict' ('Canonical' can be a bit of a loaded term).  It's currently set as ID 24.

I will likely push out a new 1.6 point release this week or next, I'll merge these in for that release.

chris

On Oct 14, 2013, at 12:58 PM, Carson Holt <carsonhh at gmail.com> wrote:

> I think adding one more codon table to the set of available tables would
> be sufficient.  Call it the 'Strict' table or 'Canonical' table.  It
> doesn't need to be the default, but should be a selectable option just as
> the other codon tables are.  There is a way to export codon tables to the
> module, which is what I've now added to MAKER, but I'm sure other BoiPerl
> users would find a strictly canonical codon table useful as well.
> 
> Thanks,
> Carson
> 
> 
> On 10/14/13 11:07 AM, "Fields, Christopher J" <cjfields at illinois.edu>
> wrote:
> 
>> Carson,
>> 
>> Regarding the CodonTable change below, should this be something that
>> needs to be fixed, or made more flexible, in bioperl?  I could see this
>> being a problem if using MAKER for bacterial annotation (where the
>> alternative start codons are actually more common).
>> 
>> chris
>> 
>> On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>>> Probably Tuesday or Wednesday.
>>> 
>>> --Carson
>>> 
>>> 
>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>> 
>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>> 
>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>> This issue just came up this week on another e-mail as well.
>>>>> 
>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>> BioPerl (use maker --debug to have maker print out the locations of
>>>>> all
>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>> around.
>>>>> 
>>>>> You change line 256 from -->
>>>>> ---M---------------M---------------M----------------------------
>>>>> 
>>>>> To-->
>>>>> -----------------------------------M----------------------------
>>>>> 
>>>>> 
>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>> codon
>>>>> used in a result it receives is acceptable or if it should look
>>>>> upstream
>>>>> or downstream for a different one. Apparently there are actually 3
>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>> one
>>>>> common), so making the edit removes the two rare ones from the list.
>>>>> 
>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>> to
>>>>> the BioPerl module, that will be used by default and should fix the
>>>>> issue.
>>>>> 
>>>>> Thanks,
>>>>> Carson
>>>>> 
>>>>> 
>>>>> 
>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>> wrote:
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I have a serious problems with maker annotations especially the start
>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>> 1/3
>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>> right gene structure including the start codon. I was thinking that
>>>>>> this
>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>> proteins with proper start codon (first column) and missing start
>>>>>> codon
>>>>>> (second column).
>>>>>> 
>>>>>> Maker		9268	4215
>>>>>> SNAP		16577	896
>>>>>> Genemark	18764	290
>>>>>> 
>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>> want
>>>>>> to check > 4000 genes for this.
>>>>>> 
>>>>>> Do you have any idea what could cause such a problem? If you need
>>>>>> some
>>>>>> example gff files I can send you.
>>>>>> 
>>>>>> Best regards
>>>>>> Felix
>>>>>> 
>>>>>> --
>>>>>> Felix Bemm
>>>>>> Department of Bioinformatics
>>>>>> University of W?rzburg, Germany
>>>>>> Tel: +49 931 - 31 83696
>>>>>> Fax: +49 931 - 31 84552
>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>> 
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> 
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>> 
>>>> -- 
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
> 
> 




From carsonhh at gmail.com  Mon Oct 14 19:59:45 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 14 Oct 2013 20:59:45 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <160BC401-0471-4285-8712-21440628A5DA@illinois.edu>
Message-ID: <CE820BA4.10C8F%carsonhh@gmail.com>

Thanks!!

--Carson


On 10/14/13 2:51 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

>Done, with some added tests.  I labeled it 'Strict' ('Canonical' can be a
>bit of a loaded term).  It's currently set as ID 24.
>
>I will likely push out a new 1.6 point release this week or next, I'll
>merge these in for that release.
>
>chris
>
>On Oct 14, 2013, at 12:58 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> I think adding one more codon table to the set of available tables would
>> be sufficient.  Call it the 'Strict' table or 'Canonical' table.  It
>> doesn't need to be the default, but should be a selectable option just
>>as
>> the other codon tables are.  There is a way to export codon tables to
>>the
>> module, which is what I've now added to MAKER, but I'm sure other
>>BoiPerl
>> users would find a strictly canonical codon table useful as well.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> On 10/14/13 11:07 AM, "Fields, Christopher J" <cjfields at illinois.edu>
>> wrote:
>> 
>>> Carson,
>>> 
>>> Regarding the CodonTable change below, should this be something that
>>> needs to be fixed, or made more flexible, in bioperl?  I could see this
>>> being a problem if using MAKER for bacterial annotation (where the
>>> alternative start codons are actually more common).
>>> 
>>> chris
>>> 
>>> On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> 
>>>> Probably Tuesday or Wednesday.
>>>> 
>>>> --Carson
>>>> 
>>>> 
>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>wrote:
>>>> 
>>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>>> 
>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>>> This issue just came up this week on another e-mail as well.
>>>>>> 
>>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>>> BioPerl (use maker --debug to have maker print out the locations of
>>>>>> all
>>>>>> modules it uses).  Such a hack should only be done as a temporary
>>>>>>work
>>>>>> around.
>>>>>> 
>>>>>> You change line 256 from -->
>>>>>> ---M---------------M---------------M----------------------------
>>>>>> 
>>>>>> To-->
>>>>>> -----------------------------------M----------------------------
>>>>>> 
>>>>>> 
>>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>>> codon
>>>>>> used in a result it receives is acceptable or if it should look
>>>>>> upstream
>>>>>> or downstream for a different one. Apparently there are actually 3
>>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>>> one
>>>>>> common), so making the edit removes the two rare ones from the list.
>>>>>> 
>>>>>> I'm also preparing a 2.30 release that exports a "strict" codon
>>>>>>table
>>>>>> to
>>>>>> the BioPerl module, that will be used by default and should fix the
>>>>>> issue.
>>>>>> 
>>>>>> Thanks,
>>>>>> Carson
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>>> wrote:
>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I have a serious problems with maker annotations especially the
>>>>>>>start
>>>>>>> codon placement. It started happening with maker version 2.27!
>>>>>>>About
>>>>>>> 1/3
>>>>>>> of my genes are missing a proper start codon. When reviewing the
>>>>>>>GFF
>>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>>> right gene structure including the start codon. I was thinking that
>>>>>>> this
>>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>>> standalone prediction I discarded that theory. Just some stats
>>>>>>>about
>>>>>>> proteins with proper start codon (first column) and missing start
>>>>>>> codon
>>>>>>> (second column).
>>>>>>> 
>>>>>>> Maker		9268	4215
>>>>>>> SNAP		16577	896
>>>>>>> Genemark	18764	290
>>>>>>> 
>>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>>> want
>>>>>>> to check > 4000 genes for this.
>>>>>>> 
>>>>>>> Do you have any idea what could cause such a problem? If you need
>>>>>>> some
>>>>>>> example gff files I can send you.
>>>>>>> 
>>>>>>> Best regards
>>>>>>> Felix
>>>>>>> 
>>>>>>> --
>>>>>>> Felix Bemm
>>>>>>> Department of Bioinformatics
>>>>>>> University of W?rzburg, Germany
>>>>>>> Tel: +49 931 - 31 83696
>>>>>>> Fax: +49 931 - 31 84552
>>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> 
>>>>>>> 
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>or
>>>>>>> g
>>>>> 
>>>>> -- 
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>> 
>> 
>





From jfierst at uoregon.edu  Mon Oct 21 12:40:06 2013
From: jfierst at uoregon.edu (Janna Fierst)
Date: Mon, 21 Oct 2013 10:40:06 -0700
Subject: [maker-devel] Fwd: exon/intron boundaries
In-Reply-To: <CE782A71.F621%carsonhh@gmail.com>
References: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
	<CE782A71.F621%carsonhh@gmail.com>
Message-ID: <CAGoyurZfiqRpEKg0C=__ou6muWD2PqCQh9b+S9y_+95-xsCfOQ@mail.gmail.com>

Hi,

thanks for your help- I have used Trinity to assemble the EST's but am
having a problem with the 2.29-beta release. Instead of starting and
finishing a set of scaffolds, it appears to re-start over and over again. I
am running it in parallel across 32 cores and I'm wondering if this is a
problem with the parallel implementation. I've gone through it several
times and not been able to find any errors or output that would suggest
what the problem is. Thanks -Janna


On Mon, Oct 7, 2013 at 6:20 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Hi Janna,
>
> There are a couple of things to do.  Download the maker-2.29p-beta from
> the lab website.  This includes some changes made to improve the
> performance of correct_est_fusion.  Whenever using the correct_est_fusion
> option, this also reduces the influence of ESTs on annotation.  So normally
> you would need to increase your protein dataset, but given that you have
> supplied 3 nematode species and all of UniProt already you should probably
> be fine. But there is one last thing you can do.  Instead of using
> cufflinks, try using trinity to assemble the ESTs.  There is a Jaccard clip
> option that reducing merging caused by overlapping UTR.  Between the
> trinity and correct_est_fusion you should be able to really reduce the
> effect of those ESTs.
>
> If those changes don't work there is one last option.  If you take the
> MAKER results and filter them for SNAP and Augustus ab initio results
> (match/match_part in the GFF3), then you can pass those in to the pred_gff
> options.  Then turn snaphmm and augustus_species off in the control files.
>  Basically what this will do is turn MAKER's hint based prediction off and
> force it to filter the ab intio results and select directly models from
> there.  Since the merging is being caused by bad hints (merged transcripts
> from mRNAseq) this would reduce that effect.  You will still need
> correct_est_fusion=1 though to trim UTR coming from the merged transcripts,
> because even though MAEKR can't process hints to rerun SNAP and Augustus
> this way, it will try and add UTR using the EST evidence.
>
> --Carson
>
>
> From: Janna Fierst <jfierst at uoregon.edu>
> Date: Friday, October 4, 2013 1:06 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Fwd: exon/intron boundaries
>
> Hi,
>
> thanks for your reply- I have been going through our annotations in detail
> and trying different parameter sets, and I think I have identified what is
> going on but I'm not sure how to set the MAKER2 parameters for our
> situation. We are working with a species of Caenorhabditid worm and there
> are long gene-dense blocks that are being incorrectly annotated as large
> single genes instead of several smaller closely spaced genes. The protein
> alignments (tblastx and protein2genome) show very clearly where the
> exon/intron boundaries are and in most cases agree with the augustus
> predictions. The assembled cufflinks output (through blastn, est2genome and
> est_gff:cufflinks) does not agree in some locations; I think this may be
> because in some cases the UTR nearly overlaps adjacent genes.
>
> I have included a screenshot of an annotated region viewed in apollo to
> try to show this. The large gene in the middle is actually 7 different
> genes that are extremely close together and MAKER2 is collapsing them into
> a single gene. I tried running without any RNASeq/cufflinks data and MAKER2
> annotates the region as two genes instead of one, but I can't get it to
> recognize the 7 as different genes. I have retrained SNAP but we have not
> been able to successfully train Augustus, we are currently using the
> default caenhorhabditis species model. I also included a species specific
> repeat library. I tried setting correct_est_fusion=1 and reducing
> pred_flank but these changes appear to really alter the annotations and we
> end up annotating almost nothing. I also tried setting est2genome=0 to
> decrease the influence of the cufflinks assembly but it didn't appear to
> help. There are some very large introns in these genes so I haven't tried
> yet decreasing the maximum intron size because I'm concerned this may
> generate too many split genes instead of our current merged gene problem.
> Thanks for your help, any advice is greatly appreciated! -Janna Fierst
>
>
> On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Are you getting gene fusions or just more exons?  Gene fusions can be
>> reduced by setting correct_est_fusion=1, or reducing pred_flank, although
>> reducing pred_flank can cause other issues (but those generally only appear
>> if setting the value below below 150).  Also if you have the maximum intron
>> size set to high (split_hit option), you may also be generating bridging
>> alignments that make evidence align across distant paralogous genes as well
>> (this can result in gene merging)
>>
>> You should also look at your results manually in a viewer like Apollo.
>>  Then see if the extra exons are supported by something such as protein
>> alignments from another species.  If this is the case, you may have a
>> poorly annotated protein set that is being used as evidence that is
>> carrying over it's erroneous exons into the species you are annotating.  If
>> the extra  exons are supported by EST evidence, then perhaps you should try
>> and rebuild the EST assembly (for example trinity has an option to use a
>> Jarccardian similarity coefficient to avoid fusing transcripts).
>>
>> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
>> produce any of the models itself (it is a pipeline not a predictor).  The
>> models are all generated using these other algorithms, MAKER just feeds
>> them hints based on protein and transcript alignments, so making sure
>> training is sufficient is important for those programs to produce their
>> best models.
>>
>> Finally make sure your repeat database is sufficient, you may need to
>> generate a species specific repeat library using something like
>> RepeatModeler.  Repeats can end up being included as extra exons in gene
>> models because they may contain reading frames the do code for proteins
>> (I.e. reverse transcriptases).
>>
>> If you have any questions on any of the above, just let us know.
>>
>> Thanks,
>> Carson
>>
>>
>> From: Janna Fierst <jfierst at uoregon.edu>
>> Date: Monday, August 26, 2013 2:54 PM
>> To: <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] exon/intron boundaries
>>
>> Hi,
>>
>> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
>> initial results appear fairly good but we seem to be be annotating too many
>> exons for multiple genes. I was wondering which parameters should be tuned
>> to change the threshold for exon/intron boundaries? Thanks for your help
>> -Janna Fierst
>> _______________________________________________ maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From graham.etherington at sainsbury-laboratory.ac.uk  Thu Oct 24 08:42:51 2013
From: graham.etherington at sainsbury-laboratory.ac.uk (graham etherington (TSL))
Date: Thu, 24 Oct 2013 13:42:51 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE7FA55D.10C4B%carsonhh@gmail.com>
Message-ID: <CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>

Hi,
I notice that the latest version of Maker available from
http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
2013). As we're also having the start codon problem we'd like to get hold
of v2.30. Do you know when this will be released?
Many thanks,
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:

>Before Wednesday, because after that I'm on a 6 day road trip, so I have
>to have it wrapped up before I leave.
>
>--Carson
>
>
>
>
>On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>>Thx Carson! Do you now when 2.30 will be available? Bests
>>
>>On 12.10.2013 17:48, Carson Holt wrote:
>>> This issue just came up this week on another e-mail as well.
>>>
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>> BioPerl (use maker --debug to have maker print out the locations of all
>>> modules it uses).  Such a hack should only be done as a temporary work
>>> around.
>>>
>>> You change line 256 from -->
>>> ---M---------------M---------------M----------------------------
>>>
>>> To-->
>>> -----------------------------------M----------------------------
>>>
>>>
>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>codon
>>> used in a result it receives is acceptable or if it should look
>>>upstream
>>> or downstream for a different one. Apparently there are actually 3
>>> acceptable start codons in the standard codon table (2 rare ones and
>>>one
>>> common), so making the edit removes the two rare ones from the list.
>>>
>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>to
>>> the BioPerl module, that will be used by default and should fix the
>>>issue.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a serious problems with maker annotations especially the start
>>>> codon placement. It started happening with maker version 2.27! About
>>>>1/3
>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>> files gene predictors and est evidence standalone would predict the
>>>> right gene structure including the start codon. I was thinking that
>>>>this
>>>> problem was somehow linked to my gene models but looking at their
>>>> standalone prediction I discarded that theory. Just some stats about
>>>> proteins with proper start codon (first column) and missing start
>>>>codon
>>>> (second column).
>>>>
>>>> Maker		9268	4215
>>>> SNAP		16577	896
>>>> Genemark	18764	290
>>>>
>>>> Numbers look the same when Augustus is used (currently retraining).
>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>want
>>>> to check > 4000 genes for this.
>>>>
>>>> Do you have any idea what could cause such a problem? If you need some
>>>> example gff files I can send you.
>>>>
>>>> Best regards
>>>> Felix
>>>>
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>-- 
>>Felix Bemm
>>Department of Bioinformatics
>>University of W?rzburg, Germany
>>Tel: +49 931 - 31 83696
>>Fax: +49 931 - 31 84552
>>felix.bemm at uni-wuerzburg.de
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From myandell at genetics.utah.edu  Thu Oct 24 08:55:05 2013
From: myandell at genetics.utah.edu (Mark Yandell)
Date: Thu, 24 Oct 2013 13:55:05 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>,
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
Message-ID: <7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>

Hi Graham,

 Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.


--mark


Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
Sent: Thursday, October 24, 2013 7:42 AM
To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
Cc: Kate Bailey (TSL)
Subject: Re: [maker-devel] Serious Start Codon Problem

Hi,
I notice that the latest version of Maker available from
http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
2013). As we're also having the start codon problem we'd like to get hold
of v2.30. Do you know when this will be released?
Many thanks,
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:

>Before Wednesday, because after that I'm on a 6 day road trip, so I have
>to have it wrapped up before I leave.
>
>--Carson
>
>
>
>
>On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>>Thx Carson! Do you now when 2.30 will be available? Bests
>>
>>On 12.10.2013 17:48, Carson Holt wrote:
>>> This issue just came up this week on another e-mail as well.
>>>
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>> BioPerl (use maker --debug to have maker print out the locations of all
>>> modules it uses).  Such a hack should only be done as a temporary work
>>> around.
>>>
>>> You change line 256 from -->
>>> ---M---------------M---------------M----------------------------
>>>
>>> To-->
>>> -----------------------------------M----------------------------
>>>
>>>
>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>codon
>>> used in a result it receives is acceptable or if it should look
>>>upstream
>>> or downstream for a different one. Apparently there are actually 3
>>> acceptable start codons in the standard codon table (2 rare ones and
>>>one
>>> common), so making the edit removes the two rare ones from the list.
>>>
>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>to
>>> the BioPerl module, that will be used by default and should fix the
>>>issue.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a serious problems with maker annotations especially the start
>>>> codon placement. It started happening with maker version 2.27! About
>>>>1/3
>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>> files gene predictors and est evidence standalone would predict the
>>>> right gene structure including the start codon. I was thinking that
>>>>this
>>>> problem was somehow linked to my gene models but looking at their
>>>> standalone prediction I discarded that theory. Just some stats about
>>>> proteins with proper start codon (first column) and missing start
>>>>codon
>>>> (second column).
>>>>
>>>> Maker              9268    4215
>>>> SNAP               16577   896
>>>> Genemark   18764   290
>>>>
>>>> Numbers look the same when Augustus is used (currently retraining).
>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>want
>>>> to check > 4000 genes for this.
>>>>
>>>> Do you have any idea what could cause such a problem? If you need some
>>>> example gff files I can send you.
>>>>
>>>> Best regards
>>>> Felix
>>>>
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>>
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>--
>>Felix Bemm
>>Department of Bioinformatics
>>University of W?rzburg, Germany
>>Tel: +49 931 - 31 83696
>>Fax: +49 931 - 31 84552
>>felix.bemm at uni-wuerzburg.de
>
>
>
>_______________________________________________
>maker-devel mailing list
>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
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


From felix.bemm at uni-wuerzburg.de  Thu Oct 24 09:03:27 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Thu, 24 Oct 2013 16:03:27 +0200
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>,
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
Message-ID: <526928AF.90108@uni-wuerzburg.de>

Hi,

I used the temporary fix of the Bio::Tools::CodonTable. It's working 
pretty nice. Almost every predicted proteins now start with a M ;)

Bests
Felix

On 24.10.2013 15:55, Mark Yandell wrote:
> Hi Graham,
>
>   Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>
>
> --mark
>
>
> Mark Yandell
> Professor of Human Genetics
> H.A. & Edna Benning Presidential Endowed Chair
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ph:801-587-7707
>
> ________________________________________
> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
> Sent: Thursday, October 24, 2013 7:42 AM
> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
> Cc: Kate Bailey (TSL)
> Subject: Re: [maker-devel] Serious Start Codon Problem
>
> Hi,
> I notice that the latest version of Maker available from
> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
> 2013). As we're also having the start codon problem we'd like to get hold
> of v2.30. Do you know when this will be released?
> Many thanks,
> Graham
>
>
> Dr. Graham Etherington
> Bioinformatics Support Officer,
> The Sainsbury Laboratory,
> Norwich Research Park,
> Norwich NR4 7UH.
> UK
> Tel: +44 (0)1603 450601
>
>
>
>
>
> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>
>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>> to have it wrapped up before I leave.
>>
>> --Carson
>>
>>
>>
>>
>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>
>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>> This issue just came up this week on another e-mail as well.
>>>>
>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>> around.
>>>>
>>>> You change line 256 from -->
>>>> ---M---------------M---------------M----------------------------
>>>>
>>>> To-->
>>>> -----------------------------------M----------------------------
>>>>
>>>>
>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>> codon
>>>> used in a result it receives is acceptable or if it should look
>>>> upstream
>>>> or downstream for a different one. Apparently there are actually 3
>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>> one
>>>> common), so making the edit removes the two rare ones from the list.
>>>>
>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>> to
>>>> the BioPerl module, that will be used by default and should fix the
>>>> issue.
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>>
>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I have a serious problems with maker annotations especially the start
>>>>> codon placement. It started happening with maker version 2.27! About
>>>>> 1/3
>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>> files gene predictors and est evidence standalone would predict the
>>>>> right gene structure including the start codon. I was thinking that
>>>>> this
>>>>> problem was somehow linked to my gene models but looking at their
>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>> proteins with proper start codon (first column) and missing start
>>>>> codon
>>>>> (second column).
>>>>>
>>>>> Maker              9268    4215
>>>>> SNAP               16577   896
>>>>> Genemark   18764   290
>>>>>
>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>> want
>>>>> to check > 4000 genes for this.
>>>>>
>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>> example gff files I can send you.
>>>>>
>>>>> Best regards
>>>>> Felix
>>>>>
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>>
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From jim.hu.biobio at gmail.com  Thu Oct 24 09:32:01 2013
From: jim.hu.biobio at gmail.com (JH Gmail)
Date: Thu, 24 Oct 2013 09:32:01 -0500
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
Message-ID: <69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>

Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 

Does maker handle ribosome profiling yet?

jim

Sent from my iPad

> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
> 
> Hi Graham,
> 
> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
> 
> 
> --mark
> 
> 
> Mark Yandell
> Professor of Human Genetics
> H.A. & Edna Benning Presidential Endowed Chair
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ph:801-587-7707
> 
> ________________________________________
> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
> Sent: Thursday, October 24, 2013 7:42 AM
> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
> Cc: Kate Bailey (TSL)
> Subject: Re: [maker-devel] Serious Start Codon Problem
> 
> Hi,
> I notice that the latest version of Maker available from
> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
> 2013). As we're also having the start codon problem we'd like to get hold
> of v2.30. Do you know when this will be released?
> Many thanks,
> Graham
> 
> 
> Dr. Graham Etherington
> Bioinformatics Support Officer,
> The Sainsbury Laboratory,
> Norwich Research Park,
> Norwich NR4 7UH.
> UK
> Tel: +44 (0)1603 450601
> 
> 
> 
> 
> 
>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>> 
>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>> to have it wrapped up before I leave.
>> 
>> --Carson
>> 
>> 
>> 
>> 
>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>> 
>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>> 
>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>> This issue just came up this week on another e-mail as well.
>>>> 
>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>> around.
>>>> 
>>>> You change line 256 from -->
>>>> ---M---------------M---------------M----------------------------
>>>> 
>>>> To-->
>>>> -----------------------------------M----------------------------
>>>> 
>>>> 
>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>> codon
>>>> used in a result it receives is acceptable or if it should look
>>>> upstream
>>>> or downstream for a different one. Apparently there are actually 3
>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>> one
>>>> common), so making the edit removes the two rare ones from the list.
>>>> 
>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>> to
>>>> the BioPerl module, that will be used by default and should fix the
>>>> issue.
>>>> 
>>>> Thanks,
>>>> Carson
>>>> 
>>>> 
>>>> 
>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> I have a serious problems with maker annotations especially the start
>>>>> codon placement. It started happening with maker version 2.27! About
>>>>> 1/3
>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>> files gene predictors and est evidence standalone would predict the
>>>>> right gene structure including the start codon. I was thinking that
>>>>> this
>>>>> problem was somehow linked to my gene models but looking at their
>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>> proteins with proper start codon (first column) and missing start
>>>>> codon
>>>>> (second column).
>>>>> 
>>>>> Maker              9268    4215
>>>>> SNAP               16577   896
>>>>> Genemark   18764   290
>>>>> 
>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>> want
>>>>> to check > 4000 genes for this.
>>>>> 
>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>> example gff files I can send you.
>>>>> 
>>>>> Best regards
>>>>> Felix
>>>>> 
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>> 
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



From amelia.ireland at gmod.org  Thu Oct 24 13:52:17 2013
From: amelia.ireland at gmod.org (Amelia Ireland)
Date: Thu, 24 Oct 2013 11:52:17 -0700
Subject: [maker-devel] GMOD 2014: San Diego
Message-ID: <CAALsq00kuy83m4_k_rcWLSpwFYwMCYm5LXEkUgwzqCOUGfryBw@mail.gmail.com>

Greetings GMOD community citizens!

Online registration is now open for the 2014 GMOD meeting, to be held at
the Best Western Seven Seas, San Diego, CA, on January 16-17, 2014 (after
PAG). The meeting is open to GMOD users, developers, and anyone interested
in the project and the software we provide.

Online registration is now open; please see the meeting page,
http://gmod.org/wiki/Jan_2014_GMOD_Meeting, for more information. Early
bird registration rates apply until Dec. 14th.

We have secured a discount on a block of rooms at the Best Western Seven
Seas; please see the wiki for more information on booking.

Please feel free to contact the GMOD helpdesk on help at gmod.org if you have
any questions. Thanks!

-- 
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject
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From barry.moore at genetics.utah.edu  Thu Oct 24 16:09:20 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Thu, 24 Oct 2013 15:09:20 -0600
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
	<69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
Message-ID: <1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>

Hi Jim,

You can and any kind of evidence you want to MAKER including ribosomal profiling data as long as you format it in GFF3 format.  You could pass in your GFF3 formatted ribosomal profiling data in maker_opt.ctl with the protein_gff option and it will be treated as protein evidence.  However if you are wondering if anyone has coded a specific addition to MAKER to accept ribosomal profiling data and treat it as a different kind of evidence then no, this hasn't been done.

B

On Oct 24, 2013, at 8:32 AM, JH Gmail wrote:

> Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 
> 
> Does maker handle ribosome profiling yet?
> 
> jim
> 
> Sent from my iPad
> 
>> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
>> 
>> Hi Graham,
>> 
>> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>> 
>> 
>> --mark
>> 
>> 
>> Mark Yandell
>> Professor of Human Genetics
>> H.A. & Edna Benning Presidential Endowed Chair
>> Eccles Institute of Human Genetics
>> University of Utah
>> 15 North 2030 East, Room 2100
>> Salt Lake City, UT 84112-5330
>> ph:801-587-7707
>> 
>> ________________________________________
>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
>> Sent: Thursday, October 24, 2013 7:42 AM
>> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
>> Cc: Kate Bailey (TSL)
>> Subject: Re: [maker-devel] Serious Start Codon Problem
>> 
>> Hi,
>> I notice that the latest version of Maker available from
>> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
>> 2013). As we're also having the start codon problem we'd like to get hold
>> of v2.30. Do you know when this will be released?
>> Many thanks,
>> Graham
>> 
>> 
>> Dr. Graham Etherington
>> Bioinformatics Support Officer,
>> The Sainsbury Laboratory,
>> Norwich Research Park,
>> Norwich NR4 7UH.
>> UK
>> Tel: +44 (0)1603 450601
>> 
>> 
>> 
>> 
>> 
>>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>>> 
>>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>>> to have it wrapped up before I leave.
>>> 
>>> --Carson
>>> 
>>> 
>>> 
>>> 
>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>> 
>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>> 
>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>> This issue just came up this week on another e-mail as well.
>>>>> 
>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>> around.
>>>>> 
>>>>> You change line 256 from -->
>>>>> ---M---------------M---------------M----------------------------
>>>>> 
>>>>> To-->
>>>>> -----------------------------------M----------------------------
>>>>> 
>>>>> 
>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>> codon
>>>>> used in a result it receives is acceptable or if it should look
>>>>> upstream
>>>>> or downstream for a different one. Apparently there are actually 3
>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>> one
>>>>> common), so making the edit removes the two rare ones from the list.
>>>>> 
>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>> to
>>>>> the BioPerl module, that will be used by default and should fix the
>>>>> issue.
>>>>> 
>>>>> Thanks,
>>>>> Carson
>>>>> 
>>>>> 
>>>>> 
>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I have a serious problems with maker annotations especially the start
>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>> 1/3
>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>> right gene structure including the start codon. I was thinking that
>>>>>> this
>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>> proteins with proper start codon (first column) and missing start
>>>>>> codon
>>>>>> (second column).
>>>>>> 
>>>>>> Maker              9268    4215
>>>>>> SNAP               16577   896
>>>>>> Genemark   18764   290
>>>>>> 
>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>> want
>>>>>> to check > 4000 genes for this.
>>>>>> 
>>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>>> example gff files I can send you.
>>>>>> 
>>>>>> Best regards
>>>>>> Felix
>>>>>> 
>>>>>> --
>>>>>> Felix Bemm
>>>>>> Department of Bioinformatics
>>>>>> University of W?rzburg, Germany
>>>>>> Tel: +49 931 - 31 83696
>>>>>> Fax: +49 931 - 31 84552
>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>> 
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> 
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> 
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> 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
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> _______________________________________________
>> maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From marc.hoeppner at imbim.uu.se  Fri Oct 25 09:20:04 2013
From: marc.hoeppner at imbim.uu.se (Marc P. Hoeppner)
Date: Fri, 25 Oct 2013 16:20:04 +0200
Subject: [maker-devel] Maker MPICH2 issue (Multiple MAKER processes have
 been started in the same directory)
Message-ID: <526A7E14.9010906@imbim.uu.se>

Dear list,

I know that MPICH2 related issues have been discussed previously, but 
the suggested solutions don't seem to work for me.
Briefly, I have set up a new cluster, with a fresh install of mpich2 (SL 
6.4, from the yum repos) and a newly compiled build of Maker 2.28.

When I start maker with mpiexec, I get spammed with
'WARNING: Multiple MAKER processes have been started in the same 
directory.'

Here is what I have tried so far - still getting the error :-< Any 
suggestions would be appreciated

--------
MPICH2
---------

which mpiexec:
/usr/lib64/mpich2/bin/mpiexec

Started the mpd ring as normal user across 5 nodes (bnode-01 to 
bnode-04, and the head node bhead)

mpdtrace:
bhead
bnode-02
bnode-03
bnode-04
bnode-01

mpdringtest:
time for 1 loops = 0.00128293037415 seconds

mpixec -n 32 -machinefile hostfile hostname:

<long list of host names, as ecpected>

I also ran the Skampi Mpi Benchmark, which ran through just fine.

-----------
MAKER
-----------

./Build status

PERL Dependencies:      VERIFIED
External Programs:      VERIFIED
External C Libraries:   VERIFIED
MPI SUPPORT:            ENABLED
MWAS Web Interface:     DISABLED
MAKER PACKAGE:          CONFIGURATION OK

During configuration/installation, Build.PL automatically detected all 
MPI data and never complained, so I have to assume that everything went 
fine there.

-- 
----------
Marc P. Hoeppner, PhD
Department of Microbiology and Medical Biochemistry
Uppsala University, Sweden
marc.hoeppner at imbim.uu.se




From jim.hu.biobio at gmail.com  Fri Oct 25 09:51:19 2013
From: jim.hu.biobio at gmail.com (JH Gmail)
Date: Fri, 25 Oct 2013 09:51:19 -0500
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
	<69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
	<1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>
Message-ID: <596400F6-3215-4F71-A896-AF52CEC8D77D@gmail.com>

Thanks Barry,

I'm thinking about this more theoretically, as we don't have immediate plans, but...

This would work for gff derived from ribosome profiling analysis, but it would be nice to be able to start with bam files of mapped reads, or coverage scores as bigwig or gff.  RNA-seq has similar issues, but IIRC Maker expects RNA-seq data to be assembled first.  It may not be possible to do de novo cds assembly from ribosome profiling because I think the nuclease step may kill the overlaps. I'd have to look at some of the available data. 

Jim

Sent from my iPad

> On Oct 24, 2013, at 4:09 PM, Barry Moore <barry.moore at genetics.utah.edu> wrote:
> 
> Hi Jim,
> 
> You can and any kind of evidence you want to MAKER including ribosomal profiling data as long as you format it in GFF3 format.  You could pass in your GFF3 formatted ribosomal profiling data in maker_opt.ctl with the protein_gff option and it will be treated as protein evidence.  However if you are wondering if anyone has coded a specific addition to MAKER to accept ribosomal profiling data and treat it as a different kind of evidence then no, this hasn't been done.
> 
> B
> 
>> On Oct 24, 2013, at 8:32 AM, JH Gmail wrote:
>> 
>> Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 
>> 
>> Does maker handle ribosome profiling yet?
>> 
>> jim
>> 
>> Sent from my iPad
>> 
>>> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
>>> 
>>> Hi Graham,
>>> 
>>> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>>> 
>>> 
>>> --mark
>>> 
>>> 
>>> Mark Yandell
>>> Professor of Human Genetics
>>> H.A. & Edna Benning Presidential Endowed Chair
>>> Eccles Institute of Human Genetics
>>> University of Utah
>>> 15 North 2030 East, Room 2100
>>> Salt Lake City, UT 84112-5330
>>> ph:801-587-7707
>>> 
>>> ________________________________________
>>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
>>> Sent: Thursday, October 24, 2013 7:42 AM
>>> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
>>> Cc: Kate Bailey (TSL)
>>> Subject: Re: [maker-devel] Serious Start Codon Problem
>>> 
>>> Hi,
>>> I notice that the latest version of Maker available from
>>> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
>>> 2013). As we're also having the start codon problem we'd like to get hold
>>> of v2.30. Do you know when this will be released?
>>> Many thanks,
>>> Graham
>>> 
>>> 
>>> Dr. Graham Etherington
>>> Bioinformatics Support Officer,
>>> The Sainsbury Laboratory,
>>> Norwich Research Park,
>>> Norwich NR4 7UH.
>>> UK
>>> Tel: +44 (0)1603 450601
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>>>> 
>>>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>>>> to have it wrapped up before I leave.
>>>> 
>>>> --Carson
>>>> 
>>>> 
>>>> 
>>>> 
>>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>> 
>>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>>> 
>>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>>> This issue just came up this week on another e-mail as well.
>>>>>> 
>>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>>> around.
>>>>>> 
>>>>>> You change line 256 from -->
>>>>>> ---M---------------M---------------M----------------------------
>>>>>> 
>>>>>> To-->
>>>>>> -----------------------------------M----------------------------
>>>>>> 
>>>>>> 
>>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>>> codon
>>>>>> used in a result it receives is acceptable or if it should look
>>>>>> upstream
>>>>>> or downstream for a different one. Apparently there are actually 3
>>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>>> one
>>>>>> common), so making the edit removes the two rare ones from the list.
>>>>>> 
>>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>>> to
>>>>>> the BioPerl module, that will be used by default and should fix the
>>>>>> issue.
>>>>>> 
>>>>>> Thanks,
>>>>>> Carson
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I have a serious problems with maker annotations especially the start
>>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>>> 1/3
>>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>>> right gene structure including the start codon. I was thinking that
>>>>>>> this
>>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>>> proteins with proper start codon (first column) and missing start
>>>>>>> codon
>>>>>>> (second column).
>>>>>>> 
>>>>>>> Maker              9268    4215
>>>>>>> SNAP               16577   896
>>>>>>> Genemark   18764   290
>>>>>>> 
>>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>>> want
>>>>>>> to check > 4000 genes for this.
>>>>>>> 
>>>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>>>> example gff files I can send you.
>>>>>>> 
>>>>>>> Best regards
>>>>>>> Felix
>>>>>>> 
>>>>>>> --
>>>>>>> Felix Bemm
>>>>>>> Department of Bioinformatics
>>>>>>> University of W?rzburg, Germany
>>>>>>> Tel: +49 931 - 31 83696
>>>>>>> Fax: +49 931 - 31 84552
>>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> 
>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>> 
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> 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
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> _______________________________________________
>>> maker-devel mailing list
>>> 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
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
> 
> 
> 
> 
-------------- next part --------------
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From barry.moore at genetics.utah.edu  Fri Oct 25 10:44:55 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Fri, 25 Oct 2013 09:44:55 -0600
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <596400F6-3215-4F71-A896-AF52CEC8D77D@gmail.com>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
	<69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
	<1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>
	<596400F6-3215-4F71-A896-AF52CEC8D77D@gmail.com>
Message-ID: <DA777487-D8DD-47E2-A852-DB123C3A1BB8@genetics.utah.edu>

Thanks Jim.

B

On Oct 25, 2013, at 8:51 AM, JH Gmail wrote:

> Thanks Barry,
> 
> I'm thinking about this more theoretically, as we don't have immediate plans, but...
> 
> This would work for gff derived from ribosome profiling analysis, but it would be nice to be able to start with bam files of mapped reads, or coverage scores as bigwig or gff.  RNA-seq has similar issues, but IIRC Maker expects RNA-seq data to be assembled first.  It may not be possible to do de novo cds assembly from ribosome profiling because I think the nuclease step may kill the overlaps. I'd have to look at some of the available data. 
> 
> Jim
> 
> Sent from my iPad
> 
> On Oct 24, 2013, at 4:09 PM, Barry Moore <barry.moore at genetics.utah.edu> wrote:
> 
>> Hi Jim,
>> 
>> You can and any kind of evidence you want to MAKER including ribosomal profiling data as long as you format it in GFF3 format.  You could pass in your GFF3 formatted ribosomal profiling data in maker_opt.ctl with the protein_gff option and it will be treated as protein evidence.  However if you are wondering if anyone has coded a specific addition to MAKER to accept ribosomal profiling data and treat it as a different kind of evidence then no, this hasn't been done.
>> 
>> B
>> 
>> On Oct 24, 2013, at 8:32 AM, JH Gmail wrote:
>> 
>>> Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 
>>> 
>>> Does maker handle ribosome profiling yet?
>>> 
>>> jim
>>> 
>>> Sent from my iPad
>>> 
>>>> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
>>>> 
>>>> Hi Graham,
>>>> 
>>>> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>>>> 
>>>> 
>>>> --mark
>>>> 
>>>> 
>>>> Mark Yandell
>>>> Professor of Human Genetics
>>>> H.A. & Edna Benning Presidential Endowed Chair
>>>> Eccles Institute of Human Genetics
>>>> University of Utah
>>>> 15 North 2030 East, Room 2100
>>>> Salt Lake City, UT 84112-5330
>>>> ph:801-587-7707
>>>> 
>>>> ________________________________________
>>>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
>>>> Sent: Thursday, October 24, 2013 7:42 AM
>>>> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
>>>> Cc: Kate Bailey (TSL)
>>>> Subject: Re: [maker-devel] Serious Start Codon Problem
>>>> 
>>>> Hi,
>>>> I notice that the latest version of Maker available from
>>>> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
>>>> 2013). As we're also having the start codon problem we'd like to get hold
>>>> of v2.30. Do you know when this will be released?
>>>> Many thanks,
>>>> Graham
>>>> 
>>>> 
>>>> Dr. Graham Etherington
>>>> Bioinformatics Support Officer,
>>>> The Sainsbury Laboratory,
>>>> Norwich Research Park,
>>>> Norwich NR4 7UH.
>>>> UK
>>>> Tel: +44 (0)1603 450601
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>>>>> 
>>>>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>>>>> to have it wrapped up before I leave.
>>>>> 
>>>>> --Carson
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>> 
>>>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>>>> 
>>>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>>>> This issue just came up this week on another e-mail as well.
>>>>>>> 
>>>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>>>> around.
>>>>>>> 
>>>>>>> You change line 256 from -->
>>>>>>> ---M---------------M---------------M----------------------------
>>>>>>> 
>>>>>>> To-->
>>>>>>> -----------------------------------M----------------------------
>>>>>>> 
>>>>>>> 
>>>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>>>> codon
>>>>>>> used in a result it receives is acceptable or if it should look
>>>>>>> upstream
>>>>>>> or downstream for a different one. Apparently there are actually 3
>>>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>>>> one
>>>>>>> common), so making the edit removes the two rare ones from the list.
>>>>>>> 
>>>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>>>> to
>>>>>>> the BioPerl module, that will be used by default and should fix the
>>>>>>> issue.
>>>>>>> 
>>>>>>> Thanks,
>>>>>>> Carson
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>>>> 
>>>>>>>> Hi,
>>>>>>>> 
>>>>>>>> I have a serious problems with maker annotations especially the start
>>>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>>>> 1/3
>>>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>>>> right gene structure including the start codon. I was thinking that
>>>>>>>> this
>>>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>>>> proteins with proper start codon (first column) and missing start
>>>>>>>> codon
>>>>>>>> (second column).
>>>>>>>> 
>>>>>>>> Maker              9268    4215
>>>>>>>> SNAP               16577   896
>>>>>>>> Genemark   18764   290
>>>>>>>> 
>>>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>>>> want
>>>>>>>> to check > 4000 genes for this.
>>>>>>>> 
>>>>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>>>>> example gff files I can send you.
>>>>>>>> 
>>>>>>>> Best regards
>>>>>>>> Felix
>>>>>>>> 
>>>>>>>> --
>>>>>>>> Felix Bemm
>>>>>>>> Department of Bioinformatics
>>>>>>>> University of W?rzburg, Germany
>>>>>>>> Tel: +49 931 - 31 83696
>>>>>>>> Fax: +49 931 - 31 84552
>>>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> maker-devel mailing list
>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>> 
>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>> 
>>>>>> --
>>>>>> Felix Bemm
>>>>>> Department of Bioinformatics
>>>>>> University of W?rzburg, Germany
>>>>>> Tel: +49 931 - 31 83696
>>>>>> Fax: +49 931 - 31 84552
>>>>>> felix.bemm at uni-wuerzburg.de
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> 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
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> 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
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> Barry Moore
>> Research Scientist
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT 84112
>> --------------------------------------------
>> (801) 585-3543
>> 
>> 
>> 
>> 

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From marc.hoeppner at imbim.uu.se  Sat Oct 26 06:54:07 2013
From: marc.hoeppner at imbim.uu.se (Marc P. Hoeppner)
Date: Sat, 26 Oct 2013 13:54:07 +0200
Subject: [maker-devel] Maker MPICH2 issue (Multiple MAKER processes have
 been started in the same directory)
In-Reply-To: <526A7E14.9010906@imbim.uu.se>
References: <526A7E14.9010906@imbim.uu.se>
Message-ID: <526BAD5F.2000800@imbim.uu.se>

Dear List,

after much more debugging, I found the solution myself. Here are the 
details:

The Maker installation instructions refer to 'mpich2' in multiple 
places, including weblinks (whchi are outdated btw). Some digging 
revealed that mpich2 has since been renamed and merged back into mpich. 
So the website is www.mpich.org and the current stable version is 
mpich-3.0.4.  Closely following the installation instruction yielded a 
working copy of mpiexec that Maker was willing to accept. Good news - 
but I suggest to update the documentation. Most importantly for either 
SL/CentOS users, mpich2 as packaged with e.g. Scientific Linux *does 
not* work with Maker. You will need to download the latest stable build 
and compile it yourself (the mpich2 version bundled with Maker doesn't 
work either btw).

Cheers,

Marc

> Dear list,
>
> I know that MPICH2 related issues have been discussed previously, but 
> the suggested solutions don't seem to work for me.
> Briefly, I have set up a new cluster, with a fresh install of mpich2 
> (SL 6.4, from the yum repos) and a newly compiled build of Maker 2.28.
>
> When I start maker with mpiexec, I get spammed with
> 'WARNING: Multiple MAKER processes have been started in the same 
> directory.'
>
> Here is what I have tried so far - still getting the error :-< Any 
> suggestions would be appreciated
>
> --------
> MPICH2
> ---------
>
> which mpiexec:
> /usr/lib64/mpich2/bin/mpiexec
>
> Started the mpd ring as normal user across 5 nodes (bnode-01 to 
> bnode-04, and the head node bhead)
>
> mpdtrace:
> bhead
> bnode-02
> bnode-03
> bnode-04
> bnode-01
>
> mpdringtest:
> time for 1 loops = 0.00128293037415 seconds
>
> mpixec -n 32 -machinefile hostfile hostname:
>
> <long list of host names, as ecpected>
>
> I also ran the Skampi Mpi Benchmark, which ran through just fine.
>
> -----------
> MAKER
> -----------
>
> ./Build status
>
> PERL Dependencies:      VERIFIED
> External Programs:      VERIFIED
> External C Libraries:   VERIFIED
> MPI SUPPORT:            ENABLED
> MWAS Web Interface:     DISABLED
> MAKER PACKAGE:          CONFIGURATION OK
>
> During configuration/installation, Build.PL automatically detected all 
> MPI data and never complained, so I have to assume that everything 
> went fine there.
>


-- 
----------
Marc P. Hoeppner, PhD
Department of Microbiology and Medical Biochemistry
Uppsala University, Sweden
marc.hoeppner at imbim.uu.se




From barry.utah at gmail.com  Sat Oct 26 09:41:24 2013
From: barry.utah at gmail.com (Barry Moore)
Date: Sat, 26 Oct 2013 08:41:24 -0600
Subject: [maker-devel] Maker MPICH2 issue (Multiple MAKER processes have
	been started in the same directory)
In-Reply-To: <526BAD5F.2000800@imbim.uu.se>
References: <526A7E14.9010906@imbim.uu.se> <526BAD5F.2000800@imbim.uu.se>
Message-ID: <DDEE11FF-9EE2-4359-9A50-3DA95770DDEC@genetics.utah.edu>

Hi Marc,

Thanks so much for sharing the results of all your hard work!  We will follow up on your feedback and incorporate the necessary updates to MAKER docs and installation procedures.

B

On Oct 26, 2013, at 5:54 AM, Marc P. Hoeppner wrote:

> Dear List,
> 
> after much more debugging, I found the solution myself. Here are the details:
> 
> The Maker installation instructions refer to 'mpich2' in multiple places, including weblinks (whchi are outdated btw). Some digging revealed that mpich2 has since been renamed and merged back into mpich. So the website is www.mpich.org and the current stable version is mpich-3.0.4.  Closely following the installation instruction yielded a working copy of mpiexec that Maker was willing to accept. Good news - but I suggest to update the documentation. Most importantly for either SL/CentOS users, mpich2 as packaged with e.g. Scientific Linux *does not* work with Maker. You will need to download the latest stable build and compile it yourself (the mpich2 version bundled with Maker doesn't work either btw).
> 
> Cheers,
> 
> Marc
> 
>> Dear list,
>> 
>> I know that MPICH2 related issues have been discussed previously, but the suggested solutions don't seem to work for me.
>> Briefly, I have set up a new cluster, with a fresh install of mpich2 (SL 6.4, from the yum repos) and a newly compiled build of Maker 2.28.
>> 
>> When I start maker with mpiexec, I get spammed with
>> 'WARNING: Multiple MAKER processes have been started in the same directory.'
>> 
>> Here is what I have tried so far - still getting the error :-< Any suggestions would be appreciated
>> 
>> --------
>> MPICH2
>> ---------
>> 
>> which mpiexec:
>> /usr/lib64/mpich2/bin/mpiexec
>> 
>> Started the mpd ring as normal user across 5 nodes (bnode-01 to bnode-04, and the head node bhead)
>> 
>> mpdtrace:
>> bhead
>> bnode-02
>> bnode-03
>> bnode-04
>> bnode-01
>> 
>> mpdringtest:
>> time for 1 loops = 0.00128293037415 seconds
>> 
>> mpixec -n 32 -machinefile hostfile hostname:
>> 
>> <long list of host names, as ecpected>
>> 
>> I also ran the Skampi Mpi Benchmark, which ran through just fine.
>> 
>> -----------
>> MAKER
>> -----------
>> 
>> ./Build status
>> 
>> PERL Dependencies:      VERIFIED
>> External Programs:      VERIFIED
>> External C Libraries:   VERIFIED
>> MPI SUPPORT:            ENABLED
>> MWAS Web Interface:     DISABLED
>> MAKER PACKAGE:          CONFIGURATION OK
>> 
>> During configuration/installation, Build.PL automatically detected all MPI data and never complained, so I have to assume that everything went fine there.
>> 
> 
> 
> -- 
> ----------
> Marc P. Hoeppner, PhD
> Department of Microbiology and Medical Biochemistry
> Uppsala University, Sweden
> marc.hoeppner at imbim.uu.se
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From wholtz at lygos.com  Wed Oct 30 13:21:52 2013
From: wholtz at lygos.com (William Holtz)
Date: Wed, 30 Oct 2013 11:21:52 -0700 (PDT)
Subject: [maker-devel] maker apollo error
Message-ID: <1383157312.95043.YahooMailNeo@web5706.biz.mail.ne1.yahoo.com>

Hi,

I'm attempting to reply to a thread on this list from before I was a member. My apologies if this gets messed up.

I've tried installing maker v2.28 and v2.29p-beta and both of them fail due to the URL of the apollo tar file being outdated as previously reported on this list.?The updated URL that Carson Holt posted,?http://sourceforge.net/code-snapshots/svn/g/gm/gmod/svn/gmod-svn-25291-apollo-trunk.zip,?is also no longer valid. I was able to find a copy of the apollo source at?http://downloads.sourceforge.net/project/gmod/Apollo/1.11.1/apollo-1.11.1.tgz. However my attempts to integrate this into the maker build process have been unsuccessful, but likely could be done by someone more skilled than I.?Any pointers on how to get past this hurdle would be appreciated.

Thanks in advance for your help.

-Will



From barry.utah at gmail.com  Wed Oct 30 17:31:58 2013
From: barry.utah at gmail.com (Barry Moore)
Date: Wed, 30 Oct 2013 16:31:58 -0600
Subject: [maker-devel] maker apollo error
In-Reply-To: <1383157312.95043.YahooMailNeo@web5706.biz.mail.ne1.yahoo.com>
References: <1383157312.95043.YahooMailNeo@web5706.biz.mail.ne1.yahoo.com>
Message-ID: <C6E0A4A7-10D2-43B4-AA77-CCF6BE62E927@genetics.utah.edu>

Hi Will,

You can edit these URLs in the following file:

maker/src/locations

In a section that looks like this:

    'apollo'       => {'Linux_x86_64'  => 'http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar',
                       'Linux_i386'    => 'http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar',
                       'Darwin_i386'   => 'http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz',
                       'Darwin_x86_64' => 'http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz',
                       'src_'          => 'http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz',
                   },

Carson may have more feedback for you as well, but he is right in the middle of a move, so there may be a few days before he can reply, so modifying this file should work for you in the mean time.

On any of the executables that are missing you can always install them manually and add them to your path and maker will find them.  Also, maker shouldn't be required for a base maker install, so you could ignore that dependency as well.

Thanks,

B




On Oct 30, 2013, at 12:21 PM, William Holtz wrote:

> Hi,
> 
> I'm attempting to reply to a thread on this list from before I was a member. My apologies if this gets messed up.
> 
> I've tried installing maker v2.28 and v2.29p-beta and both of them fail due to the URL of the apollo tar file being outdated as previously reported on this list. The updated URL that Carson Holt posted, http://sourceforge.net/code-snapshots/svn/g/gm/gmod/svn/gmod-svn-25291-apollo-trunk.zip, is also no longer valid. I was able to find a copy of the apollo source at http://downloads.sourceforge.net/project/gmod/Apollo/1.11.1/apollo-1.11.1.tgz. However my attempts to integrate this into the maker build process have been unsuccessful, but likely could be done by someone more skilled than I. Any pointers on how to get past this hurdle would be appreciated.
> 
> Thanks in advance for your help.
> 
> -Will
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From carsonhh at gmail.com  Wed Oct  2 08:14:44 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 02 Oct 2013 10:14:44 -0400
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
Message-ID: <CE709D72.EF15%carsonhh@gmail.com>

It still works, but it will be reduced.  Without ESTs you won't get any
UTR prediction, also you will be limited by how well the protein set
matches to the genes.  If you use the protein set of a close relative you
will capture most things.  You will probably capture 80-95% of what you
would by also including ESTs.  It all depending on how different the
species in the proteins evidence file are compared to the the species
being annotated.

--Carson

On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for your message and your kind help. Now conversion from
>match/match_part to gene/mRNA/exons/CDS works well after blanking out
>some options in control file.
>
>I have one more question about maker2. In case we don't have EST evidence
>(set of ESTs or assembled mRNA-seq in fasta format) for a genome, does
>maker2 function? If it does function, could you please let me know the
>performance of maker2 without providing EST evidence compared to the one
>with EST evidence?
>
>Thank you  again and I look forward to hearing from you.
>
>Best,
>Xia
>
>
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Wednesday, September 25, 2013 10:36 AM
>To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>If it is launching predictors then you have snap hmm or augustus_species
>set.  You ned to blank out all other options in the control files
>(including repeat masking options, proteins, ESTs, etc.) when trying to
>convert mathc/match_part to gene/mRNA/exons/CDS, or else those other
>programs will run.
>
>--Carson
>
>
>On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>
>>Hi Carson,
>>
>>Thank you for the message and your kind help. We tested maker2 by
>>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>But it seemed maker2 started to launch all predictors again and it took
>>long time to finish. I wonder if there is any way that we can directly
>>get gene/mRNA/exons/CDS gff file without re-running maker2 to convert
>>match/match_part features into gene/mRNA/exons/CDS.
>>
>>Thanks,
>>Xia
>>
>>-----Original Message-----
>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>Sent: Thursday, September 19, 2013 5:58 PM
>>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY;
>>maker-devel at yandell-lab.org
>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>
>>Hello Corban & Xia,
>>
>>Some scripts like gff3_preds2models are deprecated.  To get the same
>>result as was offered by gff3_preds2models, just give your
>>match/match_part features to pref_gff= in the maker_opts.ctl file, set
>>keep_preds=1, and run with all other options and predictors turned off.
>>The final MAKER result will be your match/match_part features converted
>>into gene/mRNA/exons/CDS.
>>
>>For functional annotation, you can use Interproscan, BLASTP against
>>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO
>>terms and proteins domains via the ipr_update_gff and iprscan2gff3
>>scripts.  Then add putative gene functions via BLASTP to UniProt and
>>maker_functional_fasta and maker_functional_gff scripts.
>>
>>Go ahead and take a look and that those tools and let me know if you
>>have any questions or need help you configuring them.
>>
>>Thanks,
>>Carson
>>
>>
>>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>
>>>Hi  Corban & Xia,
>>>
>>>
>>>I've forwarded your question along to the MAKER_dev list, were you can
>>>get speedy answers to your maker related questions. Thanks for using
>>>MAKER.
>>>
>>>--mark
>>>
>>>
>>>Mark Yandell
>>>Professor of Human Genetics
>>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of
>>>Human Genetics University of Utah
>>>15 North 2030 East, Room 2100
>>>Salt Lake City, UT 84112-5330
>>>ph:801-587-7707
>>>
>>>________________________________________
>>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>Sent: Thursday, September 19, 2013 11:49 AM
>>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>Subject: maker2 scripts for functional annotation
>>>
>>>Dr. Yandell,
>>>
>>>We were recently evaluating maker2 for annotation and going through
>>>the maker tutorial from 2012.
>>>
>>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>>
>>>The tutorial makes references to some scripts that we couldn?t find in
>>>the current release.  We were looking for scripts like
>>>gff3_preds2models to convert match/match_part format into annotations
>>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did
>>>not have the most up to date version.
>>>
>>>In addition to getting accurate gene annotations, I was looking for a
>>>solution to get functional assignments.  I see that there are some
>>>scripts like maker_functional_fasta that may help, but I was wondering
>>>what you would recommend.
>>>
>>>Thanks,
>>>
>>>Corban & Xia
>>>
>>>This communication is for use by the intended recipient and contains
>>>information that may be Privileged, confidential or copyrighted under
>>>applicable law. If you are not the intended recipient, you are hereby
>>>formally notified that any use, copying or distribution of this
>>>e-mail, in whole or in part, is strictly prohibited. Please notify the
>>>sender by return e-mail and delete this e-mail from your system.
>>>Unless explicitly and conspicuously designated as "E-Contract
>>>Intended", this e-mail does not constitute a contract offer, a
>>>contract amendment, or an acceptance of a contract offer. This e-mail
>>>does not constitute a consent to the use of sender's contact
>>>information for direct marketing purposes or for transfers of data to
>>>third parties.
>>>
>>>The dupont.com web address will continue in use for a transitional
>>>period for communications sent or received on behalf of DuPont
>>>Performance Coatings., which is not affiliated in any way with the
>>>DuPont Company.
>>>
>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>>Korean
>>>
>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>g
>>
>>
>>
>>This communication is for use by the intended recipient and contains
>>information that may be Privileged, confidential or copyrighted under
>>applicable law. If you are not the intended recipient, you are hereby
>>formally notified that any use, copying or distribution of this e-mail,
>>in whole or in part, is strictly prohibited. Please notify the sender
>>by return e-mail and delete this e-mail from your system. Unless
>>explicitly and conspicuously designated as "E-Contract Intended", this
>>e-mail does not constitute a contract offer, a contract amendment, or
>>an acceptance of a contract offer. This e-mail does not constitute a
>>consent to the use of sender's contact information for direct marketing
>>purposes or for transfers of data to third parties.
>>
>>The dupont.com<http://dupont.com/> web address will continue in use for
>>a transitional period for communications sent or received on behalf of
>>DuPont Performance Coatings., which is not affiliated in any way with
>>the DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>Korean
>>
>>           http://www.DuPont.com/corp/email_disclaimer.html
>>
>
>
>
>This communication is for use by the intended recipient and contains
>information that may be Privileged, confidential or copyrighted under
>applicable law. If you are not the intended recipient, you are hereby
>formally notified that any use, copying or distribution of this e-mail,
>in whole or in part, is strictly prohibited. Please notify the sender by
>return e-mail and delete this e-mail from your system. Unless explicitly
>and conspicuously designated as "E-Contract Intended", this e-mail does
>not constitute a contract offer, a contract amendment, or an acceptance
>of a contract offer. This e-mail does not constitute a consent to the
>use of sender's contact information for direct marketing purposes or for
>transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for a
>transitional period for communications sent or received on behalf of
>DuPont
>Performance Coatings., which is not affiliated in any way with the DuPont
>Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>





From Xia.Cao at dupont.com  Tue Oct  1 13:00:42 2013
From: Xia.Cao at dupont.com (Xia.Cao at dupont.com)
Date: Tue, 1 Oct 2013 19:00:42 +0000
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <CE686C71.ECAC%carsonhh@gmail.com>
References: <AAF36CDE29C45F45AE125A1D13F5D675ACE4B8@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE686C71.ECAC%carsonhh@gmail.com>
Message-ID: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>

Hi Carson,

Thank you for your message and your kind help. Now conversion from match/match_part to gene/mRNA/exons/CDS works well after blanking out some options in control file.  

I have one more question about maker2. In case we don't have EST evidence (set of ESTs or assembled mRNA-seq in fasta format) for a genome, does maker2 function? If it does function, could you please let me know the performance of maker2 without providing EST evidence compared to the one with EST evidence?

Thank you  again and I look forward to hearing from you.

Best,
Xia




-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Wednesday, September 25, 2013 10:36 AM
To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] maker2 scripts for functional annotation

If it is launching predictors then you have snap hmm or augustus_species set.  You ned to blank out all other options in the control files (including repeat masking options, proteins, ESTs, etc.) when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else those other programs will run.

--Carson


On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for the message and your kind help. We tested maker2 by 
>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun . 
>But it seemed maker2 started to launch all predictors again and it took 
>long time to finish. I wonder if there is any way that we can directly 
>get gene/mRNA/exons/CDS gff file without re-running maker2 to convert 
>match/match_part features into gene/mRNA/exons/CDS.
>
>Thanks,
>Xia
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Thursday, September 19, 2013 5:58 PM
>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; 
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>Hello Corban & Xia,
>
>Some scripts like gff3_preds2models are deprecated.  To get the same 
>result as was offered by gff3_preds2models, just give your 
>match/match_part features to pref_gff= in the maker_opts.ctl file, set 
>keep_preds=1, and run with all other options and predictors turned off.
>The final MAKER result will be your match/match_part features converted 
>into gene/mRNA/exons/CDS.
>
>For functional annotation, you can use Interproscan, BLASTP against 
>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO 
>terms and proteins domains via the ipr_update_gff and iprscan2gff3 
>scripts.  Then add putative gene functions via BLASTP to UniProt and 
>maker_functional_fasta and maker_functional_gff scripts.
>
>Go ahead and take a look and that those tools and let me know if you 
>have any questions or need help you configuring them.
>
>Thanks,
>Carson
>
>
>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>
>>Hi  Corban & Xia,
>>
>>
>>I've forwarded your question along to the MAKER_dev list, were you can 
>>get speedy answers to your maker related questions. Thanks for using 
>>MAKER.
>>
>>--mark
>>
>>
>>Mark Yandell
>>Professor of Human Genetics
>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of 
>>Human Genetics University of Utah
>>15 North 2030 East, Room 2100
>>Salt Lake City, UT 84112-5330
>>ph:801-587-7707
>>
>>________________________________________
>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>Sent: Thursday, September 19, 2013 11:49 AM
>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>Subject: maker2 scripts for functional annotation
>>
>>Dr. Yandell,
>>
>>We were recently evaluating maker2 for annotation and going through 
>>the maker tutorial from 2012.
>>
>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>
>>The tutorial makes references to some scripts that we couldn?t find in 
>>the current release.  We were looking for scripts like 
>>gff3_preds2models to convert match/match_part format into annotations 
>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did 
>>not have the most up to date version.
>>
>>In addition to getting accurate gene annotations, I was looking for a 
>>solution to get functional assignments.  I see that there are some 
>>scripts like maker_functional_fasta that may help, but I was wondering 
>>what you would recommend.
>>
>>Thanks,
>>
>>Corban & Xia
>>
>>This communication is for use by the intended recipient and contains 
>>information that may be Privileged, confidential or copyrighted under 
>>applicable law. If you are not the intended recipient, you are hereby 
>>formally notified that any use, copying or distribution of this 
>>e-mail, in whole or in part, is strictly prohibited. Please notify the 
>>sender by return e-mail and delete this e-mail from your system. 
>>Unless explicitly and conspicuously designated as "E-Contract 
>>Intended", this e-mail does not constitute a contract offer, a 
>>contract amendment, or an acceptance of a contract offer. This e-mail 
>>does not constitute a consent to the use of sender's contact 
>>information for direct marketing purposes or for transfers of data to third parties.
>>
>>The dupont.com web address will continue in use for a transitional 
>>period for communications sent or received on behalf of DuPont 
>>Performance Coatings., which is not affiliated in any way with the 
>>DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>Korean
>>
>>          http://www.DuPont.com/corp/email_disclaimer.html
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>g
>
>
>
>This communication is for use by the intended recipient and contains 
>information that may be Privileged, confidential or copyrighted under 
>applicable law. If you are not the intended recipient, you are hereby 
>formally notified that any use, copying or distribution of this e-mail, 
>in whole or in part, is strictly prohibited. Please notify the sender 
>by return e-mail and delete this e-mail from your system. Unless 
>explicitly and conspicuously designated as "E-Contract Intended", this 
>e-mail does not constitute a contract offer, a contract amendment, or 
>an acceptance of a contract offer. This e-mail does not constitute a 
>consent to the use of sender's contact information for direct marketing 
>purposes or for transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for 
>a transitional period for communications sent or received on behalf of 
>DuPont Performance Coatings., which is not affiliated in any way with 
>the DuPont Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  
>Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>



This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
applicable law. If you are not the intended recipient, you are hereby
formally notified that any use, copying or distribution of this e-mail,
in whole or in part, is strictly prohibited. Please notify the sender by
return e-mail and delete this e-mail from your system. Unless explicitly
and conspicuously designated as "E-Contract Intended", this e-mail does
not constitute a contract offer, a contract amendment, or an acceptance
of a contract offer. This e-mail does not constitute a consent to the
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transfers of data to third parties.

The dupont.com<http://dupont.com/> web address will continue in use for a
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Performance Coatings., which is not affiliated in any way with the DuPont Company.

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From carsonhh at gmail.com  Wed Oct  2 08:43:29 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 02 Oct 2013 10:43:29 -0400
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
Message-ID: <CE71A8D4.F2AD%carsonhh@gmail.com>

That's ok.  If it is very closely related, provide it directly to the est=
option, otherwise provide it to the altest= option.  The difference
between the two options is how they are aligned.  The altest= alignments
takes about 10x longer than the est= alignments.

--Carson


On 10/2/13 10:40 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for your quick and kind reply. One more question here. If we
>don't have EST evidence for the strain we sequenced/assembled, will it be
>ok to provide some EST evidence that is from some other strains which are
>close to the one we are trying to annotate? Could you please let us know
>how this will affect performance of maker2?
>
>Thank you again.
>
>Best,
>Xia
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Wednesday, October 02, 2013 10:15 AM
>To: CAO, XIA
>Cc: myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>It still works, but it will be reduced.  Without ESTs you won't get any
>UTR prediction, also you will be limited by how well the protein set
>matches to the genes.  If you use the protein set of a close relative you
>will capture most things.  You will probably capture 80-95% of what you
>would by also including ESTs.  It all depending on how different the
>species in the proteins evidence file are compared to the the species
>being annotated.
>
>--Carson
>
>On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>
>>Hi Carson,
>>
>>Thank you for your message and your kind help. Now conversion from
>>match/match_part to gene/mRNA/exons/CDS works well after blanking out
>>some options in control file.
>>
>>I have one more question about maker2. In case we don't have EST
>>evidence (set of ESTs or assembled mRNA-seq in fasta format) for a
>>genome, does
>>maker2 function? If it does function, could you please let me know the
>>performance of maker2 without providing EST evidence compared to the
>>one with EST evidence?
>>
>>Thank you  again and I look forward to hearing from you.
>>
>>Best,
>>Xia
>>
>>
>>
>>
>>-----Original Message-----
>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>Sent: Wednesday, September 25, 2013 10:36 AM
>>To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>>maker-devel at yandell-lab.org
>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>
>>If it is launching predictors then you have snap hmm or
>>augustus_species set.  You ned to blank out all other options in the
>>control files (including repeat masking options, proteins, ESTs, etc.)
>>when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else
>>those other programs will run.
>>
>>--Carson
>>
>>
>>On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>>
>>>Hi Carson,
>>>
>>>Thank you for the message and your kind help. We tested maker2 by
>>>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>>But it seemed maker2 started to launch all predictors again and it
>>>took long time to finish. I wonder if there is any way that we can
>>>directly get gene/mRNA/exons/CDS gff file without re-running maker2 to
>>>convert match/match_part features into gene/mRNA/exons/CDS.
>>>
>>>Thanks,
>>>Xia
>>>
>>>-----Original Message-----
>>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>>Sent: Thursday, September 19, 2013 5:58 PM
>>>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY;
>>>maker-devel at yandell-lab.org
>>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>>
>>>Hello Corban & Xia,
>>>
>>>Some scripts like gff3_preds2models are deprecated.  To get the same
>>>result as was offered by gff3_preds2models, just give your
>>>match/match_part features to pref_gff= in the maker_opts.ctl file, set
>>>keep_preds=1, and run with all other options and predictors turned off.
>>>The final MAKER result will be your match/match_part features
>>>converted into gene/mRNA/exons/CDS.
>>>
>>>For functional annotation, you can use Interproscan, BLASTP against
>>>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO
>>>terms and proteins domains via the ipr_update_gff and iprscan2gff3
>>>scripts.  Then add putative gene functions via BLASTP to UniProt and
>>>maker_functional_fasta and maker_functional_gff scripts.
>>>
>>>Go ahead and take a look and that those tools and let me know if you
>>>have any questions or need help you configuring them.
>>>
>>>Thanks,
>>>Carson
>>>
>>>
>>>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>>
>>>>Hi  Corban & Xia,
>>>>
>>>>
>>>>I've forwarded your question along to the MAKER_dev list, were you
>>>>can get speedy answers to your maker related questions. Thanks for
>>>>using MAKER.
>>>>
>>>>--mark
>>>>
>>>>
>>>>Mark Yandell
>>>>Professor of Human Genetics
>>>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of
>>>>Human Genetics University of Utah
>>>>15 North 2030 East, Room 2100
>>>>Salt Lake City, UT 84112-5330
>>>>ph:801-587-7707
>>>>
>>>>________________________________________
>>>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>>Sent: Thursday, September 19, 2013 11:49 AM
>>>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>>Subject: maker2 scripts for functional annotation
>>>>
>>>>Dr. Yandell,
>>>>
>>>>We were recently evaluating maker2 for annotation and going through
>>>>the maker tutorial from 2012.
>>>>
>>>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>>>
>>>>The tutorial makes references to some scripts that we couldn?t find
>>>>in the current release.  We were looking for scripts like
>>>>gff3_preds2models to convert match/match_part format into annotations
>>>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did
>>>>not have the most up to date version.
>>>>
>>>>In addition to getting accurate gene annotations, I was looking for a
>>>>solution to get functional assignments.  I see that there are some
>>>>scripts like maker_functional_fasta that may help, but I was
>>>>wondering what you would recommend.
>>>>
>>>>Thanks,
>>>>
>>>>Corban & Xia
>>>>
>>>>This communication is for use by the intended recipient and contains
>>>>information that may be Privileged, confidential or copyrighted under
>>>>applicable law. If you are not the intended recipient, you are hereby
>>>>formally notified that any use, copying or distribution of this
>>>>e-mail, in whole or in part, is strictly prohibited. Please notify
>>>>the sender by return e-mail and delete this e-mail from your system.
>>>>Unless explicitly and conspicuously designated as "E-Contract
>>>>Intended", this e-mail does not constitute a contract offer, a
>>>>contract amendment, or an acceptance of a contract offer. This e-mail
>>>>does not constitute a consent to the use of sender's contact
>>>>information for direct marketing purposes or for transfers of data to
>>>>third parties.
>>>>
>>>>The dupont.com web address will continue in use for a transitional
>>>>period for communications sent or received on behalf of DuPont
>>>>Performance Coatings., which is not affiliated in any way with the
>>>>DuPont Company.
>>>>
>>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>>>Korean
>>>>
>>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>>>
>>>>_______________________________________________
>>>>maker-devel mailing list
>>>>maker-devel at box290.bluehost.com
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>>r
>>>>g
>>>
>>>
>>>
>>>This communication is for use by the intended recipient and contains
>>>information that may be Privileged, confidential or copyrighted under
>>>applicable law. If you are not the intended recipient, you are hereby
>>>formally notified that any use, copying or distribution of this
>>>e-mail, in whole or in part, is strictly prohibited. Please notify the
>>>sender by return e-mail and delete this e-mail from your system.
>>>Unless explicitly and conspicuously designated as "E-Contract
>>>Intended", this e-mail does not constitute a contract offer, a
>>>contract amendment, or an acceptance of a contract offer. This e-mail
>>>does not constitute a consent to the use of sender's contact
>>>information for direct marketing purposes or for transfers of data to
>>>third parties.
>>>
>>>The dupont.com<http://dupont.com/> web address will continue in use
>>>for a transitional period for communications sent or received on
>>>behalf of DuPont Performance Coatings., which is not affiliated in any
>>>way with the DuPont Company.
>>>
>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>>Korean
>>>
>>>           http://www.DuPont.com/corp/email_disclaimer.html
>>>
>>
>>
>>
>>This communication is for use by the intended recipient and contains
>>information that may be Privileged, confidential or copyrighted under
>>applicable law. If you are not the intended recipient, you are hereby
>>formally notified that any use, copying or distribution of this e-mail,
>>in whole or in part, is strictly prohibited. Please notify the sender
>>by return e-mail and delete this e-mail from your system. Unless
>>explicitly and conspicuously designated as "E-Contract Intended", this
>>e-mail does not constitute a contract offer, a contract amendment, or
>>an acceptance of a contract offer. This e-mail does not constitute a
>>consent to the use of sender's contact information for direct marketing
>>purposes or for transfers of data to third parties.
>>
>>The dupont.com<http://dupont.com/> web address will continue in use for
>>a transitional period for communications sent or received on behalf of
>>DuPont Performance Coatings., which is not affiliated in any way with
>>the DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>Korean
>>
>>           http://www.DuPont.com/corp/email_disclaimer.html
>>
>
>
>
>This communication is for use by the intended recipient and contains
>information that may be Privileged, confidential or copyrighted under
>applicable law. If you are not the intended recipient, you are hereby
>formally notified that any use, copying or distribution of this e-mail,
>in whole or in part, is strictly prohibited. Please notify the sender by
>return e-mail and delete this e-mail from your system. Unless explicitly
>and conspicuously designated as "E-Contract Intended", this e-mail does
>not constitute a contract offer, a contract amendment, or an acceptance
>of a contract offer. This e-mail does not constitute a consent to the
>use of sender's contact information for direct marketing purposes or for
>transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for a
>transitional period for communications sent or received on behalf of
>DuPont
>Performance Coatings., which is not affiliated in any way with the DuPont
>Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>





From Carson.Holt at oicr.on.ca  Wed Oct  2 09:24:42 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Wed, 2 Oct 2013 15:24:42 +0000
Subject: [maker-devel] Incorrect gene model, antisense transcripts
In-Reply-To: <A21F03FBB429334EB4D450CC75E8CBF37F0454C6@CH1PRD0210MB384.namprd02.prod.outlook.com>
Message-ID: <CE71B238.F2B7%carson.holt@oicr.on.ca>

SNAP appears to be making small ab initio calls all over the place.  You may need to retrain it, or just drop it completely from your analysis and just use augustus.

Try running with protein2genome and then training SNAP off of those results.  Also make sure your repeat masking is sufficient.  You may be getting too many SANP predictions if that is the case.

Thanks,
Carson



From: Sivaranjani Namasivayam <ranjani at uga.edu<mailto:ranjani at uga.edu>>
Date: Tuesday, October 1, 2013 5:01 PM
To: "maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>" <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>>
Subject: Incorrect gene model, antisense transcripts

Hello,

I am working on annotating a genome. I have RNAseq data assembled with Cufflinks and Trinity. I am using to predict gene models. Below is the procedure I used

- For the first round of prediction I provided the following : EST evidence: assembled RNAseq, Protein evidence: proteins from related organism, Gene predictor: augustus trained on a related organism.
- The number of genes I got was much less than expected (Expect atleast 10K genes, got ~4K genes)
- Used the gene models from the first round of annotations to train SNAP (default parameters) and provided the HMM for the second round of annotation (used augustus also). All other data I passed as such in the gff3, except the gene models.I also included the some manually curated genes in the EST evidence.

- The number of genes were much higher, ~11k, but many seemed incorrect and appear to have been generated from the SNAP models. I am attaching a screen shot from Apollo showing this.

Would you have any suggestions on why this might be happening and how I can fix?
I am essentially looking for gene models for my assembled RNAseq, can I achieve this by setting est2genome to 1? Would I be losing/misrepresenting any data if I do this.

Also, I recently noticed my RNAseq data has assembled antisense transcripts. MAKER seems to be predicting a coding region for these antisense transcripts in some cases, (although the coding region predicted is much smaller than that of the sense gene model.) Is there a way to tell MAKER not to predict gene models on both strands at the same loci.

Appreciate your help.

Thanks,
Ranjani





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From Xia.Cao at dupont.com  Wed Oct  2 08:40:12 2013
From: Xia.Cao at dupont.com (Xia.Cao at dupont.com)
Date: Wed, 2 Oct 2013 14:40:12 +0000
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <CE709D72.EF15%carsonhh@gmail.com>
References: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE709D72.EF15%carsonhh@gmail.com>
Message-ID: <AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>

Hi Carson,

Thank you for your quick and kind reply. One more question here. If we don't have EST evidence for the strain we sequenced/assembled, will it be ok to provide some EST evidence that is from some other strains which are close to the one we are trying to annotate? Could you please let us know how this will affect performance of maker2?

Thank you again.

Best,
Xia

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Wednesday, October 02, 2013 10:15 AM
To: CAO, XIA
Cc: myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] maker2 scripts for functional annotation

It still works, but it will be reduced.  Without ESTs you won't get any UTR prediction, also you will be limited by how well the protein set matches to the genes.  If you use the protein set of a close relative you will capture most things.  You will probably capture 80-95% of what you would by also including ESTs.  It all depending on how different the species in the proteins evidence file are compared to the the species being annotated.

--Carson

On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for your message and your kind help. Now conversion from 
>match/match_part to gene/mRNA/exons/CDS works well after blanking out 
>some options in control file.
>
>I have one more question about maker2. In case we don't have EST 
>evidence (set of ESTs or assembled mRNA-seq in fasta format) for a 
>genome, does
>maker2 function? If it does function, could you please let me know the 
>performance of maker2 without providing EST evidence compared to the 
>one with EST evidence?
>
>Thank you  again and I look forward to hearing from you.
>
>Best,
>Xia
>
>
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Wednesday, September 25, 2013 10:36 AM
>To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; 
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>If it is launching predictors then you have snap hmm or 
>augustus_species set.  You ned to blank out all other options in the 
>control files (including repeat masking options, proteins, ESTs, etc.) 
>when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else 
>those other programs will run.
>
>--Carson
>
>
>On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>
>>Hi Carson,
>>
>>Thank you for the message and your kind help. We tested maker2 by 
>>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>But it seemed maker2 started to launch all predictors again and it 
>>took long time to finish. I wonder if there is any way that we can 
>>directly get gene/mRNA/exons/CDS gff file without re-running maker2 to 
>>convert match/match_part features into gene/mRNA/exons/CDS.
>>
>>Thanks,
>>Xia
>>
>>-----Original Message-----
>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>Sent: Thursday, September 19, 2013 5:58 PM
>>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; 
>>maker-devel at yandell-lab.org
>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>
>>Hello Corban & Xia,
>>
>>Some scripts like gff3_preds2models are deprecated.  To get the same 
>>result as was offered by gff3_preds2models, just give your 
>>match/match_part features to pref_gff= in the maker_opts.ctl file, set 
>>keep_preds=1, and run with all other options and predictors turned off.
>>The final MAKER result will be your match/match_part features 
>>converted into gene/mRNA/exons/CDS.
>>
>>For functional annotation, you can use Interproscan, BLASTP against 
>>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO 
>>terms and proteins domains via the ipr_update_gff and iprscan2gff3 
>>scripts.  Then add putative gene functions via BLASTP to UniProt and 
>>maker_functional_fasta and maker_functional_gff scripts.
>>
>>Go ahead and take a look and that those tools and let me know if you 
>>have any questions or need help you configuring them.
>>
>>Thanks,
>>Carson
>>
>>
>>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>
>>>Hi  Corban & Xia,
>>>
>>>
>>>I've forwarded your question along to the MAKER_dev list, were you 
>>>can get speedy answers to your maker related questions. Thanks for 
>>>using MAKER.
>>>
>>>--mark
>>>
>>>
>>>Mark Yandell
>>>Professor of Human Genetics
>>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of 
>>>Human Genetics University of Utah
>>>15 North 2030 East, Room 2100
>>>Salt Lake City, UT 84112-5330
>>>ph:801-587-7707
>>>
>>>________________________________________
>>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>Sent: Thursday, September 19, 2013 11:49 AM
>>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>Subject: maker2 scripts for functional annotation
>>>
>>>Dr. Yandell,
>>>
>>>We were recently evaluating maker2 for annotation and going through 
>>>the maker tutorial from 2012.
>>>
>>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>>
>>>The tutorial makes references to some scripts that we couldn?t find 
>>>in the current release.  We were looking for scripts like 
>>>gff3_preds2models to convert match/match_part format into annotations 
>>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did 
>>>not have the most up to date version.
>>>
>>>In addition to getting accurate gene annotations, I was looking for a 
>>>solution to get functional assignments.  I see that there are some 
>>>scripts like maker_functional_fasta that may help, but I was 
>>>wondering what you would recommend.
>>>
>>>Thanks,
>>>
>>>Corban & Xia
>>>
>>>This communication is for use by the intended recipient and contains 
>>>information that may be Privileged, confidential or copyrighted under 
>>>applicable law. If you are not the intended recipient, you are hereby 
>>>formally notified that any use, copying or distribution of this 
>>>e-mail, in whole or in part, is strictly prohibited. Please notify 
>>>the sender by return e-mail and delete this e-mail from your system.
>>>Unless explicitly and conspicuously designated as "E-Contract 
>>>Intended", this e-mail does not constitute a contract offer, a 
>>>contract amendment, or an acceptance of a contract offer. This e-mail 
>>>does not constitute a consent to the use of sender's contact 
>>>information for direct marketing purposes or for transfers of data to 
>>>third parties.
>>>
>>>The dupont.com web address will continue in use for a transitional 
>>>period for communications sent or received on behalf of DuPont 
>>>Performance Coatings., which is not affiliated in any way with the 
>>>DuPont Company.
>>>
>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>>Korean
>>>
>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>r
>>>g
>>
>>
>>
>>This communication is for use by the intended recipient and contains 
>>information that may be Privileged, confidential or copyrighted under 
>>applicable law. If you are not the intended recipient, you are hereby 
>>formally notified that any use, copying or distribution of this 
>>e-mail, in whole or in part, is strictly prohibited. Please notify the 
>>sender by return e-mail and delete this e-mail from your system. 
>>Unless explicitly and conspicuously designated as "E-Contract 
>>Intended", this e-mail does not constitute a contract offer, a 
>>contract amendment, or an acceptance of a contract offer. This e-mail 
>>does not constitute a consent to the use of sender's contact 
>>information for direct marketing purposes or for transfers of data to third parties.
>>
>>The dupont.com<http://dupont.com/> web address will continue in use 
>>for a transitional period for communications sent or received on 
>>behalf of DuPont Performance Coatings., which is not affiliated in any 
>>way with the DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>Korean
>>
>>           http://www.DuPont.com/corp/email_disclaimer.html
>>
>
>
>
>This communication is for use by the intended recipient and contains 
>information that may be Privileged, confidential or copyrighted under 
>applicable law. If you are not the intended recipient, you are hereby 
>formally notified that any use, copying or distribution of this e-mail, 
>in whole or in part, is strictly prohibited. Please notify the sender 
>by return e-mail and delete this e-mail from your system. Unless 
>explicitly and conspicuously designated as "E-Contract Intended", this 
>e-mail does not constitute a contract offer, a contract amendment, or 
>an acceptance of a contract offer. This e-mail does not constitute a 
>consent to the use of sender's contact information for direct marketing 
>purposes or for transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for 
>a transitional period for communications sent or received on behalf of 
>DuPont Performance Coatings., which is not affiliated in any way with 
>the DuPont Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  
>Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>



This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
applicable law. If you are not the intended recipient, you are hereby
formally notified that any use, copying or distribution of this e-mail,
in whole or in part, is strictly prohibited. Please notify the sender by
return e-mail and delete this e-mail from your system. Unless explicitly
and conspicuously designated as "E-Contract Intended", this e-mail does
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of a contract offer. This e-mail does not constitute a consent to the
use of sender's contact information for direct marketing purposes or for
transfers of data to third parties.

The dupont.com<http://dupont.com/> web address will continue in use for a
transitional period for communications sent or received on behalf of DuPont
Performance Coatings., which is not affiliated in any way with the DuPont Company.

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From markwiz at us.ibm.com  Wed Oct  2 10:52:55 2013
From: markwiz at us.ibm.com (Mark Wisner)
Date: Wed, 2 Oct 2013 12:52:55 -0400
Subject: [maker-devel] Maker2 on IBM PowerLinux?
Message-ID: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>

IBMs PowerLinux is tuned for Big Data workloads. We have had queries for 
Maker2 on PowerLinux.
How do we work with Maker2 development to create a PowerLinux port.
Thanks,

Mark K. Wisner
Linux On Power ISV PM
IBM
3039 Cornwallis Rd
RTP, NC 27709
Cell 919-649-5813
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From barry.moore at genetics.utah.edu  Wed Oct  2 11:29:36 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Wed, 2 Oct 2013 11:29:36 -0600
Subject: [maker-devel] Maker2 on IBM PowerLinux?
In-Reply-To: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>
References: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>
Message-ID: <E59BC7E8-B562-4AD6-B4CF-C793329B688B@genetics.utah.edu>

Hi Mark,

Carson Holt is the primary Maker developer, but others of us may be able to help as well.  I've added e-mails for Carson, Michael Campbell, Mark Yandell and myself who are currently developers on the project.   You can feel free to contact this mailing list - or if the conversation is getting too far afield for general interest you can contact us off list and we will do whatever we can to help.  If you feel like you need to do some modification of MAKER code to optimize it for PowerLinux I'm happy to give you a branch on the subversion repo to work with and then we can work with you to merge these changes back to the trunk when you feel like you have some improvements that benefit PowerLinux (and all other) users.

Thanks very much for your interest in MAKER - your participation in the community is most welcome!

Barry

On Oct 2, 2013, at 10:52 AM, Mark Wisner wrote:

> IBMs PowerLinux is tuned for Big Data workloads. We have had queries for Maker2 on PowerLinux. 
> How do we work with Maker2 development to create a PowerLinux port. 
> Thanks,
> 
> Mark K. Wisner
> Linux On Power ISV PM
> IBM
> 3039 Cornwallis Rd
> RTP, NC 27709
> Cell 919-649-5813
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From carsonhh at gmail.com  Wed Oct  2 11:29:50 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 02 Oct 2013 13:29:50 -0400
Subject: [maker-devel] Maker2 on IBM PowerLinux?
In-Reply-To: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>
Message-ID: <CE71CD2E.F2D8%carsonhh@gmail.com>

MAKER is written in perl, so it can work pretty much anywhere you have perl.
It is more an issue of the tools MAKER uses.  If you can get SNAP, BLAST,
exonerate, etc. to run then MAKER should be no problem.

You can let MAKER try and install and configure any missing perl libraries
as well as external tools for you (this is by far the easiest way).  You
will need an internet connection.

cd ?/maker/src/
perl Build.PL               #say 'Y' to local installation of libraries and
'N' to MPI for now
./Build installdeps     #grabs missing perl libraries from the ether, and
installs them in  the .../maker/perl/ directory
./Build installers        #grabs missing tools from the ether, installs, and
configures them in the .../maker/exe/ directory
./Build install              #just installs maker


If you want to run via MPI, I'd recommend OpenMPI, and you will need to
rerun the 'perl Build.PL' and './Build install' steps (say yes to MPI this
time around).

Here are some variables you will likly have to add to your .bash_profile to
get openmpi to run with MAKER (you must add these and source the profile
before attempting to install with OpenMPI), otherwise compilation will not
work correctly (OpenMPI shared library issue).

#you need to set $OMPIHOME to OpenMPI's location here -->
export LD_PRELOAD=$OMPIHOME/lib/libmpi.so:$LD_PRELOAD


#this one just suppresses a warning -->
export OMPI_MCA_mpi_warn_on_fork=0


And on some systems you have to add this  ' -mca btl ^openib' to the mpiexec
command when I run maker.
Example-->
mpiexec -mca btl ^openib -n 20 maker

Thanks,
Carson


From:  Mark Wisner <markwiz at us.ibm.com>
Date:  Wednesday, October 2, 2013 12:52 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker2 on IBM PowerLinux?

IBMs PowerLinux is tuned for Big Data workloads. We have had queries for
Maker2 on PowerLinux.
How do we work with Maker2 development to create a PowerLinux port.
Thanks,

Mark K. Wisner
Linux On Power ISV PM
IBM
3039 Cornwallis Rd
RTP, NC 27709
Cell 919-649-5813
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From barry.moore at genetics.utah.edu  Wed Oct  2 11:21:29 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Wed, 2 Oct 2013 11:21:29 -0600
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
References: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE709D72.EF15%carsonhh@gmail.com>
	<AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
Message-ID: <E9DC8DC1-8E1F-42E7-94CC-5D58EF0A1F21@genetics.utah.edu>

Hi Xia,

You can use EST evidence from other strains/species.  The considerations are as follows:  When you pass EST (or mRNASeq based transcripts) evidence MAKER uses blastn to align those with alignment parameters that assume they sequences will align easily with almost perfect identity - this is fast.  If you use EST/mRNA evidence from another species MAKER uses tblastx to compare the RNA evidence to the assembly, both translated into protein space - this works fine, but it is slow and often doesn't get you much more evidence than you could have gotten from proteins as evidence.  If you believe that you're other strain should have very little divergence in sequence at the nt level then you could experiment with passing EST/mRNA evidence as est in the control file.  Consider this an experiment, do it on a few contigs and examine the results carefully and skeptically.  If it works well, that would be the way to go because you've get better UTRs, but if it doesn't you'll see that you get little support for models because sequence divergence was too much for good alignment.  In that case you'll need to use alt_est and this will be slower and you'll likely get little in the way of support for UTRs - in this case as well, do a few contigs and examine the output carefully to see if the additional alignment time with tblastx is worth it in your case.

Barry


On Oct 2, 2013, at 8:40 AM, <Xia.Cao at dupont.com>
 wrote:

> Hi Carson,
> 
> Thank you for your quick and kind reply. One more question here. If we don't have EST evidence for the strain we sequenced/assembled, will it be ok to provide some EST evidence that is from some other strains which are close to the one we are trying to annotate? Could you please let us know how this will affect performance of maker2?
> 
> Thank you again.
> 
> Best,
> Xia
> 
> -----Original Message-----
> From: Carson Holt [mailto:carsonhh at gmail.com] 
> Sent: Wednesday, October 02, 2013 10:15 AM
> To: CAO, XIA
> Cc: myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org
> Subject: Re: [maker-devel] maker2 scripts for functional annotation
> 
> It still works, but it will be reduced.  Without ESTs you won't get any UTR prediction, also you will be limited by how well the protein set matches to the genes.  If you use the protein set of a close relative you will capture most things.  You will probably capture 80-95% of what you would by also including ESTs.  It all depending on how different the species in the proteins evidence file are compared to the the species being annotated.
> 
> --Carson
> 
> On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
> 
>> Hi Carson,
>> 
>> Thank you for your message and your kind help. Now conversion from 
>> match/match_part to gene/mRNA/exons/CDS works well after blanking out 
>> some options in control file.
>> 
>> I have one more question about maker2. In case we don't have EST 
>> evidence (set of ESTs or assembled mRNA-seq in fasta format) for a 
>> genome, does
>> maker2 function? If it does function, could you please let me know the 
>> performance of maker2 without providing EST evidence compared to the 
>> one with EST evidence?
>> 
>> Thank you  again and I look forward to hearing from you.
>> 
>> Best,
>> Xia
>> 
>> 
>> 
>> 
>> -----Original Message-----
>> From: Carson Holt [mailto:carsonhh at gmail.com]
>> Sent: Wednesday, September 25, 2013 10:36 AM
>> To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; 
>> maker-devel at yandell-lab.org
>> Subject: Re: [maker-devel] maker2 scripts for functional annotation
>> 
>> If it is launching predictors then you have snap hmm or 
>> augustus_species set.  You ned to blank out all other options in the 
>> control files (including repeat masking options, proteins, ESTs, etc.) 
>> when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else 
>> those other programs will run.
>> 
>> --Carson
>> 
>> 
>> On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>> 
>>> Hi Carson,
>>> 
>>> Thank you for the message and your kind help. We tested maker2 by 
>>> setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>> But it seemed maker2 started to launch all predictors again and it 
>>> took long time to finish. I wonder if there is any way that we can 
>>> directly get gene/mRNA/exons/CDS gff file without re-running maker2 to 
>>> convert match/match_part features into gene/mRNA/exons/CDS.
>>> 
>>> Thanks,
>>> Xia
>>> 
>>> -----Original Message-----
>>> From: Carson Holt [mailto:carsonhh at gmail.com]
>>> Sent: Thursday, September 19, 2013 5:58 PM
>>> To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; 
>>> maker-devel at yandell-lab.org
>>> Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>> 
>>> Hello Corban & Xia,
>>> 
>>> Some scripts like gff3_preds2models are deprecated.  To get the same 
>>> result as was offered by gff3_preds2models, just give your 
>>> match/match_part features to pref_gff= in the maker_opts.ctl file, set 
>>> keep_preds=1, and run with all other options and predictors turned off.
>>> The final MAKER result will be your match/match_part features 
>>> converted into gene/mRNA/exons/CDS.
>>> 
>>> For functional annotation, you can use Interproscan, BLASTP against 
>>> UniProt, or BALST2GO.  My preference is to use InterProScan to add GO 
>>> terms and proteins domains via the ipr_update_gff and iprscan2gff3 
>>> scripts.  Then add putative gene functions via BLASTP to UniProt and 
>>> maker_functional_fasta and maker_functional_gff scripts.
>>> 
>>> Go ahead and take a look and that those tools and let me know if you 
>>> have any questions or need help you configuring them.
>>> 
>>> Thanks,
>>> Carson
>>> 
>>> 
>>> On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>> 
>>>> Hi  Corban & Xia,
>>>> 
>>>> 
>>>> I've forwarded your question along to the MAKER_dev list, were you 
>>>> can get speedy answers to your maker related questions. Thanks for 
>>>> using MAKER.
>>>> 
>>>> --mark
>>>> 
>>>> 
>>>> Mark Yandell
>>>> Professor of Human Genetics
>>>> H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of 
>>>> Human Genetics University of Utah
>>>> 15 North 2030 East, Room 2100
>>>> Salt Lake City, UT 84112-5330
>>>> ph:801-587-7707
>>>> 
>>>> ________________________________________
>>>> From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>> Sent: Thursday, September 19, 2013 11:49 AM
>>>> To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>> Subject: maker2 scripts for functional annotation
>>>> 
>>>> Dr. Yandell,
>>>> 
>>>> We were recently evaluating maker2 for annotation and going through 
>>>> the maker tutorial from 2012.
>>>> 
>>>> http://gmod.org/wiki/MAKER_Tutorial_2012
>>>> 
>>>> The tutorial makes references to some scripts that we couldn?t find 
>>>> in the current release.  We were looking for scripts like 
>>>> gff3_preds2models to convert match/match_part format into annotations 
>>>> with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did 
>>>> not have the most up to date version.
>>>> 
>>>> In addition to getting accurate gene annotations, I was looking for a 
>>>> solution to get functional assignments.  I see that there are some 
>>>> scripts like maker_functional_fasta that may help, but I was 
>>>> wondering what you would recommend.
>>>> 
>>>> Thanks,
>>>> 
>>>> Corban & Xia
>>>> 
>>>> This communication is for use by the intended recipient and contains 
>>>> information that may be Privileged, confidential or copyrighted under 
>>>> applicable law. If you are not the intended recipient, you are hereby 
>>>> formally notified that any use, copying or distribution of this 
>>>> e-mail, in whole or in part, is strictly prohibited. Please notify 
>>>> the sender by return e-mail and delete this e-mail from your system.
>>>> Unless explicitly and conspicuously designated as "E-Contract 
>>>> Intended", this e-mail does not constitute a contract offer, a 
>>>> contract amendment, or an acceptance of a contract offer. This e-mail 
>>>> does not constitute a consent to the use of sender's contact 
>>>> information for direct marketing purposes or for transfers of data to 
>>>> third parties.
>>>> 
>>>> The dupont.com web address will continue in use for a transitional 
>>>> period for communications sent or received on behalf of DuPont 
>>>> Performance Coatings., which is not affiliated in any way with the 
>>>> DuPont Company.
>>>> 
>>>> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>>> Korean
>>>> 
>>>>         http://www.DuPont.com/corp/email_disclaimer.html
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>> r
>>>> g
>>> 
>>> 
>>> 
>>> This communication is for use by the intended recipient and contains 
>>> information that may be Privileged, confidential or copyrighted under 
>>> applicable law. If you are not the intended recipient, you are hereby 
>>> formally notified that any use, copying or distribution of this 
>>> e-mail, in whole or in part, is strictly prohibited. Please notify the 
>>> sender by return e-mail and delete this e-mail from your system. 
>>> Unless explicitly and conspicuously designated as "E-Contract 
>>> Intended", this e-mail does not constitute a contract offer, a 
>>> contract amendment, or an acceptance of a contract offer. This e-mail 
>>> does not constitute a consent to the use of sender's contact 
>>> information for direct marketing purposes or for transfers of data to third parties.
>>> 
>>> The dupont.com<http://dupont.com/> web address will continue in use 
>>> for a transitional period for communications sent or received on 
>>> behalf of DuPont Performance Coatings., which is not affiliated in any 
>>> way with the DuPont Company.
>>> 
>>> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>> Korean
>>> 
>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>> 
>> 
>> 
>> 
>> This communication is for use by the intended recipient and contains 
>> information that may be Privileged, confidential or copyrighted under 
>> applicable law. If you are not the intended recipient, you are hereby 
>> formally notified that any use, copying or distribution of this e-mail, 
>> in whole or in part, is strictly prohibited. Please notify the sender 
>> by return e-mail and delete this e-mail from your system. Unless 
>> explicitly and conspicuously designated as "E-Contract Intended", this 
>> e-mail does not constitute a contract offer, a contract amendment, or 
>> an acceptance of a contract offer. This e-mail does not constitute a 
>> consent to the use of sender's contact information for direct marketing 
>> purposes or for transfers of data to third parties.
>> 
>> The dupont.com<http://dupont.com/> web address will continue in use for 
>> a transitional period for communications sent or received on behalf of 
>> DuPont Performance Coatings., which is not affiliated in any way with 
>> the DuPont Company.
>> 
>> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  
>> Korean
>> 
>>          http://www.DuPont.com/corp/email_disclaimer.html
>> 
> 
> 
> 
> This communication is for use by the intended recipient and contains
> information that may be Privileged, confidential or copyrighted under
> applicable law. If you are not the intended recipient, you are hereby
> formally notified that any use, copying or distribution of this e-mail,
> in whole or in part, is strictly prohibited. Please notify the sender by
> return e-mail and delete this e-mail from your system. Unless explicitly
> and conspicuously designated as "E-Contract Intended", this e-mail does
> not constitute a contract offer, a contract amendment, or an acceptance
> of a contract offer. This e-mail does not constitute a consent to the
> use of sender's contact information for direct marketing purposes or for
> transfers of data to third parties.
> 
> The dupont.com<http://dupont.com/> web address will continue in use for a
> transitional period for communications sent or received on behalf of DuPont
> Performance Coatings., which is not affiliated in any way with the DuPont Company.
> 
> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean
> 
>           http://www.DuPont.com/corp/email_disclaimer.html
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From Xia.Cao at dupont.com  Wed Oct  2 11:51:26 2013
From: Xia.Cao at dupont.com (Xia.Cao at dupont.com)
Date: Wed, 2 Oct 2013 17:51:26 +0000
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <E9DC8DC1-8E1F-42E7-94CC-5D58EF0A1F21@genetics.utah.edu>
References: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE709D72.EF15%carsonhh@gmail.com>
	<AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
	<E9DC8DC1-8E1F-42E7-94CC-5D58EF0A1F21@genetics.utah.edu>
Message-ID: <AAF36CDE29C45F45AE125A1D13F5D675AE2175@033-CH1MPN2-063.033d.mgd.msft.net>

Hi Barry,

Thank you very much for the message and suggestions. It's really helpful to us.  We will do some tests to see how we can take advantage of Maker2  to produce high-quality gene models from our assembled genome.

Thank you again,
Xia


From: Barry Moore [mailto:barry.moore at genetics.utah.edu]
Sent: Wednesday, October 02, 2013 1:21 PM
To: CAO, XIA
Cc: carsonhh at gmail.com; maker-devel at yandell-lab.org; RIVERA, CORBAN GREGORY
Subject: Re: [maker-devel] maker2 scripts for functional annotation

Hi Xia,

You can use EST evidence from other strains/species.  The considerations are as follows:  When you pass EST (or mRNASeq based transcripts) evidence MAKER uses blastn to align those with alignment parameters that assume they sequences will align easily with almost perfect identity - this is fast.  If you use EST/mRNA evidence from another species MAKER uses tblastx to compare the RNA evidence to the assembly, both translated into protein space - this works fine, but it is slow and often doesn't get you much more evidence than you could have gotten from proteins as evidence.  If you believe that you're other strain should have very little divergence in sequence at the nt level then you could experiment with passing EST/mRNA evidence as est in the control file.  Consider this an experiment, do it on a few contigs and examine the results carefully and skeptically.  If it works well, that would be the way to go because you've get better UTRs, but if it doesn't you'll see that you get little support for models because sequence divergence was too much for good alignment.  In that case you'll need to use alt_est and this will be slower and you'll likely get little in the way of support for UTRs - in this case as well, do a few contigs and examine the output carefully to see if the additional alignment time with tblastx is worth it in your case.

Barry


On Oct 2, 2013, at 8:40 AM, <Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>>
 wrote:


Hi Carson,

Thank you for your quick and kind reply. One more question here. If we don't have EST evidence for the strain we sequenced/assembled, will it be ok to provide some EST evidence that is from some other strains which are close to the one we are trying to annotate? Could you please let us know how this will affect performance of maker2?

Thank you again.

Best,
Xia

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Wednesday, October 02, 2013 10:15 AM
To: CAO, XIA
Cc: myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker2 scripts for functional annotation

It still works, but it will be reduced.  Without ESTs you won't get any UTR prediction, also you will be limited by how well the protein set matches to the genes.  If you use the protein set of a close relative you will capture most things.  You will probably capture 80-95% of what you would by also including ESTs.  It all depending on how different the species in the proteins evidence file are compared to the the species being annotated.

--Carson

On 10/1/13 3:00 PM, "Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>" <Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>> wrote:


Hi Carson,

Thank you for your message and your kind help. Now conversion from
match/match_part to gene/mRNA/exons/CDS works well after blanking out
some options in control file.

I have one more question about maker2. In case we don't have EST
evidence (set of ESTs or assembled mRNA-seq in fasta format) for a
genome, does
maker2 function? If it does function, could you please let me know the
performance of maker2 without providing EST evidence compared to the
one with EST evidence?

Thank you  again and I look forward to hearing from you.

Best,
Xia




-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Wednesday, September 25, 2013 10:36 AM
To: CAO, XIA; myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>; RIVERA, CORBAN GREGORY;
maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker2 scripts for functional annotation

If it is launching predictors then you have snap hmm or
augustus_species set.  You ned to blank out all other options in the
control files (including repeat masking options, proteins, ESTs, etc.)
when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else
those other programs will run.

--Carson


On 9/25/13 10:31 AM, "Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>" <Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>> wrote:

Hi Carson,

Thank you for the message and your kind help. We tested maker2 by
setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
But it seemed maker2 started to launch all predictors again and it
took long time to finish. I wonder if there is any way that we can
directly get gene/mRNA/exons/CDS gff file without re-running maker2 to
convert match/match_part features into gene/mRNA/exons/CDS.

Thanks,
Xia

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Thursday, September 19, 2013 5:58 PM
To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY;
maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker2 scripts for functional annotation

Hello Corban & Xia,

Some scripts like gff3_preds2models are deprecated.  To get the same
result as was offered by gff3_preds2models, just give your
match/match_part features to pref_gff= in the maker_opts.ctl file, set
keep_preds=1, and run with all other options and predictors turned off.
The final MAKER result will be your match/match_part features
converted into gene/mRNA/exons/CDS.

For functional annotation, you can use Interproscan, BLASTP against
UniProt, or BALST2GO.  My preference is to use InterProScan to add GO
terms and proteins domains via the ipr_update_gff and iprscan2gff3
scripts.  Then add putative gene functions via BLASTP to UniProt and
maker_functional_fasta and maker_functional_gff scripts.

Go ahead and take a look and that those tools and let me know if you
have any questions or need help you configuring them.

Thanks,
Carson


On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>> wrote:

Hi  Corban & Xia,


I've forwarded your question along to the MAKER_dev list, were you
can get speedy answers to your maker related questions. Thanks for
using MAKER.

--mark


Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of
Human Genetics University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com> [Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>]
Sent: Thursday, September 19, 2013 11:49 AM
To: Mark Yandell; Corban-Gregory.Rivera at dupont.com<mailto:Corban-Gregory.Rivera at dupont.com>
Subject: maker2 scripts for functional annotation

Dr. Yandell,

We were recently evaluating maker2 for annotation and going through
the maker tutorial from 2012.

http://gmod.org/wiki/MAKER_Tutorial_2012

The tutorial makes references to some scripts that we couldn?t find
in the current release.  We were looking for scripts like
gff3_preds2models to convert match/match_part format into annotations
with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did
not have the most up to date version.

In addition to getting accurate gene annotations, I was looking for a
solution to get functional assignments.  I see that there are some
scripts like maker_functional_fasta that may help, but I was
wondering what you would recommend.

Thanks,

Corban & Xia

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--------------------------------------------
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From cjfields at illinois.edu  Thu Oct  3 12:44:07 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 3 Oct 2013 18:44:07 +0000
Subject: [maker-devel] NFSLock problem
Message-ID: <B9943BBA-BEFF-4B23-A6B8-7581247F3C95@illinois.edu>

I have a MAKER job running that seems to be stalled on a failed scaffold.  It's running via MPI (MAKER v2.28, openMPI 1.6.3), that appears to have worked successfully for the most part.  This is a run that only uses transcriptome and protein information in order to get a decent dseat of 

The failed scaffold seems to be holding the job from completion.  There does seem to be changes, but mainly they are on the NFSLock files:

./.NFSLock.gi_lock.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.282.start.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.281.end.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.281.end.blastn.holdover.NFSLock.STACK

Everything else seems to have completed.  

I have seen a few issues re: NFS locking problems, would this be related?  Should I stop the job?  

We're running GPFS for our NFS.  Here's 'mount':

-system-specific-4.1$ mount
/dev/sda5 on / type ext4 (rw)
proc on /proc type proc (rw)
sysfs on /sys type sysfs (rw)
devpts on /dev/pts type devpts (rw,gid=5,mode=620)
tmpfs on /dev/shm type tmpfs (rw)
/dev/sda1 on /boot type ext4 (rw)
/dev/sdb1 on /export type ext4 (rw)
/dev/sda2 on /var type ext4 (rw)
tmpfs on /var/lib/ganglia/rrds type tmpfs (rw,size=6180842000,gid=99,uid=99)
none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
nfsd on /proc/fs/nfsd type nfsd (rw)
/dev/IGBHOME0 on /home type gpfs (rw,mtime,dev=IGBHOME0)
128.174.124.79:/shares/group on /archive/group type nfs (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,proto=tcp,mountproto=tcp,addr=128.174.124.79)
128.174.124.79:/shares/CBC on /archive/CBC type nfs (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,proto=tcp,mountproto=tcp,addr=128.174.124.79)

chris


From carsonhh at gmail.com  Thu Oct  3 12:45:37 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 03 Oct 2013 14:45:37 -0400
Subject: [maker-devel] NFSLock problem
In-Reply-To: <B9943BBA-BEFF-4B23-A6B8-7581247F3C95@illinois.edu>
Message-ID: <CE73336F.F347%carsonhh@gmail.com>

Stop the job and restart it.  No need to delete anything.  Just restart it.

Thanks,
Carson


On 10/3/13 2:44 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

>I have a MAKER job running that seems to be stalled on a failed scaffold.
> It's running via MPI (MAKER v2.28, openMPI 1.6.3), that appears to have
>worked successfully for the most part.  This is a run that only uses
>transcriptome and protein information in order to get a decent dseat of
>
>The failed scaffold seems to be holding the job from completion.  There
>does seem to be changes, but mainly they are on the NFSLock files:
>
>./.NFSLock.gi_lock.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.282.start.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.end.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.end.blastn.holdover.NFSLock.STACK
>
>Everything else seems to have completed.
>
>I have seen a few issues re: NFS locking problems, would this be related?
> Should I stop the job?
>
>We're running GPFS for our NFS.  Here's 'mount':
>
>-system-specific-4.1$ mount
>/dev/sda5 on / type ext4 (rw)
>proc on /proc type proc (rw)
>sysfs on /sys type sysfs (rw)
>devpts on /dev/pts type devpts (rw,gid=5,mode=620)
>tmpfs on /dev/shm type tmpfs (rw)
>/dev/sda1 on /boot type ext4 (rw)
>/dev/sdb1 on /export type ext4 (rw)
>/dev/sda2 on /var type ext4 (rw)
>tmpfs on /var/lib/ganglia/rrds type tmpfs
>(rw,size=6180842000,gid=99,uid=99)
>none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
>sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
>nfsd on /proc/fs/nfsd type nfsd (rw)
>/dev/IGBHOME0 on /home type gpfs (rw,mtime,dev=IGBHOME0)
>128.174.124.79:/shares/group on /archive/group type nfs
>(rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>roto=tcp,mountproto=tcp,addr=128.174.124.79)
>128.174.124.79:/shares/CBC on /archive/CBC type nfs
>(rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>roto=tcp,mountproto=tcp,addr=128.174.124.79)
>
>chris
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From cjfields at illinois.edu  Thu Oct  3 20:45:29 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 4 Oct 2013 02:45:29 +0000
Subject: [maker-devel] NFSLock problem
In-Reply-To: <CE73336F.F347%carsonhh@gmail.com>
References: <CE73336F.F347%carsonhh@gmail.com>
Message-ID: <EB3895BA-F1EF-4F14-813F-233D1B4269AB@illinois.edu>

Carson,

Took a couple of restarts but finally processed through.  I saw a prior email on the mail list where you mentioned this could be due to failed jobs hanging things up; I may set up my next job to allow one processor for logging into the nodes in case there is a similar problem, maybe try to track this down.

chris

On Oct 3, 2013, at 1:45 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Stop the job and restart it.  No need to delete anything.  Just restart it.
> 
> Thanks,
> Carson
> 
> 
> On 10/3/13 2:44 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> 
>> I have a MAKER job running that seems to be stalled on a failed scaffold.
>> It's running via MPI (MAKER v2.28, openMPI 1.6.3), that appears to have
>> worked successfully for the most part.  This is a run that only uses
>> transcriptome and protein information in order to get a decent dseat of
>> 
>> The failed scaffold seems to be holding the job from completion.  There
>> does seem to be changes, but mainly they are on the NFSLock files:
>> 
>> ./.NFSLock.gi_lock.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.282.start.blastn.holdover.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.281.end.blastn.holdover.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.281.end.blastn.holdover.NFSLock.STACK
>> 
>> Everything else seems to have completed.
>> 
>> I have seen a few issues re: NFS locking problems, would this be related?
>> Should I stop the job?
>> 
>> We're running GPFS for our NFS.  Here's 'mount':
>> 
>> -system-specific-4.1$ mount
>> /dev/sda5 on / type ext4 (rw)
>> proc on /proc type proc (rw)
>> sysfs on /sys type sysfs (rw)
>> devpts on /dev/pts type devpts (rw,gid=5,mode=620)
>> tmpfs on /dev/shm type tmpfs (rw)
>> /dev/sda1 on /boot type ext4 (rw)
>> /dev/sdb1 on /export type ext4 (rw)
>> /dev/sda2 on /var type ext4 (rw)
>> tmpfs on /var/lib/ganglia/rrds type tmpfs
>> (rw,size=6180842000,gid=99,uid=99)
>> none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
>> sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
>> nfsd on /proc/fs/nfsd type nfsd (rw)
>> /dev/IGBHOME0 on /home type gpfs (rw,mtime,dev=IGBHOME0)
>> 128.174.124.79:/shares/group on /archive/group type nfs
>> (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>> roto=tcp,mountproto=tcp,addr=128.174.124.79)
>> 128.174.124.79:/shares/CBC on /archive/CBC type nfs
>> (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>> roto=tcp,mountproto=tcp,addr=128.174.124.79)
>> 
>> chris
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 




From felix.bemm at uni-wuerzburg.de  Fri Oct  4 01:10:08 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Fri, 04 Oct 2013 09:10:08 +0200
Subject: [maker-devel] Contigs failing - could not make datastore directory
Message-ID: <524E69D0.1090905@uni-wuerzburg.de>

Hi,

I have a problem with Contigs failing like this:

examining contents of the fasta file and run log
ERROR: could not make datastore directory
--> rank=11, hostname=r5n04
ERROR: Failed while examining contents of the fasta file and run log
ERROR: Chunk failed at level:0, tier_type:0
FAILED CONTIG:MA_gen_v8.05_c31675

There is enough space available on both the storage device and the tmp 
device that is being used. The datastore log files looks like this:

MA_gen_v8.05_c1149              FAILED
MA_gen_v8.05_c1153              FAILED
MA_gen_v8.05_c1154              FAILED
MA_gen_v8.05_c1155              FAILED
MA_gen_v8.05_c1156              FAILED

Since there is no datastore for this contigs, I can not provide any more 
informationen. Approx. 1/3 of the contigs were annotated, after that 
maker started to fail. It kept running for a while and finishing some of 
the contigs in the second or third try like this:

MA_gen_v8.05_c4443		FAILED
MA_gen_v8.05_c4443		FAILED
MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	STARTED
MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/ 
FINISHED

Any ideas what can cause this problems?

Best regards
Felix

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Fri Oct  4 12:15:35 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 04 Oct 2013 14:15:35 -0400
Subject: [maker-devel] Contigs failing - could not make datastore
 directory
In-Reply-To: <524E69D0.1090905@uni-wuerzburg.de>
Message-ID: <CE747D9A.F599%carsonhh@gmail.com>

Let me know what you find.  With some failures it's hard to identify the
problem especially with long running processes, which is why I made MAKER
restartable, so you can at least get completion by just launching again.

--Carson


On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi,
>
>I have a problem with Contigs failing like this:
>
>examining contents of the fasta file and run log
>ERROR: could not make datastore directory
>--> rank=11, hostname=r5n04
>ERROR: Failed while examining contents of the fasta file and run log
>ERROR: Chunk failed at level:0, tier_type:0
>FAILED CONTIG:MA_gen_v8.05_c31675
>
>There is enough space available on both the storage device and the tmp
>device that is being used. The datastore log files looks like this:
>
>MA_gen_v8.05_c1149              FAILED
>MA_gen_v8.05_c1153              FAILED
>MA_gen_v8.05_c1154              FAILED
>MA_gen_v8.05_c1155              FAILED
>MA_gen_v8.05_c1156              FAILED
>
>Since there is no datastore for this contigs, I can not provide any more
>informationen. Approx. 1/3 of the contigs were annotated, after that
>maker started to fail. It kept running for a while and finishing some of
>the contigs in the second or third try like this:
>
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	START
>ED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>FINISHED
>
>Any ideas what can cause this problems?
>
>Best regards
>Felix
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Fri Oct  4 12:21:42 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 04 Oct 2013 14:21:42 -0400
Subject: [maker-devel] Contigs failing - could not make datastore
 directory
In-Reply-To: <524E69D0.1090905@uni-wuerzburg.de>
Message-ID: <CE743B26.F369%carsonhh@gmail.com>

Hi Felix,

There are other potential issues as well, for example a file quota limit
set by your administrator or full local /tmp which will be unique to each
node and cannot be queried directly from the root node on a cluster.  On a
cluster one node may also not have the NFS location mounted.  Or it could
be system related, for example on ibrix NFS mounted systems you can get a
weird filesystem issue with ghost files and directories when using MAKER
that can neither be created nor deleted.  Try running the failed contigs
in a different directory (even if it's on the same disk).  Also what
version of MAKER are you using?

--Carson



On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi,
>
>I have a problem with Contigs failing like this:
>
>examining contents of the fasta file and run log
>ERROR: could not make datastore directory
>--> rank=11, hostname=r5n04
>ERROR: Failed while examining contents of the fasta file and run log
>ERROR: Chunk failed at level:0, tier_type:0
>FAILED CONTIG:MA_gen_v8.05_c31675
>
>There is enough space available on both the storage device and the tmp
>device that is being used. The datastore log files looks like this:
>
>MA_gen_v8.05_c1149              FAILED
>MA_gen_v8.05_c1153              FAILED
>MA_gen_v8.05_c1154              FAILED
>MA_gen_v8.05_c1155              FAILED
>MA_gen_v8.05_c1156              FAILED
>
>Since there is no datastore for this contigs, I can not provide any more
>informationen. Approx. 1/3 of the contigs were annotated, after that
>maker started to fail. It kept running for a while and finishing some of
>the contigs in the second or third try like this:
>
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	START
>ED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>FINISHED
>
>Any ideas what can cause this problems?
>
>Best regards
>Felix
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From felix.bemm at uni-wuerzburg.de  Sat Oct  5 08:09:15 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Sat, 05 Oct 2013 16:09:15 +0200
Subject: [maker-devel] Contigs failing - could not make datastore
	directory
In-Reply-To: <CE743B26.F369%carsonhh@gmail.com>
References: <CE743B26.F369%carsonhh@gmail.com>
Message-ID: <52501D8B.2060301@uni-wuerzburg.de>

Hi Carson,

there is definitely no quota neither a full local tmp device. I changed 
to another tmp device, which is unfortunately residing on nfs but now it 
seems to work. I am using the latest version of maker (2.28). The 
complete job is running on a single machine with 32 mpi threads.

Bests
Felix

Am 04.10.2013 20:21, schrieb Carson Holt:
> Hi Felix,
>
> There are other potential issues as well, for example a file quota limit
> set by your administrator or full local /tmp which will be unique to each
> node and cannot be queried directly from the root node on a cluster.  On a
> cluster one node may also not have the NFS location mounted.  Or it could
> be system related, for example on ibrix NFS mounted systems you can get a
> weird filesystem issue with ghost files and directories when using MAKER
> that can neither be created nor deleted.  Try running the failed contigs
> in a different directory (even if it's on the same disk).  Also what
> version of MAKER are you using?
>
> --Carson
>
>
>
> On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>> Hi,
>>
>> I have a problem with Contigs failing like this:
>>
>> examining contents of the fasta file and run log
>> ERROR: could not make datastore directory
>> --> rank=11, hostname=r5n04
>> ERROR: Failed while examining contents of the fasta file and run log
>> ERROR: Chunk failed at level:0, tier_type:0
>> FAILED CONTIG:MA_gen_v8.05_c31675
>>
>> There is enough space available on both the storage device and the tmp
>> device that is being used. The datastore log files looks like this:
>>
>> MA_gen_v8.05_c1149              FAILED
>> MA_gen_v8.05_c1153              FAILED
>> MA_gen_v8.05_c1154              FAILED
>> MA_gen_v8.05_c1155              FAILED
>> MA_gen_v8.05_c1156              FAILED
>>
>> Since there is no datastore for this contigs, I can not provide any more
>> informationen. Approx. 1/3 of the contigs were annotated, after that
>> maker started to fail. It kept running for a while and finishing some of
>> the contigs in the second or third try like this:
>>
>> MA_gen_v8.05_c4443		FAILED
>> MA_gen_v8.05_c4443		FAILED
>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	START
>> ED
>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>> FINISHED
>>
>> Any ideas what can cause this problems?
>>
>> Best regards
>> Felix
>>
>> --
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From jfierst at uoregon.edu  Fri Oct  4 11:06:36 2013
From: jfierst at uoregon.edu (Janna Fierst)
Date: Fri, 4 Oct 2013 10:06:36 -0700
Subject: [maker-devel] Fwd:  exon/intron boundaries
In-Reply-To: <CAGoyurYe_c3Cd6KK-z0t0WqYmGGh5VQsSZXo9_=Lt9MGMSz=kA@mail.gmail.com>
References: <CAGoyuraVoRp94vbk_mb1qLzELeXSbeybGwkvgFx-6smEVt_DcQ@mail.gmail.com>
	<CE411E31.998A%carsonhh@gmail.com>
	<CAGoyurYe_c3Cd6KK-z0t0WqYmGGh5VQsSZXo9_=Lt9MGMSz=kA@mail.gmail.com>
Message-ID: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>

Hi,

thanks for your reply- I have been going through our annotations in detail
and trying different parameter sets, and I think I have identified what is
going on but I'm not sure how to set the MAKER2 parameters for our
situation. We are working with a species of Caenorhabditid worm and there
are long gene-dense blocks that are being incorrectly annotated as large
single genes instead of several smaller closely spaced genes. The protein
alignments (tblastx and protein2genome) show very clearly where the
exon/intron boundaries are and in most cases agree with the augustus
predictions. The assembled cufflinks output (through blastn, est2genome and
est_gff:cufflinks) does not agree in some locations; I think this may be
because in some cases the UTR nearly overlaps adjacent genes.

I have included a screenshot of an annotated region viewed in apollo to try
to show this. The large gene in the middle is actually 7 different genes
that are extremely close together and MAKER2 is collapsing them into a
single gene. I tried running without any RNASeq/cufflinks data and MAKER2
annotates the region as two genes instead of one, but I can't get it to
recognize the 7 as different genes. I have retrained SNAP but we have not
been able to successfully train Augustus, we are currently using the
default caenhorhabditis species model. I also included a species specific
repeat library. I tried setting correct_est_fusion=1 and reducing
pred_flank but these changes appear to really alter the annotations and we
end up annotating almost nothing. I also tried setting est2genome=0 to
decrease the influence of the cufflinks assembly but it didn't appear to
help. There are some very large introns in these genes so I haven't tried
yet decreasing the maximum intron size because I'm concerned this may
generate too many split genes instead of our current merged gene problem.
Thanks for your help, any advice is greatly appreciated! -Janna Fierst


On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Are you getting gene fusions or just more exons?  Gene fusions can be
> reduced by setting correct_est_fusion=1, or reducing pred_flank, although
> reducing pred_flank can cause other issues (but those generally only appear
> if setting the value below below 150).  Also if you have the maximum intron
> size set to high (split_hit option), you may also be generating bridging
> alignments that make evidence align across distant paralogous genes as well
> (this can result in gene merging)
>
> You should also look at your results manually in a viewer like Apollo.
>  Then see if the extra exons are supported by something such as protein
> alignments from another species.  If this is the case, you may have a
> poorly annotated protein set that is being used as evidence that is
> carrying over it's erroneous exons into the species you are annotating.  If
> the extra  exons are supported by EST evidence, then perhaps you should try
> and rebuild the EST assembly (for example trinity has an option to use a
> Jarccardian similarity coefficient to avoid fusing transcripts).
>
> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
> produce any of the models itself (it is a pipeline not a predictor).  The
> models are all generated using these other algorithms, MAKER just feeds
> them hints based on protein and transcript alignments, so making sure
> training is sufficient is important for those programs to produce their
> best models.
>
> Finally make sure your repeat database is sufficient, you may need to
> generate a species specific repeat library using something like
> RepeatModeler.  Repeats can end up being included as extra exons in gene
> models because they may contain reading frames the do code for proteins
> (I.e. reverse transcriptases).
>
> If you have any questions on any of the above, just let us know.
>
> Thanks,
> Carson
>
>
> From: Janna Fierst <jfierst at uoregon.edu>
> Date: Monday, August 26, 2013 2:54 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] exon/intron boundaries
>
> Hi,
>
> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
> initial results appear fairly good but we seem to be be annotating too many
> exons for multiple genes. I was wondering which parameters should be tuned
> to change the threshold for exon/intron boundaries? Thanks for your help
> -Janna Fierst
>  _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From jfierst at uoregon.edu  Sat Oct  5 16:18:52 2013
From: jfierst at uoregon.edu (Janna Fierst)
Date: Sat, 5 Oct 2013 15:18:52 -0700
Subject: [maker-devel] Fwd:  exon/intron boundaries
In-Reply-To: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
References: <CAGoyuraVoRp94vbk_mb1qLzELeXSbeybGwkvgFx-6smEVt_DcQ@mail.gmail.com>
	<CE411E31.998A%carsonhh@gmail.com>
	<CAGoyurYe_c3Cd6KK-z0t0WqYmGGh5VQsSZXo9_=Lt9MGMSz=kA@mail.gmail.com>
	<CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
Message-ID: <CAGoyurYHu9ir90T2-xhBxDyv_xVY5=AGFHJJL3Fu0o2fxtvqOg@mail.gmail.com>

Hi,

thanks for your reply- I have been going through our annotations in detail
and trying different parameter sets, and I think I have identified what is
going on but I'm not sure how to set the MAKER2 parameters for our
situation. We are working with a species of Caenorhabditid worm and there
are long gene-dense blocks that are being incorrectly annotated as large
single genes instead of several smaller closely spaced genes. The protein
alignments (tblastx and protein2genome) show very clearly where the
exon/intron boundaries are and in most cases agree with the augustus
predictions. The assembled cufflinks output (through blastn, est2genome and
est_gff:cufflinks) does not agree in some locations; I think this may be
because in some cases the UTR nearly overlaps adjacent genes.

I have included a screenshot of an annotated region viewed in apollo to try
to show this. The large gene in the middle is actually 7 different genes
that are extremely close together and MAKER2 is collapsing them into a
single gene. I tried running without any RNASeq/cufflinks data and MAKER2
annotates the region as two genes instead of one, but I can't get it to
recognize the 7 as different genes. I have retrained SNAP but we have not
been able to successfully train Augustus, we are currently using the
default caenhorhabditis species model. I also included a species specific
repeat library. I tried setting correct_est_fusion=1 and reducing
pred_flank but these changes appear to really alter the annotations and we
end up annotating almost nothing. I also tried setting est2genome=0 to
decrease the influence of the cufflinks assembly but it didn't appear to
help. There are some very large introns in these genes so I haven't tried
yet decreasing the maximum intron size because I'm concerned this may
generate too many split genes instead of our current merged gene problem.
Thanks for your help, any advice is greatly appreciated! -Janna Fierst


On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Are you getting gene fusions or just more exons?  Gene fusions can be
> reduced by setting correct_est_fusion=1, or reducing pred_flank, although
> reducing pred_flank can cause other issues (but those generally only appear
> if setting the value below below 150).  Also if you have the maximum intron
> size set to high (split_hit option), you may also be generating bridging
> alignments that make evidence align across distant paralogous genes as well
> (this can result in gene merging)
>
> You should also look at your results manually in a viewer like Apollo.
>  Then see if the extra exons are supported by something such as protein
> alignments from another species.  If this is the case, you may have a
> poorly annotated protein set that is being used as evidence that is
> carrying over it's erroneous exons into the species you are annotating.  If
> the extra  exons are supported by EST evidence, then perhaps you should try
> and rebuild the EST assembly (for example trinity has an option to use a
> Jarccardian similarity coefficient to avoid fusing transcripts).
>
> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
> produce any of the models itself (it is a pipeline not a predictor).  The
> models are all generated using these other algorithms, MAKER just feeds
> them hints based on protein and transcript alignments, so making sure
> training is sufficient is important for those programs to produce their
> best models.
>
> Finally make sure your repeat database is sufficient, you may need to
> generate a species specific repeat library using something like
> RepeatModeler.  Repeats can end up being included as extra exons in gene
> models because they may contain reading frames the do code for proteins
> (I.e. reverse transcriptases).
>
> If you have any questions on any of the above, just let us know.
>
> Thanks,
> Carson
>
>
> From: Janna Fierst <jfierst at uoregon.edu>
> Date: Monday, August 26, 2013 2:54 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] exon/intron boundaries
>
> Hi,
>
> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
> initial results appear fairly good but we seem to be be annotating too many
> exons for multiple genes. I was wondering which parameters should be tuned
> to change the threshold for exon/intron boundaries? Thanks for your help
> -Janna Fierst
>  _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From myandell at genetics.utah.edu  Mon Oct  7 05:36:53 2013
From: myandell at genetics.utah.edu (Mark Yandell)
Date: Mon, 7 Oct 2013 11:36:53 +0000
Subject: [maker-devel] maker apollo error
In-Reply-To: <8687323557146056ef885dd8a1bf2ea4@buzonweb.us.es>
References: <8687323557146056ef885dd8a1bf2ea4@buzonweb.us.es>
Message-ID: <7A60AB257EFF2B48B1F4C814817EA05365E66B3C@mxb2.hg.genetics.utah.edu>


Hi Gabriel,

I've forwarded your request on to the MAKER email list...

cheers,

--mark

Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: ggpozo at us.es [ggpozo at us.es]
Sent: Monday, October 07, 2013 2:49 AM
To: Mark Yandell
Subject: maker apollo error

Dear Dr. Yandell,

First, thank you very much for provide us such a great tool as MAKER. I am traying to install it in my Linux system, everything is ok, however when I try to instal Apollo with ./Build apollo...

Downloading apollo...
--2013-10-07 10:45:37--  http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 302 Found
Localizaci?n: http://sourceforge.net/p/gmod/svn/ [siguiendo]
--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/
Resolviendo sourceforge.net... 216.34.181.60
Connecting to sourceforge.net|216.34.181.60|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 302 Found
Localizaci?n: http://sourceforge.net/p/gmod/svn/HEAD/tree/ [siguiendo]
--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/HEAD/tree/
Connecting to sourceforge.net|216.34.181.60|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 200 OK
Longitud: 37730 (37K) [text/html]
Saving to: `/home/maker/src/../exe/apollo.tar.gz'

100%[==================================================================================================================================>] 37.730      92,1K/s   in 0,4s

2013-10-07 10:45:40 (92,1 KB/s) - `/home/maker/src/../exe/apollo.tar.gz' saved [37730/37730]

Unpacking apollo tarball...

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now


ERROR: Failed installing apollo, now cleaning installation path...
You may need to install apollo manually.



It seems that the http direction  in locations file is wrong, Apollo has changed its version and now Apollo is integrated in Apolloweb, may be this the problem.



I would greatly appreciate any help you can give me.

Thank you very much.



Dr. Gabriel Gutierrez

Department of Genetcis

University of Seville

Spain




From carsonhh at gmail.com  Mon Oct  7 07:20:17 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 09:20:17 -0400
Subject: [maker-devel] Fwd:  exon/intron boundaries
In-Reply-To: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
Message-ID: <CE782A71.F621%carsonhh@gmail.com>

Hi Janna,

There are a couple of things to do.  Download the maker-2.29p-beta from the
lab website.  This includes some changes made to improve the performance of
correct_est_fusion.  Whenever using the correct_est_fusion option, this also
reduces the influence of ESTs on annotation.  So normally you would need to
increase your protein dataset, but given that you have supplied 3 nematode
species and all of UniProt already you should probably be fine. But there is
one last thing you can do.  Instead of using cufflinks, try using trinity to
assemble the ESTs.  There is a Jaccard clip option that reducing merging
caused by overlapping UTR.  Between the trinity and correct_est_fusion you
should be able to really reduce the effect of those ESTs.

If those changes don't work there is one last option.  If you take the MAKER
results and filter them for SNAP and Augustus ab initio results
(match/match_part in the GFF3), then you can pass those in to the pred_gff
options.  Then turn snaphmm and augustus_species off in the control files.
Basically what this will do is turn MAKER's hint based prediction off and
force it to filter the ab intio results and select directly models from
there.  Since the merging is being caused by bad hints (merged transcripts
from mRNAseq) this would reduce that effect.  You will still need
correct_est_fusion=1 though to trim UTR coming from the merged transcripts,
because even though MAEKR can't process hints to rerun SNAP and Augustus
this way, it will try and add UTR using the EST evidence.

--Carson


From:  Janna Fierst <jfierst at uoregon.edu>
Date:  Friday, October 4, 2013 1:06 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Fwd:  exon/intron boundaries

Hi,

thanks for your reply- I have been going through our annotations in detail
and trying different parameter sets, and I think I have identified what is
going on but I'm not sure how to set the MAKER2 parameters for our
situation. We are working with a species of Caenorhabditid worm and there
are long gene-dense blocks that are being incorrectly annotated as large
single genes instead of several smaller closely spaced genes. The protein
alignments (tblastx and protein2genome) show very clearly where the
exon/intron boundaries are and in most cases agree with the augustus
predictions. The assembled cufflinks output (through blastn, est2genome and
est_gff:cufflinks) does not agree in some locations; I think this may be
because in some cases the UTR nearly overlaps adjacent genes.

I have included a screenshot of an annotated region viewed in apollo to try
to show this. The large gene in the middle is actually 7 different genes
that are extremely close together and MAKER2 is collapsing them into a
single gene. I tried running without any RNASeq/cufflinks data and MAKER2
annotates the region as two genes instead of one, but I can't get it to
recognize the 7 as different genes. I have retrained SNAP but we have not
been able to successfully train Augustus, we are currently using the default
caenhorhabditis species model. I also included a species specific repeat
library. I tried setting correct_est_fusion=1 and reducing pred_flank but
these changes appear to really alter the annotations and we end up
annotating almost nothing. I also tried setting est2genome=0 to decrease the
influence of the cufflinks assembly but it didn't appear to help. There are
some very large introns in these genes so I haven't tried yet decreasing the
maximum intron size because I'm concerned this may generate too many split
genes instead of our current merged gene problem. Thanks for your help, any
advice is greatly appreciated! -Janna Fierst


On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:
> Are you getting gene fusions or just more exons?  Gene fusions can be reduced
> by setting correct_est_fusion=1, or reducing pred_flank, although reducing
> pred_flank can cause other issues (but those generally only appear if setting
> the value below below 150).  Also if you have the maximum intron size set to
> high (split_hit option), you may also be generating bridging alignments that
> make evidence align across distant paralogous genes as well (this can result
> in gene merging)
> 
> You should also look at your results manually in a viewer like Apollo.  Then
> see if the extra exons are supported by something such as protein alignments
> from another species.  If this is the case, you may have a poorly annotated
> protein set that is being used as evidence that is carrying over it's
> erroneous exons into the species you are annotating.  If the extra  exons are
> supported by EST evidence, then perhaps you should try and rebuild the EST
> assembly (for example trinity has an option to use a Jarccardian similarity
> coefficient to avoid fusing transcripts).
> 
> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
> produce any of the models itself (it is a pipeline not a predictor).  The
> models are all generated using these other algorithms, MAKER just feeds them
> hints based on protein and transcript alignments, so making sure training is
> sufficient is important for those programs to produce their best models.
> 
> Finally make sure your repeat database is sufficient, you may need to generate
> a species specific repeat library using something like RepeatModeler.  Repeats
> can end up being included as extra exons in gene models because they may
> contain reading frames the do code for proteins (I.e. reverse transcriptases).
> 
> If you have any questions on any of the above, just let us know.
> 
> Thanks,
> Carson
> 
> 
> From:  Janna Fierst <jfierst at uoregon.edu>
> Date:  Monday, August 26, 2013 2:54 PM
> To:  <maker-devel at yandell-lab.org>
> Subject:  [maker-devel] exon/intron boundaries
> 
> Hi,
> 
> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
> initial results appear fairly good but we seem to be be annotating too many
> exons for multiple genes. I was wondering which parameters should be tuned to
> change the threshold for exon/intron boundaries? Thanks for your help -Janna
> Fierst
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak
> er-devel_yandell-lab.org


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

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From carsonhh at gmail.com  Mon Oct  7 08:12:24 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 10:12:24 -0400
Subject: [maker-devel] maker apollo error
In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05365E66B3C@mxb2.hg.genetics.utah.edu>
Message-ID: <CE783792.F640%carsonhh@gmail.com>

This was a location from GMOD for the older Apollo.  It looks like they've
dropped it, so it now points to nothing. Perhaps there is another location
that still has the old code I can get from Ed.

--Carson



On 10/7/13 7:36 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:

>
>Hi Gabriel,
>
>I've forwarded your request on to the MAKER email list...
>
>cheers,
>
>--mark
>
>Mark Yandell
>Professor of Human Genetics
>H.A. & Edna Benning Presidential Endowed Chair
>Eccles Institute of Human Genetics
>University of Utah
>15 North 2030 East, Room 2100
>Salt Lake City, UT 84112-5330
>ph:801-587-7707
>
>________________________________________
>From: ggpozo at us.es [ggpozo at us.es]
>Sent: Monday, October 07, 2013 2:49 AM
>To: Mark Yandell
>Subject: maker apollo error
>
>Dear Dr. Yandell,
>
>First, thank you very much for provide us such a great tool as MAKER. I
>am traying to install it in my Linux system, everything is ok, however
>when I try to instal Apollo with ./Build apollo...
>
>Downloading apollo...
>--2013-10-07 10:45:37--
>http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
>Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
>Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
>Petici?n HTTP enviada, esperando respuesta... 302 Found
>Localizaci?n: http://sourceforge.net/p/gmod/svn/ [siguiendo]
>--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/
>Resolviendo sourceforge.net... 216.34.181.60
>Connecting to sourceforge.net|216.34.181.60|:80... conectado.
>Petici?n HTTP enviada, esperando respuesta... 302 Found
>Localizaci?n: http://sourceforge.net/p/gmod/svn/HEAD/tree/ [siguiendo]
>--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/HEAD/tree/
>Connecting to sourceforge.net|216.34.181.60|:80... conectado.
>Petici?n HTTP enviada, esperando respuesta... 200 OK
>Longitud: 37730 (37K) [text/html]
>Saving to: `/home/maker/src/../exe/apollo.tar.gz'
>
>100%[=====================================================================
>=============================================================>] 37.730
>  92,1K/s   in 0,4s
>
>2013-10-07 10:45:40 (92,1 KB/s) - `/home/maker/src/../exe/apollo.tar.gz'
>saved [37730/37730]
>
>Unpacking apollo tarball...
>
>gzip: stdin: not in gzip format
>tar: Child returned status 1
>tar: Error is not recoverable: exiting now
>
>
>ERROR: Failed installing apollo, now cleaning installation path...
>You may need to install apollo manually.
>
>
>
>It seems that the http direction  in locations file is wrong, Apollo has
>changed its version and now Apollo is integrated in Apolloweb, may be
>this the problem.
>
>
>
>I would greatly appreciate any help you can give me.
>
>Thank you very much.
>
>
>
>Dr. Gabriel Gutierrez
>
>Department of Genetcis
>
>University of Seville
>
>Spain
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Mon Oct  7 08:33:44 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 10:33:44 -0400
Subject: [maker-devel] Contigs failing - could not make datastore
 directory
In-Reply-To: <52501D8B.2060301@uni-wuerzburg.de>
Message-ID: <CE783CF2.F65A%carsonhh@gmail.com>

You can also try the 2.29 beta if you want (on the website).  Also when
MAKER exits, it tries to delete anything left behind in temporary folders,
so is it possible that it is creating space on exit after filling up /tmp?

Given that the issue seems to go away when you switch to another
directory, it suggests that this might be the kind of thing that is
specific to something about the current state of your your system.

Thanks,
Carson


On 10/5/13 10:09 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi Carson,
>
>there is definitely no quota neither a full local tmp device. I changed
>to another tmp device, which is unfortunately residing on nfs but now it
>seems to work. I am using the latest version of maker (2.28). The
>complete job is running on a single machine with 32 mpi threads.
>
>Bests
>Felix
>
>Am 04.10.2013 20:21, schrieb Carson Holt:
>> Hi Felix,
>>
>> There are other potential issues as well, for example a file quota limit
>> set by your administrator or full local /tmp which will be unique to
>>each
>> node and cannot be queried directly from the root node on a cluster.
>>On a
>> cluster one node may also not have the NFS location mounted.  Or it
>>could
>> be system related, for example on ibrix NFS mounted systems you can get
>>a
>> weird filesystem issue with ghost files and directories when using MAKER
>> that can neither be created nor deleted.  Try running the failed contigs
>> in a different directory (even if it's on the same disk).  Also what
>> version of MAKER are you using?
>>
>> --Carson
>>
>>
>>
>> On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Hi,
>>>
>>> I have a problem with Contigs failing like this:
>>>
>>> examining contents of the fasta file and run log
>>> ERROR: could not make datastore directory
>>> --> rank=11, hostname=r5n04
>>> ERROR: Failed while examining contents of the fasta file and run log
>>> ERROR: Chunk failed at level:0, tier_type:0
>>> FAILED CONTIG:MA_gen_v8.05_c31675
>>>
>>> There is enough space available on both the storage device and the tmp
>>> device that is being used. The datastore log files looks like this:
>>>
>>> MA_gen_v8.05_c1149              FAILED
>>> MA_gen_v8.05_c1153              FAILED
>>> MA_gen_v8.05_c1154              FAILED
>>> MA_gen_v8.05_c1155              FAILED
>>> MA_gen_v8.05_c1156              FAILED
>>>
>>> Since there is no datastore for this contigs, I can not provide any
>>>more
>>> informationen. Approx. 1/3 of the contigs were annotated, after that
>>> maker started to fail. It kept running for a while and finishing some
>>>of
>>> the contigs in the second or third try like this:
>>>
>>> MA_gen_v8.05_c4443		FAILED
>>> MA_gen_v8.05_c4443		FAILED
>>> 
>>>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	STA
>>>RT
>>> ED
>>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>>> FINISHED
>>>
>>> Any ideas what can cause this problems?
>>>
>>> Best regards
>>> Felix
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de





From felix.bemm at uni-wuerzburg.de  Mon Oct  7 10:40:12 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Mon, 07 Oct 2013 18:40:12 +0200
Subject: [maker-devel] Contigs failing - could not make datastore
	directory
In-Reply-To: <CE783CF2.F65A%carsonhh@gmail.com>
References: <CE783CF2.F65A%carsonhh@gmail.com>
Message-ID: <5252E3EC.6050908@uni-wuerzburg.de>

Do you have a changelog for 2.29b?

On 07.10.2013 16:33, Carson Holt wrote:
> You can also try the 2.29 beta if you want (on the website).  Also when
> MAKER exits, it tries to delete anything left behind in temporary folders,
> so is it possible that it is creating space on exit after filling up /tmp?

I will try to monitor that!

> Given that the issue seems to go away when you switch to another
> directory, it suggests that this might be the kind of thing that is
> specific to something about the current state of your your system.

I agree with that. Interestingly it happens with the only directory 
where I would not expect that.

> Thanks,
> Carson
>
>
> On 10/5/13 10:09 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>> Hi Carson,
>>
>> there is definitely no quota neither a full local tmp device. I changed
>> to another tmp device, which is unfortunately residing on nfs but now it
>> seems to work. I am using the latest version of maker (2.28). The
>> complete job is running on a single machine with 32 mpi threads.
>>
>> Bests
>> Felix
>>
>> Am 04.10.2013 20:21, schrieb Carson Holt:
>>> Hi Felix,
>>>
>>> There are other potential issues as well, for example a file quota limit
>>> set by your administrator or full local /tmp which will be unique to
>>> each
>>> node and cannot be queried directly from the root node on a cluster.
>>> On a
>>> cluster one node may also not have the NFS location mounted.  Or it
>>> could
>>> be system related, for example on ibrix NFS mounted systems you can get
>>> a
>>> weird filesystem issue with ghost files and directories when using MAKER
>>> that can neither be created nor deleted.  Try running the failed contigs
>>> in a different directory (even if it's on the same disk).  Also what
>>> version of MAKER are you using?
>>>
>>> --Carson
>>>
>>>
>>>
>>> On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a problem with Contigs failing like this:
>>>>
>>>> examining contents of the fasta file and run log
>>>> ERROR: could not make datastore directory
>>>> --> rank=11, hostname=r5n04
>>>> ERROR: Failed while examining contents of the fasta file and run log
>>>> ERROR: Chunk failed at level:0, tier_type:0
>>>> FAILED CONTIG:MA_gen_v8.05_c31675
>>>>
>>>> There is enough space available on both the storage device and the tmp
>>>> device that is being used. The datastore log files looks like this:
>>>>
>>>> MA_gen_v8.05_c1149              FAILED
>>>> MA_gen_v8.05_c1153              FAILED
>>>> MA_gen_v8.05_c1154              FAILED
>>>> MA_gen_v8.05_c1155              FAILED
>>>> MA_gen_v8.05_c1156              FAILED
>>>>
>>>> Since there is no datastore for this contigs, I can not provide any
>>>> more
>>>> informationen. Approx. 1/3 of the contigs were annotated, after that
>>>> maker started to fail. It kept running for a while and finishing some
>>>> of
>>>> the contigs in the second or third try like this:
>>>>
>>>> MA_gen_v8.05_c4443		FAILED
>>>> MA_gen_v8.05_c4443		FAILED
>>>>
>>>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	STA
>>>> RT
>>>> ED
>>>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>>>> FINISHED
>>>>
>>>> Any ideas what can cause this problems?
>>>>
>>>> Best regards
>>>> Felix
>>>>
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> --
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Mon Oct  7 11:25:34 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 13:25:34 -0400
Subject: [maker-devel] maker apollo error
In-Reply-To: <14a642f3dc9cb615f048b70228bad3be@buzonweb.us.es>
Message-ID: <CE78668C.F68A%carsonhh@gmail.com>

Here is a new location for the source -->
http://sourceforge.net/code-snapshots/svn/g/gm/gmod/svn/gmod-svn-25291-apoll
o-trunk.zip

--Carson


From:  <ggpozo at us.es>
Date:  Monday, October 7, 2013 12:47 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Mark Yandell <myandell at genetics.utah.edu>,
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] maker apollo error

Thanks, I have modified the locations file pointing to a personal server
where I downloaded an old version of Apollo but it did not work, but if you
can get a new one I would try it again.

Thanks

Gabriel

 
El 07/10/2013 16:12, Carson Holt escribi?:
> This was a location from GMOD for the older Apollo.  It looks like they've
> dropped it, so it now points to nothing. Perhaps there is another location
> that still has the old code I can get from Ed.
> 
> --Carson
> 
> 
> 
> On 10/7/13 7:36 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>> Hi Gabriel, I've forwarded your request on to the MAKER email list... cheers,
>> --mark Mark Yandell Professor of Human Genetics H.A. & Edna Benning
>> Presidential Endowed Chair Eccles Institute of Human Genetics University of
>> Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330
>> ph:801-587-7707 ________________________________________ From: ggpozo at us.es
>> [ggpozo at us.es] Sent: Monday, October 07, 2013 2:49 AM To: Mark Yandell
>> Subject: maker apollo error Dear Dr. Yandell, First, thank you very much for
>> provide us such a great tool as MAKER. I am traying to install it in my Linux
>> system, everything is ok, however when I try to instal Apollo with ./Build
>> apollo... Downloading apollo... --2013-10-07 10:45:37--
>> http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
>> Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
>> Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
>> Petici?n HTTP enviada, esperando respuesta... 302 Found Localizaci?n:
>> http://sourceforge.net/p/gmod/svn/ [siguiendo] --2013-10-07 10:45:38--
>> http://sourceforge.net/p/gmod/svn/ Resolviendo sourceforge.net...
>> 216.34.181.60 Connecting to sourceforge.net|216.34.181.60|:80... conectado.
>> Petici?n HTTP enviada, esperando respuesta... 302 Found Localizaci?n:
>> http://sourceforge.net/p/gmod/svn/HEAD/tree/ [siguiendo] --2013-10-07
>> 10:45:38-- http://sourceforge.net/p/gmod/svn/HEAD/tree/ Connecting to
>> sourceforge.net|216.34.181.60|:80... conectado. Petici?n HTTP enviada,
>> esperando respuesta... 200 OK Longitud: 37730 (37K) [text/html] Saving to:
>> `/home/maker/src/../exe/apollo.tar.gz'
>> 100%[=====================================================================
>> =============================================================>] 37.730
>> 92,1K/s in 0,4s 2013-10-07 10:45:40 (92,1 KB/s) -
>> `/home/maker/src/../exe/apollo.tar.gz' saved [37730/37730] Unpacking apollo
>> tarball... gzip: stdin: not in gzip format tar: Child returned status 1 tar:
>> Error is not recoverable: exiting now ERROR: Failed installing apollo, now
>> cleaning installation path... You may need to install apollo manually. It
>> seems that the http direction in locations file is wrong, Apollo has changed
>> its version and now Apollo is integrated in Apolloweb, may be this the
>> problem. I would greatly appreciate any help you can give me. Thank you very
>> much. Dr. Gabriel Gutierrez Department of Genetcis University of Seville
>> Spain _______________________________________________ maker-devel mailing
>> list maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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From ggpozo at us.es  Mon Oct  7 10:47:13 2013
From: ggpozo at us.es (ggpozo at us.es)
Date: Mon, 07 Oct 2013 18:47:13 +0200
Subject: [maker-devel] maker apollo error
In-Reply-To: <CE783792.F640%carsonhh@gmail.com>
References: <CE783792.F640%carsonhh@gmail.com>
Message-ID: <14a642f3dc9cb615f048b70228bad3be@buzonweb.us.es>

 

Thanks, I have modified the locations file pointing to a personal
server where I downloaded an old version of Apollo but it did not work,
but if you can get a new one I would try it again. 

Thanks 

Gabriel


El 07/10/2013 16:12, Carson Holt escribi?: 

> This was a location
from GMOD for the older Apollo. It looks like they've
> dropped it, so
it now points to nothing. Perhaps there is another location
> that still
has the old code I can get from Ed.
> 
> --Carson
> 
> On 10/7/13 7:36
AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
> 
>> Hi Gabriel,
I've forwarded your request on to the MAKER email list... cheers, --mark
Mark Yandell Professor of Human Genetics H.A. & Edna Benning
Presidential Endowed Chair Eccles Institute of Human Genetics University
of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330
ph:801-587-7707 ________________________________________ From:
ggpozo at us.es [1] [ggpozo at us.es [2]] Sent: Monday, October 07, 2013 2:49
AM To: Mark Yandell Subject: maker apollo error Dear Dr. Yandell, First,
thank you very much for provide us such a great tool as MAKER. I am
traying to install it in my Linux system, everything is ok, however when
I try to instal Apollo with ./Build apollo... Downloading apollo...
--2013-10-07 10:45:37--
http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar [3]
Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 302 Found Localizaci?n:
http://sourceforge.net/p/gmod/svn/ [4] [siguiendo] --2013-10-07
10:45:38-- http://sourceforge.net/p/gmod/svn/ [5] Resolviendo
sourceforge.net... 216.34.181.60 Connecting to
sourceforge.net|216.34.181.60|:80... conectado. Petici?n HTTP enviada,
esperando respuesta... 302 Found Localizaci?n:
http://sourceforge.net/p/gmod/svn/HEAD/tree/ [6] [siguiendo]
--2013-10-07 10:45:38-- http://sourceforge.net/p/gmod/svn/HEAD/tree/ [7]
Connecting to sourceforge.net|216.34.181.60|:80... conectado. Petici?n
HTTP enviada, esperando respuesta... 200 OK Longitud: 37730 (37K)
[text/html] Saving to: `/home/maker/src/../exe/apollo.tar.gz'
100%[=====================================================================
=============================================================>] 37.730
92,1K/s in 0,4s 2013-10-07 10:45:40 (92,1 KB/s) -
`/home/maker/src/../exe/apollo.tar.gz' saved [37730/37730] Unpacking
apollo tarball... gzip: stdin: not in gzip format tar: Child returned
status 1 tar: Error is not recoverable: exiting now ERROR: Failed
installing apollo, now cleaning installation path... You may need to
install apollo manually. It seems that the http direction in locations
file is wrong, Apollo has changed its version and now Apollo is
integrated in Apolloweb, may be this the problem. I would greatly
appreciate any help you can give me. Thank you very much. Dr. Gabriel
Gutierrez Department of Genetcis University of Seville Spain
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com [8]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
[9]
 

Links:
------
[1] mailto:ggpozo at us.es
[2] mailto:ggpozo at us.es
[3]
http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
[4]
http://sourceforge.net/p/gmod/svn/
[5]
http://sourceforge.net/p/gmod/svn/
[6]
http://sourceforge.net/p/gmod/svn/HEAD/tree/
[7]
http://sourceforge.net/p/gmod/svn/HEAD/tree/
[8]
mailto:maker-devel at box290.bluehost.com
[9]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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From felix.bemm at uni-wuerzburg.de  Sat Oct 12 09:06:52 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Sat, 12 Oct 2013 17:06:52 +0200
Subject: [maker-devel] Serious Start Codon Problem
Message-ID: <5259658C.4000102@uni-wuerzburg.de>

Hi,

I have a serious problems with maker annotations especially the start 
codon placement. It started happening with maker version 2.27! About 1/3 
of my genes are missing a proper start codon. When reviewing the GFF 
files gene predictors and est evidence standalone would predict the 
right gene structure including the start codon. I was thinking that this 
problem was somehow linked to my gene models but looking at their 
standalone prediction I discarded that theory. Just some stats about 
proteins with proper start codon (first column) and missing start codon 
(second column).

Maker		9268	4215
SNAP		16577	896
Genemark	18764	290

Numbers look the same when Augustus is used (currently retraining). 
Manually using EST's in Apollo often fixes the problems but I don't want 
to check > 4000 genes for this.

Do you have any idea what could cause such a problem? If you need some 
example gff files I can send you.

Best regards
Felix

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Sat Oct 12 09:48:29 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Sat, 12 Oct 2013 11:48:29 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <5259658C.4000102@uni-wuerzburg.de>
Message-ID: <CE7EE411.10C24%carsonhh@gmail.com>

This issue just came up this week on another e-mail as well.

One way to fix it, is to edit the Bio::Tools::CodonTable module from
BioPerl (use maker --debug to have maker print out the locations of all
modules it uses).  Such a hack should only be done as a temporary work
around.

You change line 256 from -->
---M---------------M---------------M----------------------------

To-->
-----------------------------------M----------------------------


Maker uses the BioPerl is_start_codon function to determine if the codon
used in a result it receives is acceptable or if it should look upstream
or downstream for a different one. Apparently there are actually 3
acceptable start codons in the standard codon table (2 rare ones and one
common), so making the edit removes the two rare ones from the list.

I'm also preparing a 2.30 release that exports a "strict" codon table to
the BioPerl module, that will be used by default and should fix the issue.

Thanks,
Carson



On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi,
>
>I have a serious problems with maker annotations especially the start
>codon placement. It started happening with maker version 2.27! About 1/3
>of my genes are missing a proper start codon. When reviewing the GFF
>files gene predictors and est evidence standalone would predict the
>right gene structure including the start codon. I was thinking that this
>problem was somehow linked to my gene models but looking at their
>standalone prediction I discarded that theory. Just some stats about
>proteins with proper start codon (first column) and missing start codon
>(second column).
>
>Maker		9268	4215
>SNAP		16577	896
>Genemark	18764	290
>
>Numbers look the same when Augustus is used (currently retraining).
>Manually using EST's in Apollo often fixes the problems but I don't want
>to check > 4000 genes for this.
>
>Do you have any idea what could cause such a problem? If you need some
>example gff files I can send you.
>
>Best regards
>Felix
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From felix.bemm at uni-wuerzburg.de  Sat Oct 12 10:16:06 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Sat, 12 Oct 2013 18:16:06 +0200
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE7EE411.10C24%carsonhh@gmail.com>
References: <CE7EE411.10C24%carsonhh@gmail.com>
Message-ID: <525975C6.4020403@uni-wuerzburg.de>

Thx Carson! Do you now when 2.30 will be available? Bests

On 12.10.2013 17:48, Carson Holt wrote:
> This issue just came up this week on another e-mail as well.
>
> One way to fix it, is to edit the Bio::Tools::CodonTable module from
> BioPerl (use maker --debug to have maker print out the locations of all
> modules it uses).  Such a hack should only be done as a temporary work
> around.
>
> You change line 256 from -->
> ---M---------------M---------------M----------------------------
>
> To-->
> -----------------------------------M----------------------------
>
>
> Maker uses the BioPerl is_start_codon function to determine if the codon
> used in a result it receives is acceptable or if it should look upstream
> or downstream for a different one. Apparently there are actually 3
> acceptable start codons in the standard codon table (2 rare ones and one
> common), so making the edit removes the two rare ones from the list.
>
> I'm also preparing a 2.30 release that exports a "strict" codon table to
> the BioPerl module, that will be used by default and should fix the issue.
>
> Thanks,
> Carson
>
>
>
> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>> Hi,
>>
>> I have a serious problems with maker annotations especially the start
>> codon placement. It started happening with maker version 2.27! About 1/3
>> of my genes are missing a proper start codon. When reviewing the GFF
>> files gene predictors and est evidence standalone would predict the
>> right gene structure including the start codon. I was thinking that this
>> problem was somehow linked to my gene models but looking at their
>> standalone prediction I discarded that theory. Just some stats about
>> proteins with proper start codon (first column) and missing start codon
>> (second column).
>>
>> Maker		9268	4215
>> SNAP		16577	896
>> Genemark	18764	290
>>
>> Numbers look the same when Augustus is used (currently retraining).
>> Manually using EST's in Apollo often fixes the problems but I don't want
>> to check > 4000 genes for this.
>>
>> Do you have any idea what could cause such a problem? If you need some
>> example gff files I can send you.
>>
>> Best regards
>> Felix
>>
>> --
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Sat Oct 12 23:26:17 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 13 Oct 2013 01:26:17 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <525975C6.4020403@uni-wuerzburg.de>
Message-ID: <CE7FA55D.10C4B%carsonhh@gmail.com>

Before Wednesday, because after that I'm on a 6 day road trip, so I have
to have it wrapped up before I leave.

--Carson




On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Thx Carson! Do you now when 2.30 will be available? Bests
>
>On 12.10.2013 17:48, Carson Holt wrote:
>> This issue just came up this week on another e-mail as well.
>>
>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>> BioPerl (use maker --debug to have maker print out the locations of all
>> modules it uses).  Such a hack should only be done as a temporary work
>> around.
>>
>> You change line 256 from -->
>> ---M---------------M---------------M----------------------------
>>
>> To-->
>> -----------------------------------M----------------------------
>>
>>
>> Maker uses the BioPerl is_start_codon function to determine if the codon
>> used in a result it receives is acceptable or if it should look upstream
>> or downstream for a different one. Apparently there are actually 3
>> acceptable start codons in the standard codon table (2 rare ones and one
>> common), so making the edit removes the two rare ones from the list.
>>
>> I'm also preparing a 2.30 release that exports a "strict" codon table to
>> the BioPerl module, that will be used by default and should fix the
>>issue.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Hi,
>>>
>>> I have a serious problems with maker annotations especially the start
>>> codon placement. It started happening with maker version 2.27! About
>>>1/3
>>> of my genes are missing a proper start codon. When reviewing the GFF
>>> files gene predictors and est evidence standalone would predict the
>>> right gene structure including the start codon. I was thinking that
>>>this
>>> problem was somehow linked to my gene models but looking at their
>>> standalone prediction I discarded that theory. Just some stats about
>>> proteins with proper start codon (first column) and missing start codon
>>> (second column).
>>>
>>> Maker		9268	4215
>>> SNAP		16577	896
>>> Genemark	18764	290
>>>
>>> Numbers look the same when Augustus is used (currently retraining).
>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>want
>>> to check > 4000 genes for this.
>>>
>>> Do you have any idea what could cause such a problem? If you need some
>>> example gff files I can send you.
>>>
>>> Best regards
>>> Felix
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de





From carsonhh at gmail.com  Mon Oct 14 08:45:25 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 14 Oct 2013 10:45:25 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <525975C6.4020403@uni-wuerzburg.de>
Message-ID: <CE817BB6.10C72%carsonhh@gmail.com>

Probably Tuesday or Wednesday.

--Carson


On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Thx Carson! Do you now when 2.30 will be available? Bests
>
>On 12.10.2013 17:48, Carson Holt wrote:
>> This issue just came up this week on another e-mail as well.
>>
>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>> BioPerl (use maker --debug to have maker print out the locations of all
>> modules it uses).  Such a hack should only be done as a temporary work
>> around.
>>
>> You change line 256 from -->
>> ---M---------------M---------------M----------------------------
>>
>> To-->
>> -----------------------------------M----------------------------
>>
>>
>> Maker uses the BioPerl is_start_codon function to determine if the codon
>> used in a result it receives is acceptable or if it should look upstream
>> or downstream for a different one. Apparently there are actually 3
>> acceptable start codons in the standard codon table (2 rare ones and one
>> common), so making the edit removes the two rare ones from the list.
>>
>> I'm also preparing a 2.30 release that exports a "strict" codon table to
>> the BioPerl module, that will be used by default and should fix the
>>issue.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Hi,
>>>
>>> I have a serious problems with maker annotations especially the start
>>> codon placement. It started happening with maker version 2.27! About
>>>1/3
>>> of my genes are missing a proper start codon. When reviewing the GFF
>>> files gene predictors and est evidence standalone would predict the
>>> right gene structure including the start codon. I was thinking that
>>>this
>>> problem was somehow linked to my gene models but looking at their
>>> standalone prediction I discarded that theory. Just some stats about
>>> proteins with proper start codon (first column) and missing start codon
>>> (second column).
>>>
>>> Maker		9268	4215
>>> SNAP		16577	896
>>> Genemark	18764	290
>>>
>>> Numbers look the same when Augustus is used (currently retraining).
>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>want
>>> to check > 4000 genes for this.
>>>
>>> Do you have any idea what could cause such a problem? If you need some
>>> example gff files I can send you.
>>>
>>> Best regards
>>> Felix
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de





From cjfields at illinois.edu  Mon Oct 14 09:07:43 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 14 Oct 2013 15:07:43 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE817BB6.10C72%carsonhh@gmail.com>
References: <CE817BB6.10C72%carsonhh@gmail.com>
Message-ID: <D51543B5-DCFB-4F2C-9BE5-3099B96E3317@illinois.edu>

Carson,

Regarding the CodonTable change below, should this be something that needs to be fixed, or made more flexible, in bioperl?  I could see this being a problem if using MAKER for bacterial annotation (where the alternative start codons are actually more common).

chris

On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Probably Tuesday or Wednesday.
> 
> --Carson
> 
> 
> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
> 
>> Thx Carson! Do you now when 2.30 will be available? Bests
>> 
>> On 12.10.2013 17:48, Carson Holt wrote:
>>> This issue just came up this week on another e-mail as well.
>>> 
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>> BioPerl (use maker --debug to have maker print out the locations of all
>>> modules it uses).  Such a hack should only be done as a temporary work
>>> around.
>>> 
>>> You change line 256 from -->
>>> ---M---------------M---------------M----------------------------
>>> 
>>> To-->
>>> -----------------------------------M----------------------------
>>> 
>>> 
>>> Maker uses the BioPerl is_start_codon function to determine if the codon
>>> used in a result it receives is acceptable or if it should look upstream
>>> or downstream for a different one. Apparently there are actually 3
>>> acceptable start codons in the standard codon table (2 rare ones and one
>>> common), so making the edit removes the two rare ones from the list.
>>> 
>>> I'm also preparing a 2.30 release that exports a "strict" codon table to
>>> the BioPerl module, that will be used by default and should fix the
>>> issue.
>>> 
>>> Thanks,
>>> Carson
>>> 
>>> 
>>> 
>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I have a serious problems with maker annotations especially the start
>>>> codon placement. It started happening with maker version 2.27! About
>>>> 1/3
>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>> files gene predictors and est evidence standalone would predict the
>>>> right gene structure including the start codon. I was thinking that
>>>> this
>>>> problem was somehow linked to my gene models but looking at their
>>>> standalone prediction I discarded that theory. Just some stats about
>>>> proteins with proper start codon (first column) and missing start codon
>>>> (second column).
>>>> 
>>>> Maker		9268	4215
>>>> SNAP		16577	896
>>>> Genemark	18764	290
>>>> 
>>>> Numbers look the same when Augustus is used (currently retraining).
>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>> want
>>>> to check > 4000 genes for this.
>>>> 
>>>> Do you have any idea what could cause such a problem? If you need some
>>>> example gff files I can send you.
>>>> 
>>>> Best regards
>>>> Felix
>>>> 
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> -- 
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Mon Oct 14 11:58:24 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 14 Oct 2013 13:58:24 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <D51543B5-DCFB-4F2C-9BE5-3099B96E3317@illinois.edu>
Message-ID: <CE81A824.10C7B%carsonhh@gmail.com>

I think adding one more codon table to the set of available tables would
be sufficient.  Call it the 'Strict' table or 'Canonical' table.  It
doesn't need to be the default, but should be a selectable option just as
the other codon tables are.  There is a way to export codon tables to the
module, which is what I've now added to MAKER, but I'm sure other BoiPerl
users would find a strictly canonical codon table useful as well.

Thanks,
Carson


On 10/14/13 11:07 AM, "Fields, Christopher J" <cjfields at illinois.edu>
wrote:

>Carson,
>
>Regarding the CodonTable change below, should this be something that
>needs to be fixed, or made more flexible, in bioperl?  I could see this
>being a problem if using MAKER for bacterial annotation (where the
>alternative start codons are actually more common).
>
>chris
>
>On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Probably Tuesday or Wednesday.
>> 
>> --Carson
>> 
>> 
>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>> 
>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>> 
>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>> This issue just came up this week on another e-mail as well.
>>>> 
>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>> BioPerl (use maker --debug to have maker print out the locations of
>>>>all
>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>> around.
>>>> 
>>>> You change line 256 from -->
>>>> ---M---------------M---------------M----------------------------
>>>> 
>>>> To-->
>>>> -----------------------------------M----------------------------
>>>> 
>>>> 
>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>codon
>>>> used in a result it receives is acceptable or if it should look
>>>>upstream
>>>> or downstream for a different one. Apparently there are actually 3
>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>one
>>>> common), so making the edit removes the two rare ones from the list.
>>>> 
>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>to
>>>> the BioPerl module, that will be used by default and should fix the
>>>> issue.
>>>> 
>>>> Thanks,
>>>> Carson
>>>> 
>>>> 
>>>> 
>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> I have a serious problems with maker annotations especially the start
>>>>> codon placement. It started happening with maker version 2.27! About
>>>>> 1/3
>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>> files gene predictors and est evidence standalone would predict the
>>>>> right gene structure including the start codon. I was thinking that
>>>>> this
>>>>> problem was somehow linked to my gene models but looking at their
>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>> proteins with proper start codon (first column) and missing start
>>>>>codon
>>>>> (second column).
>>>>> 
>>>>> Maker		9268	4215
>>>>> SNAP		16577	896
>>>>> Genemark	18764	290
>>>>> 
>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>> want
>>>>> to check > 4000 genes for this.
>>>>> 
>>>>> Do you have any idea what could cause such a problem? If you need
>>>>>some
>>>>> example gff files I can send you.
>>>>> 
>>>>> Best regards
>>>>> Felix
>>>>> 
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>> 
>>> -- 
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>> 
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>





From cjfields at illinois.edu  Mon Oct 14 12:51:28 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 14 Oct 2013 18:51:28 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE81A824.10C7B%carsonhh@gmail.com>
References: <CE81A824.10C7B%carsonhh@gmail.com>
Message-ID: <160BC401-0471-4285-8712-21440628A5DA@illinois.edu>

Done, with some added tests.  I labeled it 'Strict' ('Canonical' can be a bit of a loaded term).  It's currently set as ID 24.

I will likely push out a new 1.6 point release this week or next, I'll merge these in for that release.

chris

On Oct 14, 2013, at 12:58 PM, Carson Holt <carsonhh at gmail.com> wrote:

> I think adding one more codon table to the set of available tables would
> be sufficient.  Call it the 'Strict' table or 'Canonical' table.  It
> doesn't need to be the default, but should be a selectable option just as
> the other codon tables are.  There is a way to export codon tables to the
> module, which is what I've now added to MAKER, but I'm sure other BoiPerl
> users would find a strictly canonical codon table useful as well.
> 
> Thanks,
> Carson
> 
> 
> On 10/14/13 11:07 AM, "Fields, Christopher J" <cjfields at illinois.edu>
> wrote:
> 
>> Carson,
>> 
>> Regarding the CodonTable change below, should this be something that
>> needs to be fixed, or made more flexible, in bioperl?  I could see this
>> being a problem if using MAKER for bacterial annotation (where the
>> alternative start codons are actually more common).
>> 
>> chris
>> 
>> On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>>> Probably Tuesday or Wednesday.
>>> 
>>> --Carson
>>> 
>>> 
>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>> 
>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>> 
>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>> This issue just came up this week on another e-mail as well.
>>>>> 
>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>> BioPerl (use maker --debug to have maker print out the locations of
>>>>> all
>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>> around.
>>>>> 
>>>>> You change line 256 from -->
>>>>> ---M---------------M---------------M----------------------------
>>>>> 
>>>>> To-->
>>>>> -----------------------------------M----------------------------
>>>>> 
>>>>> 
>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>> codon
>>>>> used in a result it receives is acceptable or if it should look
>>>>> upstream
>>>>> or downstream for a different one. Apparently there are actually 3
>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>> one
>>>>> common), so making the edit removes the two rare ones from the list.
>>>>> 
>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>> to
>>>>> the BioPerl module, that will be used by default and should fix the
>>>>> issue.
>>>>> 
>>>>> Thanks,
>>>>> Carson
>>>>> 
>>>>> 
>>>>> 
>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>> wrote:
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I have a serious problems with maker annotations especially the start
>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>> 1/3
>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>> right gene structure including the start codon. I was thinking that
>>>>>> this
>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>> proteins with proper start codon (first column) and missing start
>>>>>> codon
>>>>>> (second column).
>>>>>> 
>>>>>> Maker		9268	4215
>>>>>> SNAP		16577	896
>>>>>> Genemark	18764	290
>>>>>> 
>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>> want
>>>>>> to check > 4000 genes for this.
>>>>>> 
>>>>>> Do you have any idea what could cause such a problem? If you need
>>>>>> some
>>>>>> example gff files I can send you.
>>>>>> 
>>>>>> Best regards
>>>>>> Felix
>>>>>> 
>>>>>> --
>>>>>> Felix Bemm
>>>>>> Department of Bioinformatics
>>>>>> University of W?rzburg, Germany
>>>>>> Tel: +49 931 - 31 83696
>>>>>> Fax: +49 931 - 31 84552
>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>> 
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> 
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>> 
>>>> -- 
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
> 
> 




From carsonhh at gmail.com  Mon Oct 14 18:59:45 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 14 Oct 2013 20:59:45 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <160BC401-0471-4285-8712-21440628A5DA@illinois.edu>
Message-ID: <CE820BA4.10C8F%carsonhh@gmail.com>

Thanks!!

--Carson


On 10/14/13 2:51 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

>Done, with some added tests.  I labeled it 'Strict' ('Canonical' can be a
>bit of a loaded term).  It's currently set as ID 24.
>
>I will likely push out a new 1.6 point release this week or next, I'll
>merge these in for that release.
>
>chris
>
>On Oct 14, 2013, at 12:58 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> I think adding one more codon table to the set of available tables would
>> be sufficient.  Call it the 'Strict' table or 'Canonical' table.  It
>> doesn't need to be the default, but should be a selectable option just
>>as
>> the other codon tables are.  There is a way to export codon tables to
>>the
>> module, which is what I've now added to MAKER, but I'm sure other
>>BoiPerl
>> users would find a strictly canonical codon table useful as well.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> On 10/14/13 11:07 AM, "Fields, Christopher J" <cjfields at illinois.edu>
>> wrote:
>> 
>>> Carson,
>>> 
>>> Regarding the CodonTable change below, should this be something that
>>> needs to be fixed, or made more flexible, in bioperl?  I could see this
>>> being a problem if using MAKER for bacterial annotation (where the
>>> alternative start codons are actually more common).
>>> 
>>> chris
>>> 
>>> On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> 
>>>> Probably Tuesday or Wednesday.
>>>> 
>>>> --Carson
>>>> 
>>>> 
>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>wrote:
>>>> 
>>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>>> 
>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>>> This issue just came up this week on another e-mail as well.
>>>>>> 
>>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>>> BioPerl (use maker --debug to have maker print out the locations of
>>>>>> all
>>>>>> modules it uses).  Such a hack should only be done as a temporary
>>>>>>work
>>>>>> around.
>>>>>> 
>>>>>> You change line 256 from -->
>>>>>> ---M---------------M---------------M----------------------------
>>>>>> 
>>>>>> To-->
>>>>>> -----------------------------------M----------------------------
>>>>>> 
>>>>>> 
>>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>>> codon
>>>>>> used in a result it receives is acceptable or if it should look
>>>>>> upstream
>>>>>> or downstream for a different one. Apparently there are actually 3
>>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>>> one
>>>>>> common), so making the edit removes the two rare ones from the list.
>>>>>> 
>>>>>> I'm also preparing a 2.30 release that exports a "strict" codon
>>>>>>table
>>>>>> to
>>>>>> the BioPerl module, that will be used by default and should fix the
>>>>>> issue.
>>>>>> 
>>>>>> Thanks,
>>>>>> Carson
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>>> wrote:
>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I have a serious problems with maker annotations especially the
>>>>>>>start
>>>>>>> codon placement. It started happening with maker version 2.27!
>>>>>>>About
>>>>>>> 1/3
>>>>>>> of my genes are missing a proper start codon. When reviewing the
>>>>>>>GFF
>>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>>> right gene structure including the start codon. I was thinking that
>>>>>>> this
>>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>>> standalone prediction I discarded that theory. Just some stats
>>>>>>>about
>>>>>>> proteins with proper start codon (first column) and missing start
>>>>>>> codon
>>>>>>> (second column).
>>>>>>> 
>>>>>>> Maker		9268	4215
>>>>>>> SNAP		16577	896
>>>>>>> Genemark	18764	290
>>>>>>> 
>>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>>> want
>>>>>>> to check > 4000 genes for this.
>>>>>>> 
>>>>>>> Do you have any idea what could cause such a problem? If you need
>>>>>>> some
>>>>>>> example gff files I can send you.
>>>>>>> 
>>>>>>> Best regards
>>>>>>> Felix
>>>>>>> 
>>>>>>> --
>>>>>>> Felix Bemm
>>>>>>> Department of Bioinformatics
>>>>>>> University of W?rzburg, Germany
>>>>>>> Tel: +49 931 - 31 83696
>>>>>>> Fax: +49 931 - 31 84552
>>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> 
>>>>>>> 
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>or
>>>>>>> g
>>>>> 
>>>>> -- 
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>> 
>> 
>





From jfierst at uoregon.edu  Mon Oct 21 11:40:06 2013
From: jfierst at uoregon.edu (Janna Fierst)
Date: Mon, 21 Oct 2013 10:40:06 -0700
Subject: [maker-devel] Fwd: exon/intron boundaries
In-Reply-To: <CE782A71.F621%carsonhh@gmail.com>
References: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
	<CE782A71.F621%carsonhh@gmail.com>
Message-ID: <CAGoyurZfiqRpEKg0C=__ou6muWD2PqCQh9b+S9y_+95-xsCfOQ@mail.gmail.com>

Hi,

thanks for your help- I have used Trinity to assemble the EST's but am
having a problem with the 2.29-beta release. Instead of starting and
finishing a set of scaffolds, it appears to re-start over and over again. I
am running it in parallel across 32 cores and I'm wondering if this is a
problem with the parallel implementation. I've gone through it several
times and not been able to find any errors or output that would suggest
what the problem is. Thanks -Janna


On Mon, Oct 7, 2013 at 6:20 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Hi Janna,
>
> There are a couple of things to do.  Download the maker-2.29p-beta from
> the lab website.  This includes some changes made to improve the
> performance of correct_est_fusion.  Whenever using the correct_est_fusion
> option, this also reduces the influence of ESTs on annotation.  So normally
> you would need to increase your protein dataset, but given that you have
> supplied 3 nematode species and all of UniProt already you should probably
> be fine. But there is one last thing you can do.  Instead of using
> cufflinks, try using trinity to assemble the ESTs.  There is a Jaccard clip
> option that reducing merging caused by overlapping UTR.  Between the
> trinity and correct_est_fusion you should be able to really reduce the
> effect of those ESTs.
>
> If those changes don't work there is one last option.  If you take the
> MAKER results and filter them for SNAP and Augustus ab initio results
> (match/match_part in the GFF3), then you can pass those in to the pred_gff
> options.  Then turn snaphmm and augustus_species off in the control files.
>  Basically what this will do is turn MAKER's hint based prediction off and
> force it to filter the ab intio results and select directly models from
> there.  Since the merging is being caused by bad hints (merged transcripts
> from mRNAseq) this would reduce that effect.  You will still need
> correct_est_fusion=1 though to trim UTR coming from the merged transcripts,
> because even though MAEKR can't process hints to rerun SNAP and Augustus
> this way, it will try and add UTR using the EST evidence.
>
> --Carson
>
>
> From: Janna Fierst <jfierst at uoregon.edu>
> Date: Friday, October 4, 2013 1:06 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Fwd: exon/intron boundaries
>
> Hi,
>
> thanks for your reply- I have been going through our annotations in detail
> and trying different parameter sets, and I think I have identified what is
> going on but I'm not sure how to set the MAKER2 parameters for our
> situation. We are working with a species of Caenorhabditid worm and there
> are long gene-dense blocks that are being incorrectly annotated as large
> single genes instead of several smaller closely spaced genes. The protein
> alignments (tblastx and protein2genome) show very clearly where the
> exon/intron boundaries are and in most cases agree with the augustus
> predictions. The assembled cufflinks output (through blastn, est2genome and
> est_gff:cufflinks) does not agree in some locations; I think this may be
> because in some cases the UTR nearly overlaps adjacent genes.
>
> I have included a screenshot of an annotated region viewed in apollo to
> try to show this. The large gene in the middle is actually 7 different
> genes that are extremely close together and MAKER2 is collapsing them into
> a single gene. I tried running without any RNASeq/cufflinks data and MAKER2
> annotates the region as two genes instead of one, but I can't get it to
> recognize the 7 as different genes. I have retrained SNAP but we have not
> been able to successfully train Augustus, we are currently using the
> default caenhorhabditis species model. I also included a species specific
> repeat library. I tried setting correct_est_fusion=1 and reducing
> pred_flank but these changes appear to really alter the annotations and we
> end up annotating almost nothing. I also tried setting est2genome=0 to
> decrease the influence of the cufflinks assembly but it didn't appear to
> help. There are some very large introns in these genes so I haven't tried
> yet decreasing the maximum intron size because I'm concerned this may
> generate too many split genes instead of our current merged gene problem.
> Thanks for your help, any advice is greatly appreciated! -Janna Fierst
>
>
> On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Are you getting gene fusions or just more exons?  Gene fusions can be
>> reduced by setting correct_est_fusion=1, or reducing pred_flank, although
>> reducing pred_flank can cause other issues (but those generally only appear
>> if setting the value below below 150).  Also if you have the maximum intron
>> size set to high (split_hit option), you may also be generating bridging
>> alignments that make evidence align across distant paralogous genes as well
>> (this can result in gene merging)
>>
>> You should also look at your results manually in a viewer like Apollo.
>>  Then see if the extra exons are supported by something such as protein
>> alignments from another species.  If this is the case, you may have a
>> poorly annotated protein set that is being used as evidence that is
>> carrying over it's erroneous exons into the species you are annotating.  If
>> the extra  exons are supported by EST evidence, then perhaps you should try
>> and rebuild the EST assembly (for example trinity has an option to use a
>> Jarccardian similarity coefficient to avoid fusing transcripts).
>>
>> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
>> produce any of the models itself (it is a pipeline not a predictor).  The
>> models are all generated using these other algorithms, MAKER just feeds
>> them hints based on protein and transcript alignments, so making sure
>> training is sufficient is important for those programs to produce their
>> best models.
>>
>> Finally make sure your repeat database is sufficient, you may need to
>> generate a species specific repeat library using something like
>> RepeatModeler.  Repeats can end up being included as extra exons in gene
>> models because they may contain reading frames the do code for proteins
>> (I.e. reverse transcriptases).
>>
>> If you have any questions on any of the above, just let us know.
>>
>> Thanks,
>> Carson
>>
>>
>> From: Janna Fierst <jfierst at uoregon.edu>
>> Date: Monday, August 26, 2013 2:54 PM
>> To: <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] exon/intron boundaries
>>
>> Hi,
>>
>> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
>> initial results appear fairly good but we seem to be be annotating too many
>> exons for multiple genes. I was wondering which parameters should be tuned
>> to change the threshold for exon/intron boundaries? Thanks for your help
>> -Janna Fierst
>> _______________________________________________ maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From graham.etherington at sainsbury-laboratory.ac.uk  Thu Oct 24 07:42:51 2013
From: graham.etherington at sainsbury-laboratory.ac.uk (graham etherington (TSL))
Date: Thu, 24 Oct 2013 13:42:51 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE7FA55D.10C4B%carsonhh@gmail.com>
Message-ID: <CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>

Hi,
I notice that the latest version of Maker available from
http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
2013). As we're also having the start codon problem we'd like to get hold
of v2.30. Do you know when this will be released?
Many thanks,
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:

>Before Wednesday, because after that I'm on a 6 day road trip, so I have
>to have it wrapped up before I leave.
>
>--Carson
>
>
>
>
>On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>>Thx Carson! Do you now when 2.30 will be available? Bests
>>
>>On 12.10.2013 17:48, Carson Holt wrote:
>>> This issue just came up this week on another e-mail as well.
>>>
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>> BioPerl (use maker --debug to have maker print out the locations of all
>>> modules it uses).  Such a hack should only be done as a temporary work
>>> around.
>>>
>>> You change line 256 from -->
>>> ---M---------------M---------------M----------------------------
>>>
>>> To-->
>>> -----------------------------------M----------------------------
>>>
>>>
>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>codon
>>> used in a result it receives is acceptable or if it should look
>>>upstream
>>> or downstream for a different one. Apparently there are actually 3
>>> acceptable start codons in the standard codon table (2 rare ones and
>>>one
>>> common), so making the edit removes the two rare ones from the list.
>>>
>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>to
>>> the BioPerl module, that will be used by default and should fix the
>>>issue.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a serious problems with maker annotations especially the start
>>>> codon placement. It started happening with maker version 2.27! About
>>>>1/3
>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>> files gene predictors and est evidence standalone would predict the
>>>> right gene structure including the start codon. I was thinking that
>>>>this
>>>> problem was somehow linked to my gene models but looking at their
>>>> standalone prediction I discarded that theory. Just some stats about
>>>> proteins with proper start codon (first column) and missing start
>>>>codon
>>>> (second column).
>>>>
>>>> Maker		9268	4215
>>>> SNAP		16577	896
>>>> Genemark	18764	290
>>>>
>>>> Numbers look the same when Augustus is used (currently retraining).
>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>want
>>>> to check > 4000 genes for this.
>>>>
>>>> Do you have any idea what could cause such a problem? If you need some
>>>> example gff files I can send you.
>>>>
>>>> Best regards
>>>> Felix
>>>>
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>-- 
>>Felix Bemm
>>Department of Bioinformatics
>>University of W?rzburg, Germany
>>Tel: +49 931 - 31 83696
>>Fax: +49 931 - 31 84552
>>felix.bemm at uni-wuerzburg.de
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From myandell at genetics.utah.edu  Thu Oct 24 07:55:05 2013
From: myandell at genetics.utah.edu (Mark Yandell)
Date: Thu, 24 Oct 2013 13:55:05 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>,
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
Message-ID: <7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>

Hi Graham,

 Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.


--mark


Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
Sent: Thursday, October 24, 2013 7:42 AM
To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
Cc: Kate Bailey (TSL)
Subject: Re: [maker-devel] Serious Start Codon Problem

Hi,
I notice that the latest version of Maker available from
http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
2013). As we're also having the start codon problem we'd like to get hold
of v2.30. Do you know when this will be released?
Many thanks,
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:

>Before Wednesday, because after that I'm on a 6 day road trip, so I have
>to have it wrapped up before I leave.
>
>--Carson
>
>
>
>
>On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>>Thx Carson! Do you now when 2.30 will be available? Bests
>>
>>On 12.10.2013 17:48, Carson Holt wrote:
>>> This issue just came up this week on another e-mail as well.
>>>
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>> BioPerl (use maker --debug to have maker print out the locations of all
>>> modules it uses).  Such a hack should only be done as a temporary work
>>> around.
>>>
>>> You change line 256 from -->
>>> ---M---------------M---------------M----------------------------
>>>
>>> To-->
>>> -----------------------------------M----------------------------
>>>
>>>
>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>codon
>>> used in a result it receives is acceptable or if it should look
>>>upstream
>>> or downstream for a different one. Apparently there are actually 3
>>> acceptable start codons in the standard codon table (2 rare ones and
>>>one
>>> common), so making the edit removes the two rare ones from the list.
>>>
>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>to
>>> the BioPerl module, that will be used by default and should fix the
>>>issue.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a serious problems with maker annotations especially the start
>>>> codon placement. It started happening with maker version 2.27! About
>>>>1/3
>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>> files gene predictors and est evidence standalone would predict the
>>>> right gene structure including the start codon. I was thinking that
>>>>this
>>>> problem was somehow linked to my gene models but looking at their
>>>> standalone prediction I discarded that theory. Just some stats about
>>>> proteins with proper start codon (first column) and missing start
>>>>codon
>>>> (second column).
>>>>
>>>> Maker              9268    4215
>>>> SNAP               16577   896
>>>> Genemark   18764   290
>>>>
>>>> Numbers look the same when Augustus is used (currently retraining).
>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>want
>>>> to check > 4000 genes for this.
>>>>
>>>> Do you have any idea what could cause such a problem? If you need some
>>>> example gff files I can send you.
>>>>
>>>> Best regards
>>>> Felix
>>>>
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>>
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>--
>>Felix Bemm
>>Department of Bioinformatics
>>University of W?rzburg, Germany
>>Tel: +49 931 - 31 83696
>>Fax: +49 931 - 31 84552
>>felix.bemm at uni-wuerzburg.de
>
>
>
>_______________________________________________
>maker-devel mailing list
>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
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


From felix.bemm at uni-wuerzburg.de  Thu Oct 24 08:03:27 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Thu, 24 Oct 2013 16:03:27 +0200
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>,
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
Message-ID: <526928AF.90108@uni-wuerzburg.de>

Hi,

I used the temporary fix of the Bio::Tools::CodonTable. It's working 
pretty nice. Almost every predicted proteins now start with a M ;)

Bests
Felix

On 24.10.2013 15:55, Mark Yandell wrote:
> Hi Graham,
>
>   Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>
>
> --mark
>
>
> Mark Yandell
> Professor of Human Genetics
> H.A. & Edna Benning Presidential Endowed Chair
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ph:801-587-7707
>
> ________________________________________
> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
> Sent: Thursday, October 24, 2013 7:42 AM
> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
> Cc: Kate Bailey (TSL)
> Subject: Re: [maker-devel] Serious Start Codon Problem
>
> Hi,
> I notice that the latest version of Maker available from
> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
> 2013). As we're also having the start codon problem we'd like to get hold
> of v2.30. Do you know when this will be released?
> Many thanks,
> Graham
>
>
> Dr. Graham Etherington
> Bioinformatics Support Officer,
> The Sainsbury Laboratory,
> Norwich Research Park,
> Norwich NR4 7UH.
> UK
> Tel: +44 (0)1603 450601
>
>
>
>
>
> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>
>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>> to have it wrapped up before I leave.
>>
>> --Carson
>>
>>
>>
>>
>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>
>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>> This issue just came up this week on another e-mail as well.
>>>>
>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>> around.
>>>>
>>>> You change line 256 from -->
>>>> ---M---------------M---------------M----------------------------
>>>>
>>>> To-->
>>>> -----------------------------------M----------------------------
>>>>
>>>>
>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>> codon
>>>> used in a result it receives is acceptable or if it should look
>>>> upstream
>>>> or downstream for a different one. Apparently there are actually 3
>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>> one
>>>> common), so making the edit removes the two rare ones from the list.
>>>>
>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>> to
>>>> the BioPerl module, that will be used by default and should fix the
>>>> issue.
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>>
>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I have a serious problems with maker annotations especially the start
>>>>> codon placement. It started happening with maker version 2.27! About
>>>>> 1/3
>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>> files gene predictors and est evidence standalone would predict the
>>>>> right gene structure including the start codon. I was thinking that
>>>>> this
>>>>> problem was somehow linked to my gene models but looking at their
>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>> proteins with proper start codon (first column) and missing start
>>>>> codon
>>>>> (second column).
>>>>>
>>>>> Maker              9268    4215
>>>>> SNAP               16577   896
>>>>> Genemark   18764   290
>>>>>
>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>> want
>>>>> to check > 4000 genes for this.
>>>>>
>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>> example gff files I can send you.
>>>>>
>>>>> Best regards
>>>>> Felix
>>>>>
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>>
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From jim.hu.biobio at gmail.com  Thu Oct 24 08:32:01 2013
From: jim.hu.biobio at gmail.com (JH Gmail)
Date: Thu, 24 Oct 2013 09:32:01 -0500
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
Message-ID: <69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>

Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 

Does maker handle ribosome profiling yet?

jim

Sent from my iPad

> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
> 
> Hi Graham,
> 
> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
> 
> 
> --mark
> 
> 
> Mark Yandell
> Professor of Human Genetics
> H.A. & Edna Benning Presidential Endowed Chair
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ph:801-587-7707
> 
> ________________________________________
> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
> Sent: Thursday, October 24, 2013 7:42 AM
> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
> Cc: Kate Bailey (TSL)
> Subject: Re: [maker-devel] Serious Start Codon Problem
> 
> Hi,
> I notice that the latest version of Maker available from
> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
> 2013). As we're also having the start codon problem we'd like to get hold
> of v2.30. Do you know when this will be released?
> Many thanks,
> Graham
> 
> 
> Dr. Graham Etherington
> Bioinformatics Support Officer,
> The Sainsbury Laboratory,
> Norwich Research Park,
> Norwich NR4 7UH.
> UK
> Tel: +44 (0)1603 450601
> 
> 
> 
> 
> 
>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>> 
>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>> to have it wrapped up before I leave.
>> 
>> --Carson
>> 
>> 
>> 
>> 
>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>> 
>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>> 
>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>> This issue just came up this week on another e-mail as well.
>>>> 
>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>> around.
>>>> 
>>>> You change line 256 from -->
>>>> ---M---------------M---------------M----------------------------
>>>> 
>>>> To-->
>>>> -----------------------------------M----------------------------
>>>> 
>>>> 
>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>> codon
>>>> used in a result it receives is acceptable or if it should look
>>>> upstream
>>>> or downstream for a different one. Apparently there are actually 3
>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>> one
>>>> common), so making the edit removes the two rare ones from the list.
>>>> 
>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>> to
>>>> the BioPerl module, that will be used by default and should fix the
>>>> issue.
>>>> 
>>>> Thanks,
>>>> Carson
>>>> 
>>>> 
>>>> 
>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> I have a serious problems with maker annotations especially the start
>>>>> codon placement. It started happening with maker version 2.27! About
>>>>> 1/3
>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>> files gene predictors and est evidence standalone would predict the
>>>>> right gene structure including the start codon. I was thinking that
>>>>> this
>>>>> problem was somehow linked to my gene models but looking at their
>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>> proteins with proper start codon (first column) and missing start
>>>>> codon
>>>>> (second column).
>>>>> 
>>>>> Maker              9268    4215
>>>>> SNAP               16577   896
>>>>> Genemark   18764   290
>>>>> 
>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>> want
>>>>> to check > 4000 genes for this.
>>>>> 
>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>> example gff files I can send you.
>>>>> 
>>>>> Best regards
>>>>> Felix
>>>>> 
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>> 
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



From amelia.ireland at gmod.org  Thu Oct 24 12:52:17 2013
From: amelia.ireland at gmod.org (Amelia Ireland)
Date: Thu, 24 Oct 2013 11:52:17 -0700
Subject: [maker-devel] GMOD 2014: San Diego
Message-ID: <CAALsq00kuy83m4_k_rcWLSpwFYwMCYm5LXEkUgwzqCOUGfryBw@mail.gmail.com>

Greetings GMOD community citizens!

Online registration is now open for the 2014 GMOD meeting, to be held at
the Best Western Seven Seas, San Diego, CA, on January 16-17, 2014 (after
PAG). The meeting is open to GMOD users, developers, and anyone interested
in the project and the software we provide.

Online registration is now open; please see the meeting page,
http://gmod.org/wiki/Jan_2014_GMOD_Meeting, for more information. Early
bird registration rates apply until Dec. 14th.

We have secured a discount on a block of rooms at the Best Western Seven
Seas; please see the wiki for more information on booking.

Please feel free to contact the GMOD helpdesk on help at gmod.org if you have
any questions. Thanks!

-- 
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject
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From barry.moore at genetics.utah.edu  Thu Oct 24 15:09:20 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Thu, 24 Oct 2013 15:09:20 -0600
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
	<69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
Message-ID: <1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>

Hi Jim,

You can and any kind of evidence you want to MAKER including ribosomal profiling data as long as you format it in GFF3 format.  You could pass in your GFF3 formatted ribosomal profiling data in maker_opt.ctl with the protein_gff option and it will be treated as protein evidence.  However if you are wondering if anyone has coded a specific addition to MAKER to accept ribosomal profiling data and treat it as a different kind of evidence then no, this hasn't been done.

B

On Oct 24, 2013, at 8:32 AM, JH Gmail wrote:

> Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 
> 
> Does maker handle ribosome profiling yet?
> 
> jim
> 
> Sent from my iPad
> 
>> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
>> 
>> Hi Graham,
>> 
>> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>> 
>> 
>> --mark
>> 
>> 
>> Mark Yandell
>> Professor of Human Genetics
>> H.A. & Edna Benning Presidential Endowed Chair
>> Eccles Institute of Human Genetics
>> University of Utah
>> 15 North 2030 East, Room 2100
>> Salt Lake City, UT 84112-5330
>> ph:801-587-7707
>> 
>> ________________________________________
>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
>> Sent: Thursday, October 24, 2013 7:42 AM
>> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
>> Cc: Kate Bailey (TSL)
>> Subject: Re: [maker-devel] Serious Start Codon Problem
>> 
>> Hi,
>> I notice that the latest version of Maker available from
>> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
>> 2013). As we're also having the start codon problem we'd like to get hold
>> of v2.30. Do you know when this will be released?
>> Many thanks,
>> Graham
>> 
>> 
>> Dr. Graham Etherington
>> Bioinformatics Support Officer,
>> The Sainsbury Laboratory,
>> Norwich Research Park,
>> Norwich NR4 7UH.
>> UK
>> Tel: +44 (0)1603 450601
>> 
>> 
>> 
>> 
>> 
>>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>>> 
>>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>>> to have it wrapped up before I leave.
>>> 
>>> --Carson
>>> 
>>> 
>>> 
>>> 
>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>> 
>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>> 
>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>> This issue just came up this week on another e-mail as well.
>>>>> 
>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>> around.
>>>>> 
>>>>> You change line 256 from -->
>>>>> ---M---------------M---------------M----------------------------
>>>>> 
>>>>> To-->
>>>>> -----------------------------------M----------------------------
>>>>> 
>>>>> 
>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>> codon
>>>>> used in a result it receives is acceptable or if it should look
>>>>> upstream
>>>>> or downstream for a different one. Apparently there are actually 3
>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>> one
>>>>> common), so making the edit removes the two rare ones from the list.
>>>>> 
>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>> to
>>>>> the BioPerl module, that will be used by default and should fix the
>>>>> issue.
>>>>> 
>>>>> Thanks,
>>>>> Carson
>>>>> 
>>>>> 
>>>>> 
>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I have a serious problems with maker annotations especially the start
>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>> 1/3
>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>> right gene structure including the start codon. I was thinking that
>>>>>> this
>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>> proteins with proper start codon (first column) and missing start
>>>>>> codon
>>>>>> (second column).
>>>>>> 
>>>>>> Maker              9268    4215
>>>>>> SNAP               16577   896
>>>>>> Genemark   18764   290
>>>>>> 
>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>> want
>>>>>> to check > 4000 genes for this.
>>>>>> 
>>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>>> example gff files I can send you.
>>>>>> 
>>>>>> Best regards
>>>>>> Felix
>>>>>> 
>>>>>> --
>>>>>> Felix Bemm
>>>>>> Department of Bioinformatics
>>>>>> University of W?rzburg, Germany
>>>>>> Tel: +49 931 - 31 83696
>>>>>> Fax: +49 931 - 31 84552
>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>> 
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> 
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> 
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> 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
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> _______________________________________________
>> maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From marc.hoeppner at imbim.uu.se  Fri Oct 25 08:20:04 2013
From: marc.hoeppner at imbim.uu.se (Marc P. Hoeppner)
Date: Fri, 25 Oct 2013 16:20:04 +0200
Subject: [maker-devel] Maker MPICH2 issue (Multiple MAKER processes have
 been started in the same directory)
Message-ID: <526A7E14.9010906@imbim.uu.se>

Dear list,

I know that MPICH2 related issues have been discussed previously, but 
the suggested solutions don't seem to work for me.
Briefly, I have set up a new cluster, with a fresh install of mpich2 (SL 
6.4, from the yum repos) and a newly compiled build of Maker 2.28.

When I start maker with mpiexec, I get spammed with
'WARNING: Multiple MAKER processes have been started in the same 
directory.'

Here is what I have tried so far - still getting the error :-< Any 
suggestions would be appreciated

--------
MPICH2
---------

which mpiexec:
/usr/lib64/mpich2/bin/mpiexec

Started the mpd ring as normal user across 5 nodes (bnode-01 to 
bnode-04, and the head node bhead)

mpdtrace:
bhead
bnode-02
bnode-03
bnode-04
bnode-01

mpdringtest:
time for 1 loops = 0.00128293037415 seconds

mpixec -n 32 -machinefile hostfile hostname:

<long list of host names, as ecpected>

I also ran the Skampi Mpi Benchmark, which ran through just fine.

-----------
MAKER
-----------

./Build status

PERL Dependencies:      VERIFIED
External Programs:      VERIFIED
External C Libraries:   VERIFIED
MPI SUPPORT:            ENABLED
MWAS Web Interface:     DISABLED
MAKER PACKAGE:          CONFIGURATION OK

During configuration/installation, Build.PL automatically detected all 
MPI data and never complained, so I have to assume that everything went 
fine there.

-- 
----------
Marc P. Hoeppner, PhD
Department of Microbiology and Medical Biochemistry
Uppsala University, Sweden
marc.hoeppner at imbim.uu.se




From jim.hu.biobio at gmail.com  Fri Oct 25 08:51:19 2013
From: jim.hu.biobio at gmail.com (JH Gmail)
Date: Fri, 25 Oct 2013 09:51:19 -0500
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
	<69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
	<1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>
Message-ID: <596400F6-3215-4F71-A896-AF52CEC8D77D@gmail.com>

Thanks Barry,

I'm thinking about this more theoretically, as we don't have immediate plans, but...

This would work for gff derived from ribosome profiling analysis, but it would be nice to be able to start with bam files of mapped reads, or coverage scores as bigwig or gff.  RNA-seq has similar issues, but IIRC Maker expects RNA-seq data to be assembled first.  It may not be possible to do de novo cds assembly from ribosome profiling because I think the nuclease step may kill the overlaps. I'd have to look at some of the available data. 

Jim

Sent from my iPad

> On Oct 24, 2013, at 4:09 PM, Barry Moore <barry.moore at genetics.utah.edu> wrote:
> 
> Hi Jim,
> 
> You can and any kind of evidence you want to MAKER including ribosomal profiling data as long as you format it in GFF3 format.  You could pass in your GFF3 formatted ribosomal profiling data in maker_opt.ctl with the protein_gff option and it will be treated as protein evidence.  However if you are wondering if anyone has coded a specific addition to MAKER to accept ribosomal profiling data and treat it as a different kind of evidence then no, this hasn't been done.
> 
> B
> 
>> On Oct 24, 2013, at 8:32 AM, JH Gmail wrote:
>> 
>> Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 
>> 
>> Does maker handle ribosome profiling yet?
>> 
>> jim
>> 
>> Sent from my iPad
>> 
>>> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
>>> 
>>> Hi Graham,
>>> 
>>> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>>> 
>>> 
>>> --mark
>>> 
>>> 
>>> Mark Yandell
>>> Professor of Human Genetics
>>> H.A. & Edna Benning Presidential Endowed Chair
>>> Eccles Institute of Human Genetics
>>> University of Utah
>>> 15 North 2030 East, Room 2100
>>> Salt Lake City, UT 84112-5330
>>> ph:801-587-7707
>>> 
>>> ________________________________________
>>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
>>> Sent: Thursday, October 24, 2013 7:42 AM
>>> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
>>> Cc: Kate Bailey (TSL)
>>> Subject: Re: [maker-devel] Serious Start Codon Problem
>>> 
>>> Hi,
>>> I notice that the latest version of Maker available from
>>> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
>>> 2013). As we're also having the start codon problem we'd like to get hold
>>> of v2.30. Do you know when this will be released?
>>> Many thanks,
>>> Graham
>>> 
>>> 
>>> Dr. Graham Etherington
>>> Bioinformatics Support Officer,
>>> The Sainsbury Laboratory,
>>> Norwich Research Park,
>>> Norwich NR4 7UH.
>>> UK
>>> Tel: +44 (0)1603 450601
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>>>> 
>>>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>>>> to have it wrapped up before I leave.
>>>> 
>>>> --Carson
>>>> 
>>>> 
>>>> 
>>>> 
>>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>> 
>>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>>> 
>>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>>> This issue just came up this week on another e-mail as well.
>>>>>> 
>>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>>> around.
>>>>>> 
>>>>>> You change line 256 from -->
>>>>>> ---M---------------M---------------M----------------------------
>>>>>> 
>>>>>> To-->
>>>>>> -----------------------------------M----------------------------
>>>>>> 
>>>>>> 
>>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>>> codon
>>>>>> used in a result it receives is acceptable or if it should look
>>>>>> upstream
>>>>>> or downstream for a different one. Apparently there are actually 3
>>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>>> one
>>>>>> common), so making the edit removes the two rare ones from the list.
>>>>>> 
>>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>>> to
>>>>>> the BioPerl module, that will be used by default and should fix the
>>>>>> issue.
>>>>>> 
>>>>>> Thanks,
>>>>>> Carson
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I have a serious problems with maker annotations especially the start
>>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>>> 1/3
>>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>>> right gene structure including the start codon. I was thinking that
>>>>>>> this
>>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>>> proteins with proper start codon (first column) and missing start
>>>>>>> codon
>>>>>>> (second column).
>>>>>>> 
>>>>>>> Maker              9268    4215
>>>>>>> SNAP               16577   896
>>>>>>> Genemark   18764   290
>>>>>>> 
>>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>>> want
>>>>>>> to check > 4000 genes for this.
>>>>>>> 
>>>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>>>> example gff files I can send you.
>>>>>>> 
>>>>>>> Best regards
>>>>>>> Felix
>>>>>>> 
>>>>>>> --
>>>>>>> Felix Bemm
>>>>>>> Department of Bioinformatics
>>>>>>> University of W?rzburg, Germany
>>>>>>> Tel: +49 931 - 31 83696
>>>>>>> Fax: +49 931 - 31 84552
>>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> 
>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>> 
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> 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
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> _______________________________________________
>>> maker-devel mailing list
>>> 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
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
> 
> 
> 
> 
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From barry.moore at genetics.utah.edu  Fri Oct 25 09:44:55 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Fri, 25 Oct 2013 09:44:55 -0600
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <596400F6-3215-4F71-A896-AF52CEC8D77D@gmail.com>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
	<69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
	<1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>
	<596400F6-3215-4F71-A896-AF52CEC8D77D@gmail.com>
Message-ID: <DA777487-D8DD-47E2-A852-DB123C3A1BB8@genetics.utah.edu>

Thanks Jim.

B

On Oct 25, 2013, at 8:51 AM, JH Gmail wrote:

> Thanks Barry,
> 
> I'm thinking about this more theoretically, as we don't have immediate plans, but...
> 
> This would work for gff derived from ribosome profiling analysis, but it would be nice to be able to start with bam files of mapped reads, or coverage scores as bigwig or gff.  RNA-seq has similar issues, but IIRC Maker expects RNA-seq data to be assembled first.  It may not be possible to do de novo cds assembly from ribosome profiling because I think the nuclease step may kill the overlaps. I'd have to look at some of the available data. 
> 
> Jim
> 
> Sent from my iPad
> 
> On Oct 24, 2013, at 4:09 PM, Barry Moore <barry.moore at genetics.utah.edu> wrote:
> 
>> Hi Jim,
>> 
>> You can and any kind of evidence you want to MAKER including ribosomal profiling data as long as you format it in GFF3 format.  You could pass in your GFF3 formatted ribosomal profiling data in maker_opt.ctl with the protein_gff option and it will be treated as protein evidence.  However if you are wondering if anyone has coded a specific addition to MAKER to accept ribosomal profiling data and treat it as a different kind of evidence then no, this hasn't been done.
>> 
>> B
>> 
>> On Oct 24, 2013, at 8:32 AM, JH Gmail wrote:
>> 
>>> Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 
>>> 
>>> Does maker handle ribosome profiling yet?
>>> 
>>> jim
>>> 
>>> Sent from my iPad
>>> 
>>>> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
>>>> 
>>>> Hi Graham,
>>>> 
>>>> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>>>> 
>>>> 
>>>> --mark
>>>> 
>>>> 
>>>> Mark Yandell
>>>> Professor of Human Genetics
>>>> H.A. & Edna Benning Presidential Endowed Chair
>>>> Eccles Institute of Human Genetics
>>>> University of Utah
>>>> 15 North 2030 East, Room 2100
>>>> Salt Lake City, UT 84112-5330
>>>> ph:801-587-7707
>>>> 
>>>> ________________________________________
>>>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
>>>> Sent: Thursday, October 24, 2013 7:42 AM
>>>> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
>>>> Cc: Kate Bailey (TSL)
>>>> Subject: Re: [maker-devel] Serious Start Codon Problem
>>>> 
>>>> Hi,
>>>> I notice that the latest version of Maker available from
>>>> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
>>>> 2013). As we're also having the start codon problem we'd like to get hold
>>>> of v2.30. Do you know when this will be released?
>>>> Many thanks,
>>>> Graham
>>>> 
>>>> 
>>>> Dr. Graham Etherington
>>>> Bioinformatics Support Officer,
>>>> The Sainsbury Laboratory,
>>>> Norwich Research Park,
>>>> Norwich NR4 7UH.
>>>> UK
>>>> Tel: +44 (0)1603 450601
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>>>>> 
>>>>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>>>>> to have it wrapped up before I leave.
>>>>> 
>>>>> --Carson
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>> 
>>>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>>>> 
>>>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>>>> This issue just came up this week on another e-mail as well.
>>>>>>> 
>>>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>>>> around.
>>>>>>> 
>>>>>>> You change line 256 from -->
>>>>>>> ---M---------------M---------------M----------------------------
>>>>>>> 
>>>>>>> To-->
>>>>>>> -----------------------------------M----------------------------
>>>>>>> 
>>>>>>> 
>>>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>>>> codon
>>>>>>> used in a result it receives is acceptable or if it should look
>>>>>>> upstream
>>>>>>> or downstream for a different one. Apparently there are actually 3
>>>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>>>> one
>>>>>>> common), so making the edit removes the two rare ones from the list.
>>>>>>> 
>>>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>>>> to
>>>>>>> the BioPerl module, that will be used by default and should fix the
>>>>>>> issue.
>>>>>>> 
>>>>>>> Thanks,
>>>>>>> Carson
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>>>> 
>>>>>>>> Hi,
>>>>>>>> 
>>>>>>>> I have a serious problems with maker annotations especially the start
>>>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>>>> 1/3
>>>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>>>> right gene structure including the start codon. I was thinking that
>>>>>>>> this
>>>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>>>> proteins with proper start codon (first column) and missing start
>>>>>>>> codon
>>>>>>>> (second column).
>>>>>>>> 
>>>>>>>> Maker              9268    4215
>>>>>>>> SNAP               16577   896
>>>>>>>> Genemark   18764   290
>>>>>>>> 
>>>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>>>> want
>>>>>>>> to check > 4000 genes for this.
>>>>>>>> 
>>>>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>>>>> example gff files I can send you.
>>>>>>>> 
>>>>>>>> Best regards
>>>>>>>> Felix
>>>>>>>> 
>>>>>>>> --
>>>>>>>> Felix Bemm
>>>>>>>> Department of Bioinformatics
>>>>>>>> University of W?rzburg, Germany
>>>>>>>> Tel: +49 931 - 31 83696
>>>>>>>> Fax: +49 931 - 31 84552
>>>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> maker-devel mailing list
>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>> 
>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>> 
>>>>>> --
>>>>>> Felix Bemm
>>>>>> Department of Bioinformatics
>>>>>> University of W?rzburg, Germany
>>>>>> Tel: +49 931 - 31 83696
>>>>>> Fax: +49 931 - 31 84552
>>>>>> felix.bemm at uni-wuerzburg.de
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> 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
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> 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
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> Barry Moore
>> Research Scientist
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT 84112
>> --------------------------------------------
>> (801) 585-3543
>> 
>> 
>> 
>> 

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From marc.hoeppner at imbim.uu.se  Sat Oct 26 05:54:07 2013
From: marc.hoeppner at imbim.uu.se (Marc P. Hoeppner)
Date: Sat, 26 Oct 2013 13:54:07 +0200
Subject: [maker-devel] Maker MPICH2 issue (Multiple MAKER processes have
 been started in the same directory)
In-Reply-To: <526A7E14.9010906@imbim.uu.se>
References: <526A7E14.9010906@imbim.uu.se>
Message-ID: <526BAD5F.2000800@imbim.uu.se>

Dear List,

after much more debugging, I found the solution myself. Here are the 
details:

The Maker installation instructions refer to 'mpich2' in multiple 
places, including weblinks (whchi are outdated btw). Some digging 
revealed that mpich2 has since been renamed and merged back into mpich. 
So the website is www.mpich.org and the current stable version is 
mpich-3.0.4.  Closely following the installation instruction yielded a 
working copy of mpiexec that Maker was willing to accept. Good news - 
but I suggest to update the documentation. Most importantly for either 
SL/CentOS users, mpich2 as packaged with e.g. Scientific Linux *does 
not* work with Maker. You will need to download the latest stable build 
and compile it yourself (the mpich2 version bundled with Maker doesn't 
work either btw).

Cheers,

Marc

> Dear list,
>
> I know that MPICH2 related issues have been discussed previously, but 
> the suggested solutions don't seem to work for me.
> Briefly, I have set up a new cluster, with a fresh install of mpich2 
> (SL 6.4, from the yum repos) and a newly compiled build of Maker 2.28.
>
> When I start maker with mpiexec, I get spammed with
> 'WARNING: Multiple MAKER processes have been started in the same 
> directory.'
>
> Here is what I have tried so far - still getting the error :-< Any 
> suggestions would be appreciated
>
> --------
> MPICH2
> ---------
>
> which mpiexec:
> /usr/lib64/mpich2/bin/mpiexec
>
> Started the mpd ring as normal user across 5 nodes (bnode-01 to 
> bnode-04, and the head node bhead)
>
> mpdtrace:
> bhead
> bnode-02
> bnode-03
> bnode-04
> bnode-01
>
> mpdringtest:
> time for 1 loops = 0.00128293037415 seconds
>
> mpixec -n 32 -machinefile hostfile hostname:
>
> <long list of host names, as ecpected>
>
> I also ran the Skampi Mpi Benchmark, which ran through just fine.
>
> -----------
> MAKER
> -----------
>
> ./Build status
>
> PERL Dependencies:      VERIFIED
> External Programs:      VERIFIED
> External C Libraries:   VERIFIED
> MPI SUPPORT:            ENABLED
> MWAS Web Interface:     DISABLED
> MAKER PACKAGE:          CONFIGURATION OK
>
> During configuration/installation, Build.PL automatically detected all 
> MPI data and never complained, so I have to assume that everything 
> went fine there.
>


-- 
----------
Marc P. Hoeppner, PhD
Department of Microbiology and Medical Biochemistry
Uppsala University, Sweden
marc.hoeppner at imbim.uu.se




From barry.utah at gmail.com  Sat Oct 26 08:41:24 2013
From: barry.utah at gmail.com (Barry Moore)
Date: Sat, 26 Oct 2013 08:41:24 -0600
Subject: [maker-devel] Maker MPICH2 issue (Multiple MAKER processes have
	been started in the same directory)
In-Reply-To: <526BAD5F.2000800@imbim.uu.se>
References: <526A7E14.9010906@imbim.uu.se> <526BAD5F.2000800@imbim.uu.se>
Message-ID: <DDEE11FF-9EE2-4359-9A50-3DA95770DDEC@genetics.utah.edu>

Hi Marc,

Thanks so much for sharing the results of all your hard work!  We will follow up on your feedback and incorporate the necessary updates to MAKER docs and installation procedures.

B

On Oct 26, 2013, at 5:54 AM, Marc P. Hoeppner wrote:

> Dear List,
> 
> after much more debugging, I found the solution myself. Here are the details:
> 
> The Maker installation instructions refer to 'mpich2' in multiple places, including weblinks (whchi are outdated btw). Some digging revealed that mpich2 has since been renamed and merged back into mpich. So the website is www.mpich.org and the current stable version is mpich-3.0.4.  Closely following the installation instruction yielded a working copy of mpiexec that Maker was willing to accept. Good news - but I suggest to update the documentation. Most importantly for either SL/CentOS users, mpich2 as packaged with e.g. Scientific Linux *does not* work with Maker. You will need to download the latest stable build and compile it yourself (the mpich2 version bundled with Maker doesn't work either btw).
> 
> Cheers,
> 
> Marc
> 
>> Dear list,
>> 
>> I know that MPICH2 related issues have been discussed previously, but the suggested solutions don't seem to work for me.
>> Briefly, I have set up a new cluster, with a fresh install of mpich2 (SL 6.4, from the yum repos) and a newly compiled build of Maker 2.28.
>> 
>> When I start maker with mpiexec, I get spammed with
>> 'WARNING: Multiple MAKER processes have been started in the same directory.'
>> 
>> Here is what I have tried so far - still getting the error :-< Any suggestions would be appreciated
>> 
>> --------
>> MPICH2
>> ---------
>> 
>> which mpiexec:
>> /usr/lib64/mpich2/bin/mpiexec
>> 
>> Started the mpd ring as normal user across 5 nodes (bnode-01 to bnode-04, and the head node bhead)
>> 
>> mpdtrace:
>> bhead
>> bnode-02
>> bnode-03
>> bnode-04
>> bnode-01
>> 
>> mpdringtest:
>> time for 1 loops = 0.00128293037415 seconds
>> 
>> mpixec -n 32 -machinefile hostfile hostname:
>> 
>> <long list of host names, as ecpected>
>> 
>> I also ran the Skampi Mpi Benchmark, which ran through just fine.
>> 
>> -----------
>> MAKER
>> -----------
>> 
>> ./Build status
>> 
>> PERL Dependencies:      VERIFIED
>> External Programs:      VERIFIED
>> External C Libraries:   VERIFIED
>> MPI SUPPORT:            ENABLED
>> MWAS Web Interface:     DISABLED
>> MAKER PACKAGE:          CONFIGURATION OK
>> 
>> During configuration/installation, Build.PL automatically detected all MPI data and never complained, so I have to assume that everything went fine there.
>> 
> 
> 
> -- 
> ----------
> Marc P. Hoeppner, PhD
> Department of Microbiology and Medical Biochemistry
> Uppsala University, Sweden
> marc.hoeppner at imbim.uu.se
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From wholtz at lygos.com  Wed Oct 30 12:21:52 2013
From: wholtz at lygos.com (William Holtz)
Date: Wed, 30 Oct 2013 11:21:52 -0700 (PDT)
Subject: [maker-devel] maker apollo error
Message-ID: <1383157312.95043.YahooMailNeo@web5706.biz.mail.ne1.yahoo.com>

Hi,

I'm attempting to reply to a thread on this list from before I was a member. My apologies if this gets messed up.

I've tried installing maker v2.28 and v2.29p-beta and both of them fail due to the URL of the apollo tar file being outdated as previously reported on this list.?The updated URL that Carson Holt posted,?http://sourceforge.net/code-snapshots/svn/g/gm/gmod/svn/gmod-svn-25291-apollo-trunk.zip,?is also no longer valid. I was able to find a copy of the apollo source at?http://downloads.sourceforge.net/project/gmod/Apollo/1.11.1/apollo-1.11.1.tgz. However my attempts to integrate this into the maker build process have been unsuccessful, but likely could be done by someone more skilled than I.?Any pointers on how to get past this hurdle would be appreciated.

Thanks in advance for your help.

-Will



From barry.utah at gmail.com  Wed Oct 30 16:31:58 2013
From: barry.utah at gmail.com (Barry Moore)
Date: Wed, 30 Oct 2013 16:31:58 -0600
Subject: [maker-devel] maker apollo error
In-Reply-To: <1383157312.95043.YahooMailNeo@web5706.biz.mail.ne1.yahoo.com>
References: <1383157312.95043.YahooMailNeo@web5706.biz.mail.ne1.yahoo.com>
Message-ID: <C6E0A4A7-10D2-43B4-AA77-CCF6BE62E927@genetics.utah.edu>

Hi Will,

You can edit these URLs in the following file:

maker/src/locations

In a section that looks like this:

    'apollo'       => {'Linux_x86_64'  => 'http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar',
                       'Linux_i386'    => 'http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar',
                       'Darwin_i386'   => 'http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz',
                       'Darwin_x86_64' => 'http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz',
                       'src_'          => 'http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz',
                   },

Carson may have more feedback for you as well, but he is right in the middle of a move, so there may be a few days before he can reply, so modifying this file should work for you in the mean time.

On any of the executables that are missing you can always install them manually and add them to your path and maker will find them.  Also, maker shouldn't be required for a base maker install, so you could ignore that dependency as well.

Thanks,

B




On Oct 30, 2013, at 12:21 PM, William Holtz wrote:

> Hi,
> 
> I'm attempting to reply to a thread on this list from before I was a member. My apologies if this gets messed up.
> 
> I've tried installing maker v2.28 and v2.29p-beta and both of them fail due to the URL of the apollo tar file being outdated as previously reported on this list. The updated URL that Carson Holt posted, http://sourceforge.net/code-snapshots/svn/g/gm/gmod/svn/gmod-svn-25291-apollo-trunk.zip, is also no longer valid. I was able to find a copy of the apollo source at http://downloads.sourceforge.net/project/gmod/Apollo/1.11.1/apollo-1.11.1.tgz. However my attempts to integrate this into the maker build process have been unsuccessful, but likely could be done by someone more skilled than I. Any pointers on how to get past this hurdle would be appreciated.
> 
> Thanks in advance for your help.
> 
> -Will
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From carsonhh at gmail.com  Wed Oct  2 08:14:44 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 02 Oct 2013 10:14:44 -0400
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
Message-ID: <CE709D72.EF15%carsonhh@gmail.com>

It still works, but it will be reduced.  Without ESTs you won't get any
UTR prediction, also you will be limited by how well the protein set
matches to the genes.  If you use the protein set of a close relative you
will capture most things.  You will probably capture 80-95% of what you
would by also including ESTs.  It all depending on how different the
species in the proteins evidence file are compared to the the species
being annotated.

--Carson

On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for your message and your kind help. Now conversion from
>match/match_part to gene/mRNA/exons/CDS works well after blanking out
>some options in control file.
>
>I have one more question about maker2. In case we don't have EST evidence
>(set of ESTs or assembled mRNA-seq in fasta format) for a genome, does
>maker2 function? If it does function, could you please let me know the
>performance of maker2 without providing EST evidence compared to the one
>with EST evidence?
>
>Thank you  again and I look forward to hearing from you.
>
>Best,
>Xia
>
>
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Wednesday, September 25, 2013 10:36 AM
>To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>If it is launching predictors then you have snap hmm or augustus_species
>set.  You ned to blank out all other options in the control files
>(including repeat masking options, proteins, ESTs, etc.) when trying to
>convert mathc/match_part to gene/mRNA/exons/CDS, or else those other
>programs will run.
>
>--Carson
>
>
>On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>
>>Hi Carson,
>>
>>Thank you for the message and your kind help. We tested maker2 by
>>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>But it seemed maker2 started to launch all predictors again and it took
>>long time to finish. I wonder if there is any way that we can directly
>>get gene/mRNA/exons/CDS gff file without re-running maker2 to convert
>>match/match_part features into gene/mRNA/exons/CDS.
>>
>>Thanks,
>>Xia
>>
>>-----Original Message-----
>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>Sent: Thursday, September 19, 2013 5:58 PM
>>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY;
>>maker-devel at yandell-lab.org
>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>
>>Hello Corban & Xia,
>>
>>Some scripts like gff3_preds2models are deprecated.  To get the same
>>result as was offered by gff3_preds2models, just give your
>>match/match_part features to pref_gff= in the maker_opts.ctl file, set
>>keep_preds=1, and run with all other options and predictors turned off.
>>The final MAKER result will be your match/match_part features converted
>>into gene/mRNA/exons/CDS.
>>
>>For functional annotation, you can use Interproscan, BLASTP against
>>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO
>>terms and proteins domains via the ipr_update_gff and iprscan2gff3
>>scripts.  Then add putative gene functions via BLASTP to UniProt and
>>maker_functional_fasta and maker_functional_gff scripts.
>>
>>Go ahead and take a look and that those tools and let me know if you
>>have any questions or need help you configuring them.
>>
>>Thanks,
>>Carson
>>
>>
>>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>
>>>Hi  Corban & Xia,
>>>
>>>
>>>I've forwarded your question along to the MAKER_dev list, were you can
>>>get speedy answers to your maker related questions. Thanks for using
>>>MAKER.
>>>
>>>--mark
>>>
>>>
>>>Mark Yandell
>>>Professor of Human Genetics
>>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of
>>>Human Genetics University of Utah
>>>15 North 2030 East, Room 2100
>>>Salt Lake City, UT 84112-5330
>>>ph:801-587-7707
>>>
>>>________________________________________
>>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>Sent: Thursday, September 19, 2013 11:49 AM
>>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>Subject: maker2 scripts for functional annotation
>>>
>>>Dr. Yandell,
>>>
>>>We were recently evaluating maker2 for annotation and going through
>>>the maker tutorial from 2012.
>>>
>>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>>
>>>The tutorial makes references to some scripts that we couldn?t find in
>>>the current release.  We were looking for scripts like
>>>gff3_preds2models to convert match/match_part format into annotations
>>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did
>>>not have the most up to date version.
>>>
>>>In addition to getting accurate gene annotations, I was looking for a
>>>solution to get functional assignments.  I see that there are some
>>>scripts like maker_functional_fasta that may help, but I was wondering
>>>what you would recommend.
>>>
>>>Thanks,
>>>
>>>Corban & Xia
>>>
>>>This communication is for use by the intended recipient and contains
>>>information that may be Privileged, confidential or copyrighted under
>>>applicable law. If you are not the intended recipient, you are hereby
>>>formally notified that any use, copying or distribution of this
>>>e-mail, in whole or in part, is strictly prohibited. Please notify the
>>>sender by return e-mail and delete this e-mail from your system.
>>>Unless explicitly and conspicuously designated as "E-Contract
>>>Intended", this e-mail does not constitute a contract offer, a
>>>contract amendment, or an acceptance of a contract offer. This e-mail
>>>does not constitute a consent to the use of sender's contact
>>>information for direct marketing purposes or for transfers of data to
>>>third parties.
>>>
>>>The dupont.com web address will continue in use for a transitional
>>>period for communications sent or received on behalf of DuPont
>>>Performance Coatings., which is not affiliated in any way with the
>>>DuPont Company.
>>>
>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>>Korean
>>>
>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>g
>>
>>
>>
>>This communication is for use by the intended recipient and contains
>>information that may be Privileged, confidential or copyrighted under
>>applicable law. If you are not the intended recipient, you are hereby
>>formally notified that any use, copying or distribution of this e-mail,
>>in whole or in part, is strictly prohibited. Please notify the sender
>>by return e-mail and delete this e-mail from your system. Unless
>>explicitly and conspicuously designated as "E-Contract Intended", this
>>e-mail does not constitute a contract offer, a contract amendment, or
>>an acceptance of a contract offer. This e-mail does not constitute a
>>consent to the use of sender's contact information for direct marketing
>>purposes or for transfers of data to third parties.
>>
>>The dupont.com<http://dupont.com/> web address will continue in use for
>>a transitional period for communications sent or received on behalf of
>>DuPont Performance Coatings., which is not affiliated in any way with
>>the DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>Korean
>>
>>           http://www.DuPont.com/corp/email_disclaimer.html
>>
>
>
>
>This communication is for use by the intended recipient and contains
>information that may be Privileged, confidential or copyrighted under
>applicable law. If you are not the intended recipient, you are hereby
>formally notified that any use, copying or distribution of this e-mail,
>in whole or in part, is strictly prohibited. Please notify the sender by
>return e-mail and delete this e-mail from your system. Unless explicitly
>and conspicuously designated as "E-Contract Intended", this e-mail does
>not constitute a contract offer, a contract amendment, or an acceptance
>of a contract offer. This e-mail does not constitute a consent to the
>use of sender's contact information for direct marketing purposes or for
>transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for a
>transitional period for communications sent or received on behalf of
>DuPont
>Performance Coatings., which is not affiliated in any way with the DuPont
>Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>





From Xia.Cao at dupont.com  Tue Oct  1 13:00:42 2013
From: Xia.Cao at dupont.com (Xia.Cao at dupont.com)
Date: Tue, 1 Oct 2013 19:00:42 +0000
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <CE686C71.ECAC%carsonhh@gmail.com>
References: <AAF36CDE29C45F45AE125A1D13F5D675ACE4B8@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE686C71.ECAC%carsonhh@gmail.com>
Message-ID: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>

Hi Carson,

Thank you for your message and your kind help. Now conversion from match/match_part to gene/mRNA/exons/CDS works well after blanking out some options in control file.  

I have one more question about maker2. In case we don't have EST evidence (set of ESTs or assembled mRNA-seq in fasta format) for a genome, does maker2 function? If it does function, could you please let me know the performance of maker2 without providing EST evidence compared to the one with EST evidence?

Thank you  again and I look forward to hearing from you.

Best,
Xia




-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Wednesday, September 25, 2013 10:36 AM
To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] maker2 scripts for functional annotation

If it is launching predictors then you have snap hmm or augustus_species set.  You ned to blank out all other options in the control files (including repeat masking options, proteins, ESTs, etc.) when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else those other programs will run.

--Carson


On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for the message and your kind help. We tested maker2 by 
>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun . 
>But it seemed maker2 started to launch all predictors again and it took 
>long time to finish. I wonder if there is any way that we can directly 
>get gene/mRNA/exons/CDS gff file without re-running maker2 to convert 
>match/match_part features into gene/mRNA/exons/CDS.
>
>Thanks,
>Xia
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Thursday, September 19, 2013 5:58 PM
>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; 
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>Hello Corban & Xia,
>
>Some scripts like gff3_preds2models are deprecated.  To get the same 
>result as was offered by gff3_preds2models, just give your 
>match/match_part features to pref_gff= in the maker_opts.ctl file, set 
>keep_preds=1, and run with all other options and predictors turned off.
>The final MAKER result will be your match/match_part features converted 
>into gene/mRNA/exons/CDS.
>
>For functional annotation, you can use Interproscan, BLASTP against 
>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO 
>terms and proteins domains via the ipr_update_gff and iprscan2gff3 
>scripts.  Then add putative gene functions via BLASTP to UniProt and 
>maker_functional_fasta and maker_functional_gff scripts.
>
>Go ahead and take a look and that those tools and let me know if you 
>have any questions or need help you configuring them.
>
>Thanks,
>Carson
>
>
>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>
>>Hi  Corban & Xia,
>>
>>
>>I've forwarded your question along to the MAKER_dev list, were you can 
>>get speedy answers to your maker related questions. Thanks for using 
>>MAKER.
>>
>>--mark
>>
>>
>>Mark Yandell
>>Professor of Human Genetics
>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of 
>>Human Genetics University of Utah
>>15 North 2030 East, Room 2100
>>Salt Lake City, UT 84112-5330
>>ph:801-587-7707
>>
>>________________________________________
>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>Sent: Thursday, September 19, 2013 11:49 AM
>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>Subject: maker2 scripts for functional annotation
>>
>>Dr. Yandell,
>>
>>We were recently evaluating maker2 for annotation and going through 
>>the maker tutorial from 2012.
>>
>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>
>>The tutorial makes references to some scripts that we couldn?t find in 
>>the current release.  We were looking for scripts like 
>>gff3_preds2models to convert match/match_part format into annotations 
>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did 
>>not have the most up to date version.
>>
>>In addition to getting accurate gene annotations, I was looking for a 
>>solution to get functional assignments.  I see that there are some 
>>scripts like maker_functional_fasta that may help, but I was wondering 
>>what you would recommend.
>>
>>Thanks,
>>
>>Corban & Xia
>>
>>This communication is for use by the intended recipient and contains 
>>information that may be Privileged, confidential or copyrighted under 
>>applicable law. If you are not the intended recipient, you are hereby 
>>formally notified that any use, copying or distribution of this 
>>e-mail, in whole or in part, is strictly prohibited. Please notify the 
>>sender by return e-mail and delete this e-mail from your system. 
>>Unless explicitly and conspicuously designated as "E-Contract 
>>Intended", this e-mail does not constitute a contract offer, a 
>>contract amendment, or an acceptance of a contract offer. This e-mail 
>>does not constitute a consent to the use of sender's contact 
>>information for direct marketing purposes or for transfers of data to third parties.
>>
>>The dupont.com web address will continue in use for a transitional 
>>period for communications sent or received on behalf of DuPont 
>>Performance Coatings., which is not affiliated in any way with the 
>>DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>Korean
>>
>>          http://www.DuPont.com/corp/email_disclaimer.html
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>g
>
>
>
>This communication is for use by the intended recipient and contains 
>information that may be Privileged, confidential or copyrighted under 
>applicable law. If you are not the intended recipient, you are hereby 
>formally notified that any use, copying or distribution of this e-mail, 
>in whole or in part, is strictly prohibited. Please notify the sender 
>by return e-mail and delete this e-mail from your system. Unless 
>explicitly and conspicuously designated as "E-Contract Intended", this 
>e-mail does not constitute a contract offer, a contract amendment, or 
>an acceptance of a contract offer. This e-mail does not constitute a 
>consent to the use of sender's contact information for direct marketing 
>purposes or for transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for 
>a transitional period for communications sent or received on behalf of 
>DuPont Performance Coatings., which is not affiliated in any way with 
>the DuPont Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  
>Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>



This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
applicable law. If you are not the intended recipient, you are hereby
formally notified that any use, copying or distribution of this e-mail,
in whole or in part, is strictly prohibited. Please notify the sender by
return e-mail and delete this e-mail from your system. Unless explicitly
and conspicuously designated as "E-Contract Intended", this e-mail does
not constitute a contract offer, a contract amendment, or an acceptance
of a contract offer. This e-mail does not constitute a consent to the
use of sender's contact information for direct marketing purposes or for
transfers of data to third parties.

The dupont.com<http://dupont.com/> web address will continue in use for a
transitional period for communications sent or received on behalf of DuPont
Performance Coatings., which is not affiliated in any way with the DuPont Company.

Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean

           http://www.DuPont.com/corp/email_disclaimer.html




From carsonhh at gmail.com  Wed Oct  2 08:43:29 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 02 Oct 2013 10:43:29 -0400
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
Message-ID: <CE71A8D4.F2AD%carsonhh@gmail.com>

That's ok.  If it is very closely related, provide it directly to the est=
option, otherwise provide it to the altest= option.  The difference
between the two options is how they are aligned.  The altest= alignments
takes about 10x longer than the est= alignments.

--Carson


On 10/2/13 10:40 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for your quick and kind reply. One more question here. If we
>don't have EST evidence for the strain we sequenced/assembled, will it be
>ok to provide some EST evidence that is from some other strains which are
>close to the one we are trying to annotate? Could you please let us know
>how this will affect performance of maker2?
>
>Thank you again.
>
>Best,
>Xia
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Wednesday, October 02, 2013 10:15 AM
>To: CAO, XIA
>Cc: myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>It still works, but it will be reduced.  Without ESTs you won't get any
>UTR prediction, also you will be limited by how well the protein set
>matches to the genes.  If you use the protein set of a close relative you
>will capture most things.  You will probably capture 80-95% of what you
>would by also including ESTs.  It all depending on how different the
>species in the proteins evidence file are compared to the the species
>being annotated.
>
>--Carson
>
>On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>
>>Hi Carson,
>>
>>Thank you for your message and your kind help. Now conversion from
>>match/match_part to gene/mRNA/exons/CDS works well after blanking out
>>some options in control file.
>>
>>I have one more question about maker2. In case we don't have EST
>>evidence (set of ESTs or assembled mRNA-seq in fasta format) for a
>>genome, does
>>maker2 function? If it does function, could you please let me know the
>>performance of maker2 without providing EST evidence compared to the
>>one with EST evidence?
>>
>>Thank you  again and I look forward to hearing from you.
>>
>>Best,
>>Xia
>>
>>
>>
>>
>>-----Original Message-----
>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>Sent: Wednesday, September 25, 2013 10:36 AM
>>To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>>maker-devel at yandell-lab.org
>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>
>>If it is launching predictors then you have snap hmm or
>>augustus_species set.  You ned to blank out all other options in the
>>control files (including repeat masking options, proteins, ESTs, etc.)
>>when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else
>>those other programs will run.
>>
>>--Carson
>>
>>
>>On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>>
>>>Hi Carson,
>>>
>>>Thank you for the message and your kind help. We tested maker2 by
>>>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>>But it seemed maker2 started to launch all predictors again and it
>>>took long time to finish. I wonder if there is any way that we can
>>>directly get gene/mRNA/exons/CDS gff file without re-running maker2 to
>>>convert match/match_part features into gene/mRNA/exons/CDS.
>>>
>>>Thanks,
>>>Xia
>>>
>>>-----Original Message-----
>>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>>Sent: Thursday, September 19, 2013 5:58 PM
>>>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY;
>>>maker-devel at yandell-lab.org
>>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>>
>>>Hello Corban & Xia,
>>>
>>>Some scripts like gff3_preds2models are deprecated.  To get the same
>>>result as was offered by gff3_preds2models, just give your
>>>match/match_part features to pref_gff= in the maker_opts.ctl file, set
>>>keep_preds=1, and run with all other options and predictors turned off.
>>>The final MAKER result will be your match/match_part features
>>>converted into gene/mRNA/exons/CDS.
>>>
>>>For functional annotation, you can use Interproscan, BLASTP against
>>>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO
>>>terms and proteins domains via the ipr_update_gff and iprscan2gff3
>>>scripts.  Then add putative gene functions via BLASTP to UniProt and
>>>maker_functional_fasta and maker_functional_gff scripts.
>>>
>>>Go ahead and take a look and that those tools and let me know if you
>>>have any questions or need help you configuring them.
>>>
>>>Thanks,
>>>Carson
>>>
>>>
>>>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>>
>>>>Hi  Corban & Xia,
>>>>
>>>>
>>>>I've forwarded your question along to the MAKER_dev list, were you
>>>>can get speedy answers to your maker related questions. Thanks for
>>>>using MAKER.
>>>>
>>>>--mark
>>>>
>>>>
>>>>Mark Yandell
>>>>Professor of Human Genetics
>>>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of
>>>>Human Genetics University of Utah
>>>>15 North 2030 East, Room 2100
>>>>Salt Lake City, UT 84112-5330
>>>>ph:801-587-7707
>>>>
>>>>________________________________________
>>>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>>Sent: Thursday, September 19, 2013 11:49 AM
>>>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>>Subject: maker2 scripts for functional annotation
>>>>
>>>>Dr. Yandell,
>>>>
>>>>We were recently evaluating maker2 for annotation and going through
>>>>the maker tutorial from 2012.
>>>>
>>>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>>>
>>>>The tutorial makes references to some scripts that we couldn?t find
>>>>in the current release.  We were looking for scripts like
>>>>gff3_preds2models to convert match/match_part format into annotations
>>>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did
>>>>not have the most up to date version.
>>>>
>>>>In addition to getting accurate gene annotations, I was looking for a
>>>>solution to get functional assignments.  I see that there are some
>>>>scripts like maker_functional_fasta that may help, but I was
>>>>wondering what you would recommend.
>>>>
>>>>Thanks,
>>>>
>>>>Corban & Xia
>>>>
>>>>This communication is for use by the intended recipient and contains
>>>>information that may be Privileged, confidential or copyrighted under
>>>>applicable law. If you are not the intended recipient, you are hereby
>>>>formally notified that any use, copying or distribution of this
>>>>e-mail, in whole or in part, is strictly prohibited. Please notify
>>>>the sender by return e-mail and delete this e-mail from your system.
>>>>Unless explicitly and conspicuously designated as "E-Contract
>>>>Intended", this e-mail does not constitute a contract offer, a
>>>>contract amendment, or an acceptance of a contract offer. This e-mail
>>>>does not constitute a consent to the use of sender's contact
>>>>information for direct marketing purposes or for transfers of data to
>>>>third parties.
>>>>
>>>>The dupont.com web address will continue in use for a transitional
>>>>period for communications sent or received on behalf of DuPont
>>>>Performance Coatings., which is not affiliated in any way with the
>>>>DuPont Company.
>>>>
>>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>>>Korean
>>>>
>>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>>>
>>>>_______________________________________________
>>>>maker-devel mailing list
>>>>maker-devel at box290.bluehost.com
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>>r
>>>>g
>>>
>>>
>>>
>>>This communication is for use by the intended recipient and contains
>>>information that may be Privileged, confidential or copyrighted under
>>>applicable law. If you are not the intended recipient, you are hereby
>>>formally notified that any use, copying or distribution of this
>>>e-mail, in whole or in part, is strictly prohibited. Please notify the
>>>sender by return e-mail and delete this e-mail from your system.
>>>Unless explicitly and conspicuously designated as "E-Contract
>>>Intended", this e-mail does not constitute a contract offer, a
>>>contract amendment, or an acceptance of a contract offer. This e-mail
>>>does not constitute a consent to the use of sender's contact
>>>information for direct marketing purposes or for transfers of data to
>>>third parties.
>>>
>>>The dupont.com<http://dupont.com/> web address will continue in use
>>>for a transitional period for communications sent or received on
>>>behalf of DuPont Performance Coatings., which is not affiliated in any
>>>way with the DuPont Company.
>>>
>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>>Korean
>>>
>>>           http://www.DuPont.com/corp/email_disclaimer.html
>>>
>>
>>
>>
>>This communication is for use by the intended recipient and contains
>>information that may be Privileged, confidential or copyrighted under
>>applicable law. If you are not the intended recipient, you are hereby
>>formally notified that any use, copying or distribution of this e-mail,
>>in whole or in part, is strictly prohibited. Please notify the sender
>>by return e-mail and delete this e-mail from your system. Unless
>>explicitly and conspicuously designated as "E-Contract Intended", this
>>e-mail does not constitute a contract offer, a contract amendment, or
>>an acceptance of a contract offer. This e-mail does not constitute a
>>consent to the use of sender's contact information for direct marketing
>>purposes or for transfers of data to third parties.
>>
>>The dupont.com<http://dupont.com/> web address will continue in use for
>>a transitional period for communications sent or received on behalf of
>>DuPont Performance Coatings., which is not affiliated in any way with
>>the DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>Korean
>>
>>           http://www.DuPont.com/corp/email_disclaimer.html
>>
>
>
>
>This communication is for use by the intended recipient and contains
>information that may be Privileged, confidential or copyrighted under
>applicable law. If you are not the intended recipient, you are hereby
>formally notified that any use, copying or distribution of this e-mail,
>in whole or in part, is strictly prohibited. Please notify the sender by
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>not constitute a contract offer, a contract amendment, or an acceptance
>of a contract offer. This e-mail does not constitute a consent to the
>use of sender's contact information for direct marketing purposes or for
>transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for a
>transitional period for communications sent or received on behalf of
>DuPont
>Performance Coatings., which is not affiliated in any way with the DuPont
>Company.
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>
>           http://www.DuPont.com/corp/email_disclaimer.html
>





From Carson.Holt at oicr.on.ca  Wed Oct  2 09:24:42 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Wed, 2 Oct 2013 15:24:42 +0000
Subject: [maker-devel] Incorrect gene model, antisense transcripts
In-Reply-To: <A21F03FBB429334EB4D450CC75E8CBF37F0454C6@CH1PRD0210MB384.namprd02.prod.outlook.com>
Message-ID: <CE71B238.F2B7%carson.holt@oicr.on.ca>

SNAP appears to be making small ab initio calls all over the place.  You may need to retrain it, or just drop it completely from your analysis and just use augustus.

Try running with protein2genome and then training SNAP off of those results.  Also make sure your repeat masking is sufficient.  You may be getting too many SANP predictions if that is the case.

Thanks,
Carson



From: Sivaranjani Namasivayam <ranjani at uga.edu<mailto:ranjani at uga.edu>>
Date: Tuesday, October 1, 2013 5:01 PM
To: "maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>" <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>>
Subject: Incorrect gene model, antisense transcripts

Hello,

I am working on annotating a genome. I have RNAseq data assembled with Cufflinks and Trinity. I am using to predict gene models. Below is the procedure I used

- For the first round of prediction I provided the following : EST evidence: assembled RNAseq, Protein evidence: proteins from related organism, Gene predictor: augustus trained on a related organism.
- The number of genes I got was much less than expected (Expect atleast 10K genes, got ~4K genes)
- Used the gene models from the first round of annotations to train SNAP (default parameters) and provided the HMM for the second round of annotation (used augustus also). All other data I passed as such in the gff3, except the gene models.I also included the some manually curated genes in the EST evidence.

- The number of genes were much higher, ~11k, but many seemed incorrect and appear to have been generated from the SNAP models. I am attaching a screen shot from Apollo showing this.

Would you have any suggestions on why this might be happening and how I can fix?
I am essentially looking for gene models for my assembled RNAseq, can I achieve this by setting est2genome to 1? Would I be losing/misrepresenting any data if I do this.

Also, I recently noticed my RNAseq data has assembled antisense transcripts. MAKER seems to be predicting a coding region for these antisense transcripts in some cases, (although the coding region predicted is much smaller than that of the sense gene model.) Is there a way to tell MAKER not to predict gene models on both strands at the same loci.

Appreciate your help.

Thanks,
Ranjani





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From Xia.Cao at dupont.com  Wed Oct  2 08:40:12 2013
From: Xia.Cao at dupont.com (Xia.Cao at dupont.com)
Date: Wed, 2 Oct 2013 14:40:12 +0000
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <CE709D72.EF15%carsonhh@gmail.com>
References: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE709D72.EF15%carsonhh@gmail.com>
Message-ID: <AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>

Hi Carson,

Thank you for your quick and kind reply. One more question here. If we don't have EST evidence for the strain we sequenced/assembled, will it be ok to provide some EST evidence that is from some other strains which are close to the one we are trying to annotate? Could you please let us know how this will affect performance of maker2?

Thank you again.

Best,
Xia

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Wednesday, October 02, 2013 10:15 AM
To: CAO, XIA
Cc: myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] maker2 scripts for functional annotation

It still works, but it will be reduced.  Without ESTs you won't get any UTR prediction, also you will be limited by how well the protein set matches to the genes.  If you use the protein set of a close relative you will capture most things.  You will probably capture 80-95% of what you would by also including ESTs.  It all depending on how different the species in the proteins evidence file are compared to the the species being annotated.

--Carson

On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for your message and your kind help. Now conversion from 
>match/match_part to gene/mRNA/exons/CDS works well after blanking out 
>some options in control file.
>
>I have one more question about maker2. In case we don't have EST 
>evidence (set of ESTs or assembled mRNA-seq in fasta format) for a 
>genome, does
>maker2 function? If it does function, could you please let me know the 
>performance of maker2 without providing EST evidence compared to the 
>one with EST evidence?
>
>Thank you  again and I look forward to hearing from you.
>
>Best,
>Xia
>
>
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Wednesday, September 25, 2013 10:36 AM
>To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; 
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>If it is launching predictors then you have snap hmm or 
>augustus_species set.  You ned to blank out all other options in the 
>control files (including repeat masking options, proteins, ESTs, etc.) 
>when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else 
>those other programs will run.
>
>--Carson
>
>
>On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>
>>Hi Carson,
>>
>>Thank you for the message and your kind help. We tested maker2 by 
>>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>But it seemed maker2 started to launch all predictors again and it 
>>took long time to finish. I wonder if there is any way that we can 
>>directly get gene/mRNA/exons/CDS gff file without re-running maker2 to 
>>convert match/match_part features into gene/mRNA/exons/CDS.
>>
>>Thanks,
>>Xia
>>
>>-----Original Message-----
>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>Sent: Thursday, September 19, 2013 5:58 PM
>>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; 
>>maker-devel at yandell-lab.org
>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>
>>Hello Corban & Xia,
>>
>>Some scripts like gff3_preds2models are deprecated.  To get the same 
>>result as was offered by gff3_preds2models, just give your 
>>match/match_part features to pref_gff= in the maker_opts.ctl file, set 
>>keep_preds=1, and run with all other options and predictors turned off.
>>The final MAKER result will be your match/match_part features 
>>converted into gene/mRNA/exons/CDS.
>>
>>For functional annotation, you can use Interproscan, BLASTP against 
>>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO 
>>terms and proteins domains via the ipr_update_gff and iprscan2gff3 
>>scripts.  Then add putative gene functions via BLASTP to UniProt and 
>>maker_functional_fasta and maker_functional_gff scripts.
>>
>>Go ahead and take a look and that those tools and let me know if you 
>>have any questions or need help you configuring them.
>>
>>Thanks,
>>Carson
>>
>>
>>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>
>>>Hi  Corban & Xia,
>>>
>>>
>>>I've forwarded your question along to the MAKER_dev list, were you 
>>>can get speedy answers to your maker related questions. Thanks for 
>>>using MAKER.
>>>
>>>--mark
>>>
>>>
>>>Mark Yandell
>>>Professor of Human Genetics
>>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of 
>>>Human Genetics University of Utah
>>>15 North 2030 East, Room 2100
>>>Salt Lake City, UT 84112-5330
>>>ph:801-587-7707
>>>
>>>________________________________________
>>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>Sent: Thursday, September 19, 2013 11:49 AM
>>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>Subject: maker2 scripts for functional annotation
>>>
>>>Dr. Yandell,
>>>
>>>We were recently evaluating maker2 for annotation and going through 
>>>the maker tutorial from 2012.
>>>
>>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>>
>>>The tutorial makes references to some scripts that we couldn?t find 
>>>in the current release.  We were looking for scripts like 
>>>gff3_preds2models to convert match/match_part format into annotations 
>>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did 
>>>not have the most up to date version.
>>>
>>>In addition to getting accurate gene annotations, I was looking for a 
>>>solution to get functional assignments.  I see that there are some 
>>>scripts like maker_functional_fasta that may help, but I was 
>>>wondering what you would recommend.
>>>
>>>Thanks,
>>>
>>>Corban & Xia
>>>
>>>This communication is for use by the intended recipient and contains 
>>>information that may be Privileged, confidential or copyrighted under 
>>>applicable law. If you are not the intended recipient, you are hereby 
>>>formally notified that any use, copying or distribution of this 
>>>e-mail, in whole or in part, is strictly prohibited. Please notify 
>>>the sender by return e-mail and delete this e-mail from your system.
>>>Unless explicitly and conspicuously designated as "E-Contract 
>>>Intended", this e-mail does not constitute a contract offer, a 
>>>contract amendment, or an acceptance of a contract offer. This e-mail 
>>>does not constitute a consent to the use of sender's contact 
>>>information for direct marketing purposes or for transfers of data to 
>>>third parties.
>>>
>>>The dupont.com web address will continue in use for a transitional 
>>>period for communications sent or received on behalf of DuPont 
>>>Performance Coatings., which is not affiliated in any way with the 
>>>DuPont Company.
>>>
>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>>Korean
>>>
>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>r
>>>g
>>
>>
>>
>>This communication is for use by the intended recipient and contains 
>>information that may be Privileged, confidential or copyrighted under 
>>applicable law. If you are not the intended recipient, you are hereby 
>>formally notified that any use, copying or distribution of this 
>>e-mail, in whole or in part, is strictly prohibited. Please notify the 
>>sender by return e-mail and delete this e-mail from your system. 
>>Unless explicitly and conspicuously designated as "E-Contract 
>>Intended", this e-mail does not constitute a contract offer, a 
>>contract amendment, or an acceptance of a contract offer. This e-mail 
>>does not constitute a consent to the use of sender's contact 
>>information for direct marketing purposes or for transfers of data to third parties.
>>
>>The dupont.com<http://dupont.com/> web address will continue in use 
>>for a transitional period for communications sent or received on 
>>behalf of DuPont Performance Coatings., which is not affiliated in any 
>>way with the DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>Korean
>>
>>           http://www.DuPont.com/corp/email_disclaimer.html
>>
>
>
>
>This communication is for use by the intended recipient and contains 
>information that may be Privileged, confidential or copyrighted under 
>applicable law. If you are not the intended recipient, you are hereby 
>formally notified that any use, copying or distribution of this e-mail, 
>in whole or in part, is strictly prohibited. Please notify the sender 
>by return e-mail and delete this e-mail from your system. Unless 
>explicitly and conspicuously designated as "E-Contract Intended", this 
>e-mail does not constitute a contract offer, a contract amendment, or 
>an acceptance of a contract offer. This e-mail does not constitute a 
>consent to the use of sender's contact information for direct marketing 
>purposes or for transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for 
>a transitional period for communications sent or received on behalf of 
>DuPont Performance Coatings., which is not affiliated in any way with 
>the DuPont Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  
>Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>



This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
applicable law. If you are not the intended recipient, you are hereby
formally notified that any use, copying or distribution of this e-mail,
in whole or in part, is strictly prohibited. Please notify the sender by
return e-mail and delete this e-mail from your system. Unless explicitly
and conspicuously designated as "E-Contract Intended", this e-mail does
not constitute a contract offer, a contract amendment, or an acceptance
of a contract offer. This e-mail does not constitute a consent to the
use of sender's contact information for direct marketing purposes or for
transfers of data to third parties.

The dupont.com<http://dupont.com/> web address will continue in use for a
transitional period for communications sent or received on behalf of DuPont
Performance Coatings., which is not affiliated in any way with the DuPont Company.

Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean

           http://www.DuPont.com/corp/email_disclaimer.html




From markwiz at us.ibm.com  Wed Oct  2 10:52:55 2013
From: markwiz at us.ibm.com (Mark Wisner)
Date: Wed, 2 Oct 2013 12:52:55 -0400
Subject: [maker-devel] Maker2 on IBM PowerLinux?
Message-ID: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>

IBMs PowerLinux is tuned for Big Data workloads. We have had queries for 
Maker2 on PowerLinux.
How do we work with Maker2 development to create a PowerLinux port.
Thanks,

Mark K. Wisner
Linux On Power ISV PM
IBM
3039 Cornwallis Rd
RTP, NC 27709
Cell 919-649-5813
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From barry.moore at genetics.utah.edu  Wed Oct  2 11:29:36 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Wed, 2 Oct 2013 11:29:36 -0600
Subject: [maker-devel] Maker2 on IBM PowerLinux?
In-Reply-To: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>
References: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>
Message-ID: <E59BC7E8-B562-4AD6-B4CF-C793329B688B@genetics.utah.edu>

Hi Mark,

Carson Holt is the primary Maker developer, but others of us may be able to help as well.  I've added e-mails for Carson, Michael Campbell, Mark Yandell and myself who are currently developers on the project.   You can feel free to contact this mailing list - or if the conversation is getting too far afield for general interest you can contact us off list and we will do whatever we can to help.  If you feel like you need to do some modification of MAKER code to optimize it for PowerLinux I'm happy to give you a branch on the subversion repo to work with and then we can work with you to merge these changes back to the trunk when you feel like you have some improvements that benefit PowerLinux (and all other) users.

Thanks very much for your interest in MAKER - your participation in the community is most welcome!

Barry

On Oct 2, 2013, at 10:52 AM, Mark Wisner wrote:

> IBMs PowerLinux is tuned for Big Data workloads. We have had queries for Maker2 on PowerLinux. 
> How do we work with Maker2 development to create a PowerLinux port. 
> Thanks,
> 
> Mark K. Wisner
> Linux On Power ISV PM
> IBM
> 3039 Cornwallis Rd
> RTP, NC 27709
> Cell 919-649-5813
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From carsonhh at gmail.com  Wed Oct  2 11:29:50 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 02 Oct 2013 13:29:50 -0400
Subject: [maker-devel] Maker2 on IBM PowerLinux?
In-Reply-To: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>
Message-ID: <CE71CD2E.F2D8%carsonhh@gmail.com>

MAKER is written in perl, so it can work pretty much anywhere you have perl.
It is more an issue of the tools MAKER uses.  If you can get SNAP, BLAST,
exonerate, etc. to run then MAKER should be no problem.

You can let MAKER try and install and configure any missing perl libraries
as well as external tools for you (this is by far the easiest way).  You
will need an internet connection.

cd ?/maker/src/
perl Build.PL               #say 'Y' to local installation of libraries and
'N' to MPI for now
./Build installdeps     #grabs missing perl libraries from the ether, and
installs them in  the .../maker/perl/ directory
./Build installers        #grabs missing tools from the ether, installs, and
configures them in the .../maker/exe/ directory
./Build install              #just installs maker


If you want to run via MPI, I'd recommend OpenMPI, and you will need to
rerun the 'perl Build.PL' and './Build install' steps (say yes to MPI this
time around).

Here are some variables you will likly have to add to your .bash_profile to
get openmpi to run with MAKER (you must add these and source the profile
before attempting to install with OpenMPI), otherwise compilation will not
work correctly (OpenMPI shared library issue).

#you need to set $OMPIHOME to OpenMPI's location here -->
export LD_PRELOAD=$OMPIHOME/lib/libmpi.so:$LD_PRELOAD


#this one just suppresses a warning -->
export OMPI_MCA_mpi_warn_on_fork=0


And on some systems you have to add this  ' -mca btl ^openib' to the mpiexec
command when I run maker.
Example-->
mpiexec -mca btl ^openib -n 20 maker

Thanks,
Carson


From:  Mark Wisner <markwiz at us.ibm.com>
Date:  Wednesday, October 2, 2013 12:52 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker2 on IBM PowerLinux?

IBMs PowerLinux is tuned for Big Data workloads. We have had queries for
Maker2 on PowerLinux.
How do we work with Maker2 development to create a PowerLinux port.
Thanks,

Mark K. Wisner
Linux On Power ISV PM
IBM
3039 Cornwallis Rd
RTP, NC 27709
Cell 919-649-5813
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From barry.moore at genetics.utah.edu  Wed Oct  2 11:21:29 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Wed, 2 Oct 2013 11:21:29 -0600
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
References: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE709D72.EF15%carsonhh@gmail.com>
	<AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
Message-ID: <E9DC8DC1-8E1F-42E7-94CC-5D58EF0A1F21@genetics.utah.edu>

Hi Xia,

You can use EST evidence from other strains/species.  The considerations are as follows:  When you pass EST (or mRNASeq based transcripts) evidence MAKER uses blastn to align those with alignment parameters that assume they sequences will align easily with almost perfect identity - this is fast.  If you use EST/mRNA evidence from another species MAKER uses tblastx to compare the RNA evidence to the assembly, both translated into protein space - this works fine, but it is slow and often doesn't get you much more evidence than you could have gotten from proteins as evidence.  If you believe that you're other strain should have very little divergence in sequence at the nt level then you could experiment with passing EST/mRNA evidence as est in the control file.  Consider this an experiment, do it on a few contigs and examine the results carefully and skeptically.  If it works well, that would be the way to go because you've get better UTRs, but if it doesn't you'll see that you get little support for models because sequence divergence was too much for good alignment.  In that case you'll need to use alt_est and this will be slower and you'll likely get little in the way of support for UTRs - in this case as well, do a few contigs and examine the output carefully to see if the additional alignment time with tblastx is worth it in your case.

Barry


On Oct 2, 2013, at 8:40 AM, <Xia.Cao at dupont.com>
 wrote:

> Hi Carson,
> 
> Thank you for your quick and kind reply. One more question here. If we don't have EST evidence for the strain we sequenced/assembled, will it be ok to provide some EST evidence that is from some other strains which are close to the one we are trying to annotate? Could you please let us know how this will affect performance of maker2?
> 
> Thank you again.
> 
> Best,
> Xia
> 
> -----Original Message-----
> From: Carson Holt [mailto:carsonhh at gmail.com] 
> Sent: Wednesday, October 02, 2013 10:15 AM
> To: CAO, XIA
> Cc: myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org
> Subject: Re: [maker-devel] maker2 scripts for functional annotation
> 
> It still works, but it will be reduced.  Without ESTs you won't get any UTR prediction, also you will be limited by how well the protein set matches to the genes.  If you use the protein set of a close relative you will capture most things.  You will probably capture 80-95% of what you would by also including ESTs.  It all depending on how different the species in the proteins evidence file are compared to the the species being annotated.
> 
> --Carson
> 
> On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
> 
>> Hi Carson,
>> 
>> Thank you for your message and your kind help. Now conversion from 
>> match/match_part to gene/mRNA/exons/CDS works well after blanking out 
>> some options in control file.
>> 
>> I have one more question about maker2. In case we don't have EST 
>> evidence (set of ESTs or assembled mRNA-seq in fasta format) for a 
>> genome, does
>> maker2 function? If it does function, could you please let me know the 
>> performance of maker2 without providing EST evidence compared to the 
>> one with EST evidence?
>> 
>> Thank you  again and I look forward to hearing from you.
>> 
>> Best,
>> Xia
>> 
>> 
>> 
>> 
>> -----Original Message-----
>> From: Carson Holt [mailto:carsonhh at gmail.com]
>> Sent: Wednesday, September 25, 2013 10:36 AM
>> To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; 
>> maker-devel at yandell-lab.org
>> Subject: Re: [maker-devel] maker2 scripts for functional annotation
>> 
>> If it is launching predictors then you have snap hmm or 
>> augustus_species set.  You ned to blank out all other options in the 
>> control files (including repeat masking options, proteins, ESTs, etc.) 
>> when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else 
>> those other programs will run.
>> 
>> --Carson
>> 
>> 
>> On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>> 
>>> Hi Carson,
>>> 
>>> Thank you for the message and your kind help. We tested maker2 by 
>>> setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>> But it seemed maker2 started to launch all predictors again and it 
>>> took long time to finish. I wonder if there is any way that we can 
>>> directly get gene/mRNA/exons/CDS gff file without re-running maker2 to 
>>> convert match/match_part features into gene/mRNA/exons/CDS.
>>> 
>>> Thanks,
>>> Xia
>>> 
>>> -----Original Message-----
>>> From: Carson Holt [mailto:carsonhh at gmail.com]
>>> Sent: Thursday, September 19, 2013 5:58 PM
>>> To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; 
>>> maker-devel at yandell-lab.org
>>> Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>> 
>>> Hello Corban & Xia,
>>> 
>>> Some scripts like gff3_preds2models are deprecated.  To get the same 
>>> result as was offered by gff3_preds2models, just give your 
>>> match/match_part features to pref_gff= in the maker_opts.ctl file, set 
>>> keep_preds=1, and run with all other options and predictors turned off.
>>> The final MAKER result will be your match/match_part features 
>>> converted into gene/mRNA/exons/CDS.
>>> 
>>> For functional annotation, you can use Interproscan, BLASTP against 
>>> UniProt, or BALST2GO.  My preference is to use InterProScan to add GO 
>>> terms and proteins domains via the ipr_update_gff and iprscan2gff3 
>>> scripts.  Then add putative gene functions via BLASTP to UniProt and 
>>> maker_functional_fasta and maker_functional_gff scripts.
>>> 
>>> Go ahead and take a look and that those tools and let me know if you 
>>> have any questions or need help you configuring them.
>>> 
>>> Thanks,
>>> Carson
>>> 
>>> 
>>> On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>> 
>>>> Hi  Corban & Xia,
>>>> 
>>>> 
>>>> I've forwarded your question along to the MAKER_dev list, were you 
>>>> can get speedy answers to your maker related questions. Thanks for 
>>>> using MAKER.
>>>> 
>>>> --mark
>>>> 
>>>> 
>>>> Mark Yandell
>>>> Professor of Human Genetics
>>>> H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of 
>>>> Human Genetics University of Utah
>>>> 15 North 2030 East, Room 2100
>>>> Salt Lake City, UT 84112-5330
>>>> ph:801-587-7707
>>>> 
>>>> ________________________________________
>>>> From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>> Sent: Thursday, September 19, 2013 11:49 AM
>>>> To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>> Subject: maker2 scripts for functional annotation
>>>> 
>>>> Dr. Yandell,
>>>> 
>>>> We were recently evaluating maker2 for annotation and going through 
>>>> the maker tutorial from 2012.
>>>> 
>>>> http://gmod.org/wiki/MAKER_Tutorial_2012
>>>> 
>>>> The tutorial makes references to some scripts that we couldn?t find 
>>>> in the current release.  We were looking for scripts like 
>>>> gff3_preds2models to convert match/match_part format into annotations 
>>>> with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did 
>>>> not have the most up to date version.
>>>> 
>>>> In addition to getting accurate gene annotations, I was looking for a 
>>>> solution to get functional assignments.  I see that there are some 
>>>> scripts like maker_functional_fasta that may help, but I was 
>>>> wondering what you would recommend.
>>>> 
>>>> Thanks,
>>>> 
>>>> Corban & Xia
>>>> 
>>>> This communication is for use by the intended recipient and contains 
>>>> information that may be Privileged, confidential or copyrighted under 
>>>> applicable law. If you are not the intended recipient, you are hereby 
>>>> formally notified that any use, copying or distribution of this 
>>>> e-mail, in whole or in part, is strictly prohibited. Please notify 
>>>> the sender by return e-mail and delete this e-mail from your system.
>>>> Unless explicitly and conspicuously designated as "E-Contract 
>>>> Intended", this e-mail does not constitute a contract offer, a 
>>>> contract amendment, or an acceptance of a contract offer. This e-mail 
>>>> does not constitute a consent to the use of sender's contact 
>>>> information for direct marketing purposes or for transfers of data to 
>>>> third parties.
>>>> 
>>>> The dupont.com web address will continue in use for a transitional 
>>>> period for communications sent or received on behalf of DuPont 
>>>> Performance Coatings., which is not affiliated in any way with the 
>>>> DuPont Company.
>>>> 
>>>> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>>> Korean
>>>> 
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>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
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>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>> r
>>>> g
>>> 
>>> 
>>> 
>>> This communication is for use by the intended recipient and contains 
>>> information that may be Privileged, confidential or copyrighted under 
>>> applicable law. If you are not the intended recipient, you are hereby 
>>> formally notified that any use, copying or distribution of this 
>>> e-mail, in whole or in part, is strictly prohibited. Please notify the 
>>> sender by return e-mail and delete this e-mail from your system. 
>>> Unless explicitly and conspicuously designated as "E-Contract 
>>> Intended", this e-mail does not constitute a contract offer, a 
>>> contract amendment, or an acceptance of a contract offer. This e-mail 
>>> does not constitute a consent to the use of sender's contact 
>>> information for direct marketing purposes or for transfers of data to third parties.
>>> 
>>> The dupont.com<http://dupont.com/> web address will continue in use 
>>> for a transitional period for communications sent or received on 
>>> behalf of DuPont Performance Coatings., which is not affiliated in any 
>>> way with the DuPont Company.
>>> 
>>> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>> Korean
>>> 
>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>> 
>> 
>> 
>> 
>> This communication is for use by the intended recipient and contains 
>> information that may be Privileged, confidential or copyrighted under 
>> applicable law. If you are not the intended recipient, you are hereby 
>> formally notified that any use, copying or distribution of this e-mail, 
>> in whole or in part, is strictly prohibited. Please notify the sender 
>> by return e-mail and delete this e-mail from your system. Unless 
>> explicitly and conspicuously designated as "E-Contract Intended", this 
>> e-mail does not constitute a contract offer, a contract amendment, or 
>> an acceptance of a contract offer. This e-mail does not constitute a 
>> consent to the use of sender's contact information for direct marketing 
>> purposes or for transfers of data to third parties.
>> 
>> The dupont.com<http://dupont.com/> web address will continue in use for 
>> a transitional period for communications sent or received on behalf of 
>> DuPont Performance Coatings., which is not affiliated in any way with 
>> the DuPont Company.
>> 
>> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  
>> Korean
>> 
>>          http://www.DuPont.com/corp/email_disclaimer.html
>> 
> 
> 
> 
> This communication is for use by the intended recipient and contains
> information that may be Privileged, confidential or copyrighted under
> applicable law. If you are not the intended recipient, you are hereby
> formally notified that any use, copying or distribution of this e-mail,
> in whole or in part, is strictly prohibited. Please notify the sender by
> return e-mail and delete this e-mail from your system. Unless explicitly
> and conspicuously designated as "E-Contract Intended", this e-mail does
> not constitute a contract offer, a contract amendment, or an acceptance
> of a contract offer. This e-mail does not constitute a consent to the
> use of sender's contact information for direct marketing purposes or for
> transfers of data to third parties.
> 
> The dupont.com<http://dupont.com/> web address will continue in use for a
> transitional period for communications sent or received on behalf of DuPont
> Performance Coatings., which is not affiliated in any way with the DuPont Company.
> 
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> 
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> 
> 
> _______________________________________________
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> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From Xia.Cao at dupont.com  Wed Oct  2 11:51:26 2013
From: Xia.Cao at dupont.com (Xia.Cao at dupont.com)
Date: Wed, 2 Oct 2013 17:51:26 +0000
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <E9DC8DC1-8E1F-42E7-94CC-5D58EF0A1F21@genetics.utah.edu>
References: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE709D72.EF15%carsonhh@gmail.com>
	<AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
	<E9DC8DC1-8E1F-42E7-94CC-5D58EF0A1F21@genetics.utah.edu>
Message-ID: <AAF36CDE29C45F45AE125A1D13F5D675AE2175@033-CH1MPN2-063.033d.mgd.msft.net>

Hi Barry,

Thank you very much for the message and suggestions. It's really helpful to us.  We will do some tests to see how we can take advantage of Maker2  to produce high-quality gene models from our assembled genome.

Thank you again,
Xia


From: Barry Moore [mailto:barry.moore at genetics.utah.edu]
Sent: Wednesday, October 02, 2013 1:21 PM
To: CAO, XIA
Cc: carsonhh at gmail.com; maker-devel at yandell-lab.org; RIVERA, CORBAN GREGORY
Subject: Re: [maker-devel] maker2 scripts for functional annotation

Hi Xia,

You can use EST evidence from other strains/species.  The considerations are as follows:  When you pass EST (or mRNASeq based transcripts) evidence MAKER uses blastn to align those with alignment parameters that assume they sequences will align easily with almost perfect identity - this is fast.  If you use EST/mRNA evidence from another species MAKER uses tblastx to compare the RNA evidence to the assembly, both translated into protein space - this works fine, but it is slow and often doesn't get you much more evidence than you could have gotten from proteins as evidence.  If you believe that you're other strain should have very little divergence in sequence at the nt level then you could experiment with passing EST/mRNA evidence as est in the control file.  Consider this an experiment, do it on a few contigs and examine the results carefully and skeptically.  If it works well, that would be the way to go because you've get better UTRs, but if it doesn't you'll see that you get little support for models because sequence divergence was too much for good alignment.  In that case you'll need to use alt_est and this will be slower and you'll likely get little in the way of support for UTRs - in this case as well, do a few contigs and examine the output carefully to see if the additional alignment time with tblastx is worth it in your case.

Barry


On Oct 2, 2013, at 8:40 AM, <Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>>
 wrote:


Hi Carson,

Thank you for your quick and kind reply. One more question here. If we don't have EST evidence for the strain we sequenced/assembled, will it be ok to provide some EST evidence that is from some other strains which are close to the one we are trying to annotate? Could you please let us know how this will affect performance of maker2?

Thank you again.

Best,
Xia

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Wednesday, October 02, 2013 10:15 AM
To: CAO, XIA
Cc: myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker2 scripts for functional annotation

It still works, but it will be reduced.  Without ESTs you won't get any UTR prediction, also you will be limited by how well the protein set matches to the genes.  If you use the protein set of a close relative you will capture most things.  You will probably capture 80-95% of what you would by also including ESTs.  It all depending on how different the species in the proteins evidence file are compared to the the species being annotated.

--Carson

On 10/1/13 3:00 PM, "Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>" <Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>> wrote:


Hi Carson,

Thank you for your message and your kind help. Now conversion from
match/match_part to gene/mRNA/exons/CDS works well after blanking out
some options in control file.

I have one more question about maker2. In case we don't have EST
evidence (set of ESTs or assembled mRNA-seq in fasta format) for a
genome, does
maker2 function? If it does function, could you please let me know the
performance of maker2 without providing EST evidence compared to the
one with EST evidence?

Thank you  again and I look forward to hearing from you.

Best,
Xia




-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Wednesday, September 25, 2013 10:36 AM
To: CAO, XIA; myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>; RIVERA, CORBAN GREGORY;
maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker2 scripts for functional annotation

If it is launching predictors then you have snap hmm or
augustus_species set.  You ned to blank out all other options in the
control files (including repeat masking options, proteins, ESTs, etc.)
when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else
those other programs will run.

--Carson


On 9/25/13 10:31 AM, "Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>" <Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>> wrote:

Hi Carson,

Thank you for the message and your kind help. We tested maker2 by
setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
But it seemed maker2 started to launch all predictors again and it
took long time to finish. I wonder if there is any way that we can
directly get gene/mRNA/exons/CDS gff file without re-running maker2 to
convert match/match_part features into gene/mRNA/exons/CDS.

Thanks,
Xia

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Thursday, September 19, 2013 5:58 PM
To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY;
maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker2 scripts for functional annotation

Hello Corban & Xia,

Some scripts like gff3_preds2models are deprecated.  To get the same
result as was offered by gff3_preds2models, just give your
match/match_part features to pref_gff= in the maker_opts.ctl file, set
keep_preds=1, and run with all other options and predictors turned off.
The final MAKER result will be your match/match_part features
converted into gene/mRNA/exons/CDS.

For functional annotation, you can use Interproscan, BLASTP against
UniProt, or BALST2GO.  My preference is to use InterProScan to add GO
terms and proteins domains via the ipr_update_gff and iprscan2gff3
scripts.  Then add putative gene functions via BLASTP to UniProt and
maker_functional_fasta and maker_functional_gff scripts.

Go ahead and take a look and that those tools and let me know if you
have any questions or need help you configuring them.

Thanks,
Carson


On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>> wrote:

Hi  Corban & Xia,


I've forwarded your question along to the MAKER_dev list, were you
can get speedy answers to your maker related questions. Thanks for
using MAKER.

--mark


Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of
Human Genetics University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com> [Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>]
Sent: Thursday, September 19, 2013 11:49 AM
To: Mark Yandell; Corban-Gregory.Rivera at dupont.com<mailto:Corban-Gregory.Rivera at dupont.com>
Subject: maker2 scripts for functional annotation

Dr. Yandell,

We were recently evaluating maker2 for annotation and going through
the maker tutorial from 2012.

http://gmod.org/wiki/MAKER_Tutorial_2012

The tutorial makes references to some scripts that we couldn?t find
in the current release.  We were looking for scripts like
gff3_preds2models to convert match/match_part format into annotations
with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did
not have the most up to date version.

In addition to getting accurate gene annotations, I was looking for a
solution to get functional assignments.  I see that there are some
scripts like maker_functional_fasta that may help, but I was
wondering what you would recommend.

Thanks,

Corban & Xia

This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
applicable law. If you are not the intended recipient, you are hereby
formally notified that any use, copying or distribution of this
e-mail, in whole or in part, is strictly prohibited. Please notify
the sender by return e-mail and delete this e-mail from your system.
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The dupont.com<http://dupont.com> web address will continue in use for a transitional
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DuPont Company.

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Korean

        http://www.DuPont.com/corp/email_disclaimer.html

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r
g



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Korean

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This communication is for use by the intended recipient and contains
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The dupont.com<http://dupont.com><http://dupont.com/> web address will continue in use for
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Korean

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This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
applicable law. If you are not the intended recipient, you are hereby
formally notified that any use, copying or distribution of this e-mail,
in whole or in part, is strictly prohibited. Please notify the sender by
return e-mail and delete this e-mail from your system. Unless explicitly
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The dupont.com<http://dupont.com><http://dupont.com/> web address will continue in use for a
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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543





This communication is for use by the intended recipient and contains
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From cjfields at illinois.edu  Thu Oct  3 12:44:07 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 3 Oct 2013 18:44:07 +0000
Subject: [maker-devel] NFSLock problem
Message-ID: <B9943BBA-BEFF-4B23-A6B8-7581247F3C95@illinois.edu>

I have a MAKER job running that seems to be stalled on a failed scaffold.  It's running via MPI (MAKER v2.28, openMPI 1.6.3), that appears to have worked successfully for the most part.  This is a run that only uses transcriptome and protein information in order to get a decent dseat of 

The failed scaffold seems to be holding the job from completion.  There does seem to be changes, but mainly they are on the NFSLock files:

./.NFSLock.gi_lock.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.282.start.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.281.end.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.281.end.blastn.holdover.NFSLock.STACK

Everything else seems to have completed.  

I have seen a few issues re: NFS locking problems, would this be related?  Should I stop the job?  

We're running GPFS for our NFS.  Here's 'mount':

-system-specific-4.1$ mount
/dev/sda5 on / type ext4 (rw)
proc on /proc type proc (rw)
sysfs on /sys type sysfs (rw)
devpts on /dev/pts type devpts (rw,gid=5,mode=620)
tmpfs on /dev/shm type tmpfs (rw)
/dev/sda1 on /boot type ext4 (rw)
/dev/sdb1 on /export type ext4 (rw)
/dev/sda2 on /var type ext4 (rw)
tmpfs on /var/lib/ganglia/rrds type tmpfs (rw,size=6180842000,gid=99,uid=99)
none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
nfsd on /proc/fs/nfsd type nfsd (rw)
/dev/IGBHOME0 on /home type gpfs (rw,mtime,dev=IGBHOME0)
128.174.124.79:/shares/group on /archive/group type nfs (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,proto=tcp,mountproto=tcp,addr=128.174.124.79)
128.174.124.79:/shares/CBC on /archive/CBC type nfs (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,proto=tcp,mountproto=tcp,addr=128.174.124.79)

chris


From carsonhh at gmail.com  Thu Oct  3 12:45:37 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 03 Oct 2013 14:45:37 -0400
Subject: [maker-devel] NFSLock problem
In-Reply-To: <B9943BBA-BEFF-4B23-A6B8-7581247F3C95@illinois.edu>
Message-ID: <CE73336F.F347%carsonhh@gmail.com>

Stop the job and restart it.  No need to delete anything.  Just restart it.

Thanks,
Carson


On 10/3/13 2:44 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

>I have a MAKER job running that seems to be stalled on a failed scaffold.
> It's running via MPI (MAKER v2.28, openMPI 1.6.3), that appears to have
>worked successfully for the most part.  This is a run that only uses
>transcriptome and protein information in order to get a decent dseat of
>
>The failed scaffold seems to be holding the job from completion.  There
>does seem to be changes, but mainly they are on the NFSLock files:
>
>./.NFSLock.gi_lock.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.282.start.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.end.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.end.blastn.holdover.NFSLock.STACK
>
>Everything else seems to have completed.
>
>I have seen a few issues re: NFS locking problems, would this be related?
> Should I stop the job?
>
>We're running GPFS for our NFS.  Here's 'mount':
>
>-system-specific-4.1$ mount
>/dev/sda5 on / type ext4 (rw)
>proc on /proc type proc (rw)
>sysfs on /sys type sysfs (rw)
>devpts on /dev/pts type devpts (rw,gid=5,mode=620)
>tmpfs on /dev/shm type tmpfs (rw)
>/dev/sda1 on /boot type ext4 (rw)
>/dev/sdb1 on /export type ext4 (rw)
>/dev/sda2 on /var type ext4 (rw)
>tmpfs on /var/lib/ganglia/rrds type tmpfs
>(rw,size=6180842000,gid=99,uid=99)
>none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
>sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
>nfsd on /proc/fs/nfsd type nfsd (rw)
>/dev/IGBHOME0 on /home type gpfs (rw,mtime,dev=IGBHOME0)
>128.174.124.79:/shares/group on /archive/group type nfs
>(rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>roto=tcp,mountproto=tcp,addr=128.174.124.79)
>128.174.124.79:/shares/CBC on /archive/CBC type nfs
>(rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>roto=tcp,mountproto=tcp,addr=128.174.124.79)
>
>chris
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From cjfields at illinois.edu  Thu Oct  3 20:45:29 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 4 Oct 2013 02:45:29 +0000
Subject: [maker-devel] NFSLock problem
In-Reply-To: <CE73336F.F347%carsonhh@gmail.com>
References: <CE73336F.F347%carsonhh@gmail.com>
Message-ID: <EB3895BA-F1EF-4F14-813F-233D1B4269AB@illinois.edu>

Carson,

Took a couple of restarts but finally processed through.  I saw a prior email on the mail list where you mentioned this could be due to failed jobs hanging things up; I may set up my next job to allow one processor for logging into the nodes in case there is a similar problem, maybe try to track this down.

chris

On Oct 3, 2013, at 1:45 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Stop the job and restart it.  No need to delete anything.  Just restart it.
> 
> Thanks,
> Carson
> 
> 
> On 10/3/13 2:44 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> 
>> I have a MAKER job running that seems to be stalled on a failed scaffold.
>> It's running via MPI (MAKER v2.28, openMPI 1.6.3), that appears to have
>> worked successfully for the most part.  This is a run that only uses
>> transcriptome and protein information in order to get a decent dseat of
>> 
>> The failed scaffold seems to be holding the job from completion.  There
>> does seem to be changes, but mainly they are on the NFSLock files:
>> 
>> ./.NFSLock.gi_lock.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.282.start.blastn.holdover.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.281.end.blastn.holdover.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.281.end.blastn.holdover.NFSLock.STACK
>> 
>> Everything else seems to have completed.
>> 
>> I have seen a few issues re: NFS locking problems, would this be related?
>> Should I stop the job?
>> 
>> We're running GPFS for our NFS.  Here's 'mount':
>> 
>> -system-specific-4.1$ mount
>> /dev/sda5 on / type ext4 (rw)
>> proc on /proc type proc (rw)
>> sysfs on /sys type sysfs (rw)
>> devpts on /dev/pts type devpts (rw,gid=5,mode=620)
>> tmpfs on /dev/shm type tmpfs (rw)
>> /dev/sda1 on /boot type ext4 (rw)
>> /dev/sdb1 on /export type ext4 (rw)
>> /dev/sda2 on /var type ext4 (rw)
>> tmpfs on /var/lib/ganglia/rrds type tmpfs
>> (rw,size=6180842000,gid=99,uid=99)
>> none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
>> sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
>> nfsd on /proc/fs/nfsd type nfsd (rw)
>> /dev/IGBHOME0 on /home type gpfs (rw,mtime,dev=IGBHOME0)
>> 128.174.124.79:/shares/group on /archive/group type nfs
>> (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>> roto=tcp,mountproto=tcp,addr=128.174.124.79)
>> 128.174.124.79:/shares/CBC on /archive/CBC type nfs
>> (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>> roto=tcp,mountproto=tcp,addr=128.174.124.79)
>> 
>> chris
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 




From felix.bemm at uni-wuerzburg.de  Fri Oct  4 01:10:08 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Fri, 04 Oct 2013 09:10:08 +0200
Subject: [maker-devel] Contigs failing - could not make datastore directory
Message-ID: <524E69D0.1090905@uni-wuerzburg.de>

Hi,

I have a problem with Contigs failing like this:

examining contents of the fasta file and run log
ERROR: could not make datastore directory
--> rank=11, hostname=r5n04
ERROR: Failed while examining contents of the fasta file and run log
ERROR: Chunk failed at level:0, tier_type:0
FAILED CONTIG:MA_gen_v8.05_c31675

There is enough space available on both the storage device and the tmp 
device that is being used. The datastore log files looks like this:

MA_gen_v8.05_c1149              FAILED
MA_gen_v8.05_c1153              FAILED
MA_gen_v8.05_c1154              FAILED
MA_gen_v8.05_c1155              FAILED
MA_gen_v8.05_c1156              FAILED

Since there is no datastore for this contigs, I can not provide any more 
informationen. Approx. 1/3 of the contigs were annotated, after that 
maker started to fail. It kept running for a while and finishing some of 
the contigs in the second or third try like this:

MA_gen_v8.05_c4443		FAILED
MA_gen_v8.05_c4443		FAILED
MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	STARTED
MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/ 
FINISHED

Any ideas what can cause this problems?

Best regards
Felix

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Fri Oct  4 12:15:35 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 04 Oct 2013 14:15:35 -0400
Subject: [maker-devel] Contigs failing - could not make datastore
 directory
In-Reply-To: <524E69D0.1090905@uni-wuerzburg.de>
Message-ID: <CE747D9A.F599%carsonhh@gmail.com>

Let me know what you find.  With some failures it's hard to identify the
problem especially with long running processes, which is why I made MAKER
restartable, so you can at least get completion by just launching again.

--Carson


On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi,
>
>I have a problem with Contigs failing like this:
>
>examining contents of the fasta file and run log
>ERROR: could not make datastore directory
>--> rank=11, hostname=r5n04
>ERROR: Failed while examining contents of the fasta file and run log
>ERROR: Chunk failed at level:0, tier_type:0
>FAILED CONTIG:MA_gen_v8.05_c31675
>
>There is enough space available on both the storage device and the tmp
>device that is being used. The datastore log files looks like this:
>
>MA_gen_v8.05_c1149              FAILED
>MA_gen_v8.05_c1153              FAILED
>MA_gen_v8.05_c1154              FAILED
>MA_gen_v8.05_c1155              FAILED
>MA_gen_v8.05_c1156              FAILED
>
>Since there is no datastore for this contigs, I can not provide any more
>informationen. Approx. 1/3 of the contigs were annotated, after that
>maker started to fail. It kept running for a while and finishing some of
>the contigs in the second or third try like this:
>
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	START
>ED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>FINISHED
>
>Any ideas what can cause this problems?
>
>Best regards
>Felix
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Fri Oct  4 12:21:42 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 04 Oct 2013 14:21:42 -0400
Subject: [maker-devel] Contigs failing - could not make datastore
 directory
In-Reply-To: <524E69D0.1090905@uni-wuerzburg.de>
Message-ID: <CE743B26.F369%carsonhh@gmail.com>

Hi Felix,

There are other potential issues as well, for example a file quota limit
set by your administrator or full local /tmp which will be unique to each
node and cannot be queried directly from the root node on a cluster.  On a
cluster one node may also not have the NFS location mounted.  Or it could
be system related, for example on ibrix NFS mounted systems you can get a
weird filesystem issue with ghost files and directories when using MAKER
that can neither be created nor deleted.  Try running the failed contigs
in a different directory (even if it's on the same disk).  Also what
version of MAKER are you using?

--Carson



On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi,
>
>I have a problem with Contigs failing like this:
>
>examining contents of the fasta file and run log
>ERROR: could not make datastore directory
>--> rank=11, hostname=r5n04
>ERROR: Failed while examining contents of the fasta file and run log
>ERROR: Chunk failed at level:0, tier_type:0
>FAILED CONTIG:MA_gen_v8.05_c31675
>
>There is enough space available on both the storage device and the tmp
>device that is being used. The datastore log files looks like this:
>
>MA_gen_v8.05_c1149              FAILED
>MA_gen_v8.05_c1153              FAILED
>MA_gen_v8.05_c1154              FAILED
>MA_gen_v8.05_c1155              FAILED
>MA_gen_v8.05_c1156              FAILED
>
>Since there is no datastore for this contigs, I can not provide any more
>informationen. Approx. 1/3 of the contigs were annotated, after that
>maker started to fail. It kept running for a while and finishing some of
>the contigs in the second or third try like this:
>
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	START
>ED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>FINISHED
>
>Any ideas what can cause this problems?
>
>Best regards
>Felix
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From felix.bemm at uni-wuerzburg.de  Sat Oct  5 08:09:15 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Sat, 05 Oct 2013 16:09:15 +0200
Subject: [maker-devel] Contigs failing - could not make datastore
	directory
In-Reply-To: <CE743B26.F369%carsonhh@gmail.com>
References: <CE743B26.F369%carsonhh@gmail.com>
Message-ID: <52501D8B.2060301@uni-wuerzburg.de>

Hi Carson,

there is definitely no quota neither a full local tmp device. I changed 
to another tmp device, which is unfortunately residing on nfs but now it 
seems to work. I am using the latest version of maker (2.28). The 
complete job is running on a single machine with 32 mpi threads.

Bests
Felix

Am 04.10.2013 20:21, schrieb Carson Holt:
> Hi Felix,
>
> There are other potential issues as well, for example a file quota limit
> set by your administrator or full local /tmp which will be unique to each
> node and cannot be queried directly from the root node on a cluster.  On a
> cluster one node may also not have the NFS location mounted.  Or it could
> be system related, for example on ibrix NFS mounted systems you can get a
> weird filesystem issue with ghost files and directories when using MAKER
> that can neither be created nor deleted.  Try running the failed contigs
> in a different directory (even if it's on the same disk).  Also what
> version of MAKER are you using?
>
> --Carson
>
>
>
> On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>> Hi,
>>
>> I have a problem with Contigs failing like this:
>>
>> examining contents of the fasta file and run log
>> ERROR: could not make datastore directory
>> --> rank=11, hostname=r5n04
>> ERROR: Failed while examining contents of the fasta file and run log
>> ERROR: Chunk failed at level:0, tier_type:0
>> FAILED CONTIG:MA_gen_v8.05_c31675
>>
>> There is enough space available on both the storage device and the tmp
>> device that is being used. The datastore log files looks like this:
>>
>> MA_gen_v8.05_c1149              FAILED
>> MA_gen_v8.05_c1153              FAILED
>> MA_gen_v8.05_c1154              FAILED
>> MA_gen_v8.05_c1155              FAILED
>> MA_gen_v8.05_c1156              FAILED
>>
>> Since there is no datastore for this contigs, I can not provide any more
>> informationen. Approx. 1/3 of the contigs were annotated, after that
>> maker started to fail. It kept running for a while and finishing some of
>> the contigs in the second or third try like this:
>>
>> MA_gen_v8.05_c4443		FAILED
>> MA_gen_v8.05_c4443		FAILED
>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	START
>> ED
>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>> FINISHED
>>
>> Any ideas what can cause this problems?
>>
>> Best regards
>> Felix
>>
>> --
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From jfierst at uoregon.edu  Fri Oct  4 11:06:36 2013
From: jfierst at uoregon.edu (Janna Fierst)
Date: Fri, 4 Oct 2013 10:06:36 -0700
Subject: [maker-devel] Fwd:  exon/intron boundaries
In-Reply-To: <CAGoyurYe_c3Cd6KK-z0t0WqYmGGh5VQsSZXo9_=Lt9MGMSz=kA@mail.gmail.com>
References: <CAGoyuraVoRp94vbk_mb1qLzELeXSbeybGwkvgFx-6smEVt_DcQ@mail.gmail.com>
	<CE411E31.998A%carsonhh@gmail.com>
	<CAGoyurYe_c3Cd6KK-z0t0WqYmGGh5VQsSZXo9_=Lt9MGMSz=kA@mail.gmail.com>
Message-ID: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>

Hi,

thanks for your reply- I have been going through our annotations in detail
and trying different parameter sets, and I think I have identified what is
going on but I'm not sure how to set the MAKER2 parameters for our
situation. We are working with a species of Caenorhabditid worm and there
are long gene-dense blocks that are being incorrectly annotated as large
single genes instead of several smaller closely spaced genes. The protein
alignments (tblastx and protein2genome) show very clearly where the
exon/intron boundaries are and in most cases agree with the augustus
predictions. The assembled cufflinks output (through blastn, est2genome and
est_gff:cufflinks) does not agree in some locations; I think this may be
because in some cases the UTR nearly overlaps adjacent genes.

I have included a screenshot of an annotated region viewed in apollo to try
to show this. The large gene in the middle is actually 7 different genes
that are extremely close together and MAKER2 is collapsing them into a
single gene. I tried running without any RNASeq/cufflinks data and MAKER2
annotates the region as two genes instead of one, but I can't get it to
recognize the 7 as different genes. I have retrained SNAP but we have not
been able to successfully train Augustus, we are currently using the
default caenhorhabditis species model. I also included a species specific
repeat library. I tried setting correct_est_fusion=1 and reducing
pred_flank but these changes appear to really alter the annotations and we
end up annotating almost nothing. I also tried setting est2genome=0 to
decrease the influence of the cufflinks assembly but it didn't appear to
help. There are some very large introns in these genes so I haven't tried
yet decreasing the maximum intron size because I'm concerned this may
generate too many split genes instead of our current merged gene problem.
Thanks for your help, any advice is greatly appreciated! -Janna Fierst


On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Are you getting gene fusions or just more exons?  Gene fusions can be
> reduced by setting correct_est_fusion=1, or reducing pred_flank, although
> reducing pred_flank can cause other issues (but those generally only appear
> if setting the value below below 150).  Also if you have the maximum intron
> size set to high (split_hit option), you may also be generating bridging
> alignments that make evidence align across distant paralogous genes as well
> (this can result in gene merging)
>
> You should also look at your results manually in a viewer like Apollo.
>  Then see if the extra exons are supported by something such as protein
> alignments from another species.  If this is the case, you may have a
> poorly annotated protein set that is being used as evidence that is
> carrying over it's erroneous exons into the species you are annotating.  If
> the extra  exons are supported by EST evidence, then perhaps you should try
> and rebuild the EST assembly (for example trinity has an option to use a
> Jarccardian similarity coefficient to avoid fusing transcripts).
>
> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
> produce any of the models itself (it is a pipeline not a predictor).  The
> models are all generated using these other algorithms, MAKER just feeds
> them hints based on protein and transcript alignments, so making sure
> training is sufficient is important for those programs to produce their
> best models.
>
> Finally make sure your repeat database is sufficient, you may need to
> generate a species specific repeat library using something like
> RepeatModeler.  Repeats can end up being included as extra exons in gene
> models because they may contain reading frames the do code for proteins
> (I.e. reverse transcriptases).
>
> If you have any questions on any of the above, just let us know.
>
> Thanks,
> Carson
>
>
> From: Janna Fierst <jfierst at uoregon.edu>
> Date: Monday, August 26, 2013 2:54 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] exon/intron boundaries
>
> Hi,
>
> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
> initial results appear fairly good but we seem to be be annotating too many
> exons for multiple genes. I was wondering which parameters should be tuned
> to change the threshold for exon/intron boundaries? Thanks for your help
> -Janna Fierst
>  _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From jfierst at uoregon.edu  Sat Oct  5 16:18:52 2013
From: jfierst at uoregon.edu (Janna Fierst)
Date: Sat, 5 Oct 2013 15:18:52 -0700
Subject: [maker-devel] Fwd:  exon/intron boundaries
In-Reply-To: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
References: <CAGoyuraVoRp94vbk_mb1qLzELeXSbeybGwkvgFx-6smEVt_DcQ@mail.gmail.com>
	<CE411E31.998A%carsonhh@gmail.com>
	<CAGoyurYe_c3Cd6KK-z0t0WqYmGGh5VQsSZXo9_=Lt9MGMSz=kA@mail.gmail.com>
	<CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
Message-ID: <CAGoyurYHu9ir90T2-xhBxDyv_xVY5=AGFHJJL3Fu0o2fxtvqOg@mail.gmail.com>

Hi,

thanks for your reply- I have been going through our annotations in detail
and trying different parameter sets, and I think I have identified what is
going on but I'm not sure how to set the MAKER2 parameters for our
situation. We are working with a species of Caenorhabditid worm and there
are long gene-dense blocks that are being incorrectly annotated as large
single genes instead of several smaller closely spaced genes. The protein
alignments (tblastx and protein2genome) show very clearly where the
exon/intron boundaries are and in most cases agree with the augustus
predictions. The assembled cufflinks output (through blastn, est2genome and
est_gff:cufflinks) does not agree in some locations; I think this may be
because in some cases the UTR nearly overlaps adjacent genes.

I have included a screenshot of an annotated region viewed in apollo to try
to show this. The large gene in the middle is actually 7 different genes
that are extremely close together and MAKER2 is collapsing them into a
single gene. I tried running without any RNASeq/cufflinks data and MAKER2
annotates the region as two genes instead of one, but I can't get it to
recognize the 7 as different genes. I have retrained SNAP but we have not
been able to successfully train Augustus, we are currently using the
default caenhorhabditis species model. I also included a species specific
repeat library. I tried setting correct_est_fusion=1 and reducing
pred_flank but these changes appear to really alter the annotations and we
end up annotating almost nothing. I also tried setting est2genome=0 to
decrease the influence of the cufflinks assembly but it didn't appear to
help. There are some very large introns in these genes so I haven't tried
yet decreasing the maximum intron size because I'm concerned this may
generate too many split genes instead of our current merged gene problem.
Thanks for your help, any advice is greatly appreciated! -Janna Fierst


On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Are you getting gene fusions or just more exons?  Gene fusions can be
> reduced by setting correct_est_fusion=1, or reducing pred_flank, although
> reducing pred_flank can cause other issues (but those generally only appear
> if setting the value below below 150).  Also if you have the maximum intron
> size set to high (split_hit option), you may also be generating bridging
> alignments that make evidence align across distant paralogous genes as well
> (this can result in gene merging)
>
> You should also look at your results manually in a viewer like Apollo.
>  Then see if the extra exons are supported by something such as protein
> alignments from another species.  If this is the case, you may have a
> poorly annotated protein set that is being used as evidence that is
> carrying over it's erroneous exons into the species you are annotating.  If
> the extra  exons are supported by EST evidence, then perhaps you should try
> and rebuild the EST assembly (for example trinity has an option to use a
> Jarccardian similarity coefficient to avoid fusing transcripts).
>
> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
> produce any of the models itself (it is a pipeline not a predictor).  The
> models are all generated using these other algorithms, MAKER just feeds
> them hints based on protein and transcript alignments, so making sure
> training is sufficient is important for those programs to produce their
> best models.
>
> Finally make sure your repeat database is sufficient, you may need to
> generate a species specific repeat library using something like
> RepeatModeler.  Repeats can end up being included as extra exons in gene
> models because they may contain reading frames the do code for proteins
> (I.e. reverse transcriptases).
>
> If you have any questions on any of the above, just let us know.
>
> Thanks,
> Carson
>
>
> From: Janna Fierst <jfierst at uoregon.edu>
> Date: Monday, August 26, 2013 2:54 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] exon/intron boundaries
>
> Hi,
>
> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
> initial results appear fairly good but we seem to be be annotating too many
> exons for multiple genes. I was wondering which parameters should be tuned
> to change the threshold for exon/intron boundaries? Thanks for your help
> -Janna Fierst
>  _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From myandell at genetics.utah.edu  Mon Oct  7 05:36:53 2013
From: myandell at genetics.utah.edu (Mark Yandell)
Date: Mon, 7 Oct 2013 11:36:53 +0000
Subject: [maker-devel] maker apollo error
In-Reply-To: <8687323557146056ef885dd8a1bf2ea4@buzonweb.us.es>
References: <8687323557146056ef885dd8a1bf2ea4@buzonweb.us.es>
Message-ID: <7A60AB257EFF2B48B1F4C814817EA05365E66B3C@mxb2.hg.genetics.utah.edu>


Hi Gabriel,

I've forwarded your request on to the MAKER email list...

cheers,

--mark

Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: ggpozo at us.es [ggpozo at us.es]
Sent: Monday, October 07, 2013 2:49 AM
To: Mark Yandell
Subject: maker apollo error

Dear Dr. Yandell,

First, thank you very much for provide us such a great tool as MAKER. I am traying to install it in my Linux system, everything is ok, however when I try to instal Apollo with ./Build apollo...

Downloading apollo...
--2013-10-07 10:45:37--  http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 302 Found
Localizaci?n: http://sourceforge.net/p/gmod/svn/ [siguiendo]
--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/
Resolviendo sourceforge.net... 216.34.181.60
Connecting to sourceforge.net|216.34.181.60|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 302 Found
Localizaci?n: http://sourceforge.net/p/gmod/svn/HEAD/tree/ [siguiendo]
--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/HEAD/tree/
Connecting to sourceforge.net|216.34.181.60|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 200 OK
Longitud: 37730 (37K) [text/html]
Saving to: `/home/maker/src/../exe/apollo.tar.gz'

100%[==================================================================================================================================>] 37.730      92,1K/s   in 0,4s

2013-10-07 10:45:40 (92,1 KB/s) - `/home/maker/src/../exe/apollo.tar.gz' saved [37730/37730]

Unpacking apollo tarball...

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now


ERROR: Failed installing apollo, now cleaning installation path...
You may need to install apollo manually.



It seems that the http direction  in locations file is wrong, Apollo has changed its version and now Apollo is integrated in Apolloweb, may be this the problem.



I would greatly appreciate any help you can give me.

Thank you very much.



Dr. Gabriel Gutierrez

Department of Genetcis

University of Seville

Spain




From carsonhh at gmail.com  Mon Oct  7 07:20:17 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 09:20:17 -0400
Subject: [maker-devel] Fwd:  exon/intron boundaries
In-Reply-To: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
Message-ID: <CE782A71.F621%carsonhh@gmail.com>

Hi Janna,

There are a couple of things to do.  Download the maker-2.29p-beta from the
lab website.  This includes some changes made to improve the performance of
correct_est_fusion.  Whenever using the correct_est_fusion option, this also
reduces the influence of ESTs on annotation.  So normally you would need to
increase your protein dataset, but given that you have supplied 3 nematode
species and all of UniProt already you should probably be fine. But there is
one last thing you can do.  Instead of using cufflinks, try using trinity to
assemble the ESTs.  There is a Jaccard clip option that reducing merging
caused by overlapping UTR.  Between the trinity and correct_est_fusion you
should be able to really reduce the effect of those ESTs.

If those changes don't work there is one last option.  If you take the MAKER
results and filter them for SNAP and Augustus ab initio results
(match/match_part in the GFF3), then you can pass those in to the pred_gff
options.  Then turn snaphmm and augustus_species off in the control files.
Basically what this will do is turn MAKER's hint based prediction off and
force it to filter the ab intio results and select directly models from
there.  Since the merging is being caused by bad hints (merged transcripts
from mRNAseq) this would reduce that effect.  You will still need
correct_est_fusion=1 though to trim UTR coming from the merged transcripts,
because even though MAEKR can't process hints to rerun SNAP and Augustus
this way, it will try and add UTR using the EST evidence.

--Carson


From:  Janna Fierst <jfierst at uoregon.edu>
Date:  Friday, October 4, 2013 1:06 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Fwd:  exon/intron boundaries

Hi,

thanks for your reply- I have been going through our annotations in detail
and trying different parameter sets, and I think I have identified what is
going on but I'm not sure how to set the MAKER2 parameters for our
situation. We are working with a species of Caenorhabditid worm and there
are long gene-dense blocks that are being incorrectly annotated as large
single genes instead of several smaller closely spaced genes. The protein
alignments (tblastx and protein2genome) show very clearly where the
exon/intron boundaries are and in most cases agree with the augustus
predictions. The assembled cufflinks output (through blastn, est2genome and
est_gff:cufflinks) does not agree in some locations; I think this may be
because in some cases the UTR nearly overlaps adjacent genes.

I have included a screenshot of an annotated region viewed in apollo to try
to show this. The large gene in the middle is actually 7 different genes
that are extremely close together and MAKER2 is collapsing them into a
single gene. I tried running without any RNASeq/cufflinks data and MAKER2
annotates the region as two genes instead of one, but I can't get it to
recognize the 7 as different genes. I have retrained SNAP but we have not
been able to successfully train Augustus, we are currently using the default
caenhorhabditis species model. I also included a species specific repeat
library. I tried setting correct_est_fusion=1 and reducing pred_flank but
these changes appear to really alter the annotations and we end up
annotating almost nothing. I also tried setting est2genome=0 to decrease the
influence of the cufflinks assembly but it didn't appear to help. There are
some very large introns in these genes so I haven't tried yet decreasing the
maximum intron size because I'm concerned this may generate too many split
genes instead of our current merged gene problem. Thanks for your help, any
advice is greatly appreciated! -Janna Fierst


On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:
> Are you getting gene fusions or just more exons?  Gene fusions can be reduced
> by setting correct_est_fusion=1, or reducing pred_flank, although reducing
> pred_flank can cause other issues (but those generally only appear if setting
> the value below below 150).  Also if you have the maximum intron size set to
> high (split_hit option), you may also be generating bridging alignments that
> make evidence align across distant paralogous genes as well (this can result
> in gene merging)
> 
> You should also look at your results manually in a viewer like Apollo.  Then
> see if the extra exons are supported by something such as protein alignments
> from another species.  If this is the case, you may have a poorly annotated
> protein set that is being used as evidence that is carrying over it's
> erroneous exons into the species you are annotating.  If the extra  exons are
> supported by EST evidence, then perhaps you should try and rebuild the EST
> assembly (for example trinity has an option to use a Jarccardian similarity
> coefficient to avoid fusing transcripts).
> 
> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
> produce any of the models itself (it is a pipeline not a predictor).  The
> models are all generated using these other algorithms, MAKER just feeds them
> hints based on protein and transcript alignments, so making sure training is
> sufficient is important for those programs to produce their best models.
> 
> Finally make sure your repeat database is sufficient, you may need to generate
> a species specific repeat library using something like RepeatModeler.  Repeats
> can end up being included as extra exons in gene models because they may
> contain reading frames the do code for proteins (I.e. reverse transcriptases).
> 
> If you have any questions on any of the above, just let us know.
> 
> Thanks,
> Carson
> 
> 
> From:  Janna Fierst <jfierst at uoregon.edu>
> Date:  Monday, August 26, 2013 2:54 PM
> To:  <maker-devel at yandell-lab.org>
> Subject:  [maker-devel] exon/intron boundaries
> 
> Hi,
> 
> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
> initial results appear fairly good but we seem to be be annotating too many
> exons for multiple genes. I was wondering which parameters should be tuned to
> change the threshold for exon/intron boundaries? Thanks for your help -Janna
> Fierst
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak
> er-devel_yandell-lab.org


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

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From carsonhh at gmail.com  Mon Oct  7 08:12:24 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 10:12:24 -0400
Subject: [maker-devel] maker apollo error
In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05365E66B3C@mxb2.hg.genetics.utah.edu>
Message-ID: <CE783792.F640%carsonhh@gmail.com>

This was a location from GMOD for the older Apollo.  It looks like they've
dropped it, so it now points to nothing. Perhaps there is another location
that still has the old code I can get from Ed.

--Carson



On 10/7/13 7:36 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:

>
>Hi Gabriel,
>
>I've forwarded your request on to the MAKER email list...
>
>cheers,
>
>--mark
>
>Mark Yandell
>Professor of Human Genetics
>H.A. & Edna Benning Presidential Endowed Chair
>Eccles Institute of Human Genetics
>University of Utah
>15 North 2030 East, Room 2100
>Salt Lake City, UT 84112-5330
>ph:801-587-7707
>
>________________________________________
>From: ggpozo at us.es [ggpozo at us.es]
>Sent: Monday, October 07, 2013 2:49 AM
>To: Mark Yandell
>Subject: maker apollo error
>
>Dear Dr. Yandell,
>
>First, thank you very much for provide us such a great tool as MAKER. I
>am traying to install it in my Linux system, everything is ok, however
>when I try to instal Apollo with ./Build apollo...
>
>Downloading apollo...
>--2013-10-07 10:45:37--
>http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
>Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
>Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
>Petici?n HTTP enviada, esperando respuesta... 302 Found
>Localizaci?n: http://sourceforge.net/p/gmod/svn/ [siguiendo]
>--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/
>Resolviendo sourceforge.net... 216.34.181.60
>Connecting to sourceforge.net|216.34.181.60|:80... conectado.
>Petici?n HTTP enviada, esperando respuesta... 302 Found
>Localizaci?n: http://sourceforge.net/p/gmod/svn/HEAD/tree/ [siguiendo]
>--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/HEAD/tree/
>Connecting to sourceforge.net|216.34.181.60|:80... conectado.
>Petici?n HTTP enviada, esperando respuesta... 200 OK
>Longitud: 37730 (37K) [text/html]
>Saving to: `/home/maker/src/../exe/apollo.tar.gz'
>
>100%[=====================================================================
>=============================================================>] 37.730
>  92,1K/s   in 0,4s
>
>2013-10-07 10:45:40 (92,1 KB/s) - `/home/maker/src/../exe/apollo.tar.gz'
>saved [37730/37730]
>
>Unpacking apollo tarball...
>
>gzip: stdin: not in gzip format
>tar: Child returned status 1
>tar: Error is not recoverable: exiting now
>
>
>ERROR: Failed installing apollo, now cleaning installation path...
>You may need to install apollo manually.
>
>
>
>It seems that the http direction  in locations file is wrong, Apollo has
>changed its version and now Apollo is integrated in Apolloweb, may be
>this the problem.
>
>
>
>I would greatly appreciate any help you can give me.
>
>Thank you very much.
>
>
>
>Dr. Gabriel Gutierrez
>
>Department of Genetcis
>
>University of Seville
>
>Spain
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Mon Oct  7 08:33:44 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 10:33:44 -0400
Subject: [maker-devel] Contigs failing - could not make datastore
 directory
In-Reply-To: <52501D8B.2060301@uni-wuerzburg.de>
Message-ID: <CE783CF2.F65A%carsonhh@gmail.com>

You can also try the 2.29 beta if you want (on the website).  Also when
MAKER exits, it tries to delete anything left behind in temporary folders,
so is it possible that it is creating space on exit after filling up /tmp?

Given that the issue seems to go away when you switch to another
directory, it suggests that this might be the kind of thing that is
specific to something about the current state of your your system.

Thanks,
Carson


On 10/5/13 10:09 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi Carson,
>
>there is definitely no quota neither a full local tmp device. I changed
>to another tmp device, which is unfortunately residing on nfs but now it
>seems to work. I am using the latest version of maker (2.28). The
>complete job is running on a single machine with 32 mpi threads.
>
>Bests
>Felix
>
>Am 04.10.2013 20:21, schrieb Carson Holt:
>> Hi Felix,
>>
>> There are other potential issues as well, for example a file quota limit
>> set by your administrator or full local /tmp which will be unique to
>>each
>> node and cannot be queried directly from the root node on a cluster.
>>On a
>> cluster one node may also not have the NFS location mounted.  Or it
>>could
>> be system related, for example on ibrix NFS mounted systems you can get
>>a
>> weird filesystem issue with ghost files and directories when using MAKER
>> that can neither be created nor deleted.  Try running the failed contigs
>> in a different directory (even if it's on the same disk).  Also what
>> version of MAKER are you using?
>>
>> --Carson
>>
>>
>>
>> On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Hi,
>>>
>>> I have a problem with Contigs failing like this:
>>>
>>> examining contents of the fasta file and run log
>>> ERROR: could not make datastore directory
>>> --> rank=11, hostname=r5n04
>>> ERROR: Failed while examining contents of the fasta file and run log
>>> ERROR: Chunk failed at level:0, tier_type:0
>>> FAILED CONTIG:MA_gen_v8.05_c31675
>>>
>>> There is enough space available on both the storage device and the tmp
>>> device that is being used. The datastore log files looks like this:
>>>
>>> MA_gen_v8.05_c1149              FAILED
>>> MA_gen_v8.05_c1153              FAILED
>>> MA_gen_v8.05_c1154              FAILED
>>> MA_gen_v8.05_c1155              FAILED
>>> MA_gen_v8.05_c1156              FAILED
>>>
>>> Since there is no datastore for this contigs, I can not provide any
>>>more
>>> informationen. Approx. 1/3 of the contigs were annotated, after that
>>> maker started to fail. It kept running for a while and finishing some
>>>of
>>> the contigs in the second or third try like this:
>>>
>>> MA_gen_v8.05_c4443		FAILED
>>> MA_gen_v8.05_c4443		FAILED
>>> 
>>>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	STA
>>>RT
>>> ED
>>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>>> FINISHED
>>>
>>> Any ideas what can cause this problems?
>>>
>>> Best regards
>>> Felix
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de





From felix.bemm at uni-wuerzburg.de  Mon Oct  7 10:40:12 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Mon, 07 Oct 2013 18:40:12 +0200
Subject: [maker-devel] Contigs failing - could not make datastore
	directory
In-Reply-To: <CE783CF2.F65A%carsonhh@gmail.com>
References: <CE783CF2.F65A%carsonhh@gmail.com>
Message-ID: <5252E3EC.6050908@uni-wuerzburg.de>

Do you have a changelog for 2.29b?

On 07.10.2013 16:33, Carson Holt wrote:
> You can also try the 2.29 beta if you want (on the website).  Also when
> MAKER exits, it tries to delete anything left behind in temporary folders,
> so is it possible that it is creating space on exit after filling up /tmp?

I will try to monitor that!

> Given that the issue seems to go away when you switch to another
> directory, it suggests that this might be the kind of thing that is
> specific to something about the current state of your your system.

I agree with that. Interestingly it happens with the only directory 
where I would not expect that.

> Thanks,
> Carson
>
>
> On 10/5/13 10:09 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>> Hi Carson,
>>
>> there is definitely no quota neither a full local tmp device. I changed
>> to another tmp device, which is unfortunately residing on nfs but now it
>> seems to work. I am using the latest version of maker (2.28). The
>> complete job is running on a single machine with 32 mpi threads.
>>
>> Bests
>> Felix
>>
>> Am 04.10.2013 20:21, schrieb Carson Holt:
>>> Hi Felix,
>>>
>>> There are other potential issues as well, for example a file quota limit
>>> set by your administrator or full local /tmp which will be unique to
>>> each
>>> node and cannot be queried directly from the root node on a cluster.
>>> On a
>>> cluster one node may also not have the NFS location mounted.  Or it
>>> could
>>> be system related, for example on ibrix NFS mounted systems you can get
>>> a
>>> weird filesystem issue with ghost files and directories when using MAKER
>>> that can neither be created nor deleted.  Try running the failed contigs
>>> in a different directory (even if it's on the same disk).  Also what
>>> version of MAKER are you using?
>>>
>>> --Carson
>>>
>>>
>>>
>>> On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a problem with Contigs failing like this:
>>>>
>>>> examining contents of the fasta file and run log
>>>> ERROR: could not make datastore directory
>>>> --> rank=11, hostname=r5n04
>>>> ERROR: Failed while examining contents of the fasta file and run log
>>>> ERROR: Chunk failed at level:0, tier_type:0
>>>> FAILED CONTIG:MA_gen_v8.05_c31675
>>>>
>>>> There is enough space available on both the storage device and the tmp
>>>> device that is being used. The datastore log files looks like this:
>>>>
>>>> MA_gen_v8.05_c1149              FAILED
>>>> MA_gen_v8.05_c1153              FAILED
>>>> MA_gen_v8.05_c1154              FAILED
>>>> MA_gen_v8.05_c1155              FAILED
>>>> MA_gen_v8.05_c1156              FAILED
>>>>
>>>> Since there is no datastore for this contigs, I can not provide any
>>>> more
>>>> informationen. Approx. 1/3 of the contigs were annotated, after that
>>>> maker started to fail. It kept running for a while and finishing some
>>>> of
>>>> the contigs in the second or third try like this:
>>>>
>>>> MA_gen_v8.05_c4443		FAILED
>>>> MA_gen_v8.05_c4443		FAILED
>>>>
>>>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	STA
>>>> RT
>>>> ED
>>>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>>>> FINISHED
>>>>
>>>> Any ideas what can cause this problems?
>>>>
>>>> Best regards
>>>> Felix
>>>>
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> --
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Mon Oct  7 11:25:34 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 13:25:34 -0400
Subject: [maker-devel] maker apollo error
In-Reply-To: <14a642f3dc9cb615f048b70228bad3be@buzonweb.us.es>
Message-ID: <CE78668C.F68A%carsonhh@gmail.com>

Here is a new location for the source -->
http://sourceforge.net/code-snapshots/svn/g/gm/gmod/svn/gmod-svn-25291-apoll
o-trunk.zip

--Carson


From:  <ggpozo at us.es>
Date:  Monday, October 7, 2013 12:47 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Mark Yandell <myandell at genetics.utah.edu>,
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] maker apollo error

Thanks, I have modified the locations file pointing to a personal server
where I downloaded an old version of Apollo but it did not work, but if you
can get a new one I would try it again.

Thanks

Gabriel

 
El 07/10/2013 16:12, Carson Holt escribi?:
> This was a location from GMOD for the older Apollo.  It looks like they've
> dropped it, so it now points to nothing. Perhaps there is another location
> that still has the old code I can get from Ed.
> 
> --Carson
> 
> 
> 
> On 10/7/13 7:36 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>> Hi Gabriel, I've forwarded your request on to the MAKER email list... cheers,
>> --mark Mark Yandell Professor of Human Genetics H.A. & Edna Benning
>> Presidential Endowed Chair Eccles Institute of Human Genetics University of
>> Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330
>> ph:801-587-7707 ________________________________________ From: ggpozo at us.es
>> [ggpozo at us.es] Sent: Monday, October 07, 2013 2:49 AM To: Mark Yandell
>> Subject: maker apollo error Dear Dr. Yandell, First, thank you very much for
>> provide us such a great tool as MAKER. I am traying to install it in my Linux
>> system, everything is ok, however when I try to instal Apollo with ./Build
>> apollo... Downloading apollo... --2013-10-07 10:45:37--
>> http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
>> Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
>> Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
>> Petici?n HTTP enviada, esperando respuesta... 302 Found Localizaci?n:
>> http://sourceforge.net/p/gmod/svn/ [siguiendo] --2013-10-07 10:45:38--
>> http://sourceforge.net/p/gmod/svn/ Resolviendo sourceforge.net...
>> 216.34.181.60 Connecting to sourceforge.net|216.34.181.60|:80... conectado.
>> Petici?n HTTP enviada, esperando respuesta... 302 Found Localizaci?n:
>> http://sourceforge.net/p/gmod/svn/HEAD/tree/ [siguiendo] --2013-10-07
>> 10:45:38-- http://sourceforge.net/p/gmod/svn/HEAD/tree/ Connecting to
>> sourceforge.net|216.34.181.60|:80... conectado. Petici?n HTTP enviada,
>> esperando respuesta... 200 OK Longitud: 37730 (37K) [text/html] Saving to:
>> `/home/maker/src/../exe/apollo.tar.gz'
>> 100%[=====================================================================
>> =============================================================>] 37.730
>> 92,1K/s in 0,4s 2013-10-07 10:45:40 (92,1 KB/s) -
>> `/home/maker/src/../exe/apollo.tar.gz' saved [37730/37730] Unpacking apollo
>> tarball... gzip: stdin: not in gzip format tar: Child returned status 1 tar:
>> Error is not recoverable: exiting now ERROR: Failed installing apollo, now
>> cleaning installation path... You may need to install apollo manually. It
>> seems that the http direction in locations file is wrong, Apollo has changed
>> its version and now Apollo is integrated in Apolloweb, may be this the
>> problem. I would greatly appreciate any help you can give me. Thank you very
>> much. Dr. Gabriel Gutierrez Department of Genetcis University of Seville
>> Spain _______________________________________________ maker-devel mailing
>> list maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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From ggpozo at us.es  Mon Oct  7 10:47:13 2013
From: ggpozo at us.es (ggpozo at us.es)
Date: Mon, 07 Oct 2013 18:47:13 +0200
Subject: [maker-devel] maker apollo error
In-Reply-To: <CE783792.F640%carsonhh@gmail.com>
References: <CE783792.F640%carsonhh@gmail.com>
Message-ID: <14a642f3dc9cb615f048b70228bad3be@buzonweb.us.es>

 

Thanks, I have modified the locations file pointing to a personal
server where I downloaded an old version of Apollo but it did not work,
but if you can get a new one I would try it again. 

Thanks 

Gabriel


El 07/10/2013 16:12, Carson Holt escribi?: 

> This was a location
from GMOD for the older Apollo. It looks like they've
> dropped it, so
it now points to nothing. Perhaps there is another location
> that still
has the old code I can get from Ed.
> 
> --Carson
> 
> On 10/7/13 7:36
AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
> 
>> Hi Gabriel,
I've forwarded your request on to the MAKER email list... cheers, --mark
Mark Yandell Professor of Human Genetics H.A. & Edna Benning
Presidential Endowed Chair Eccles Institute of Human Genetics University
of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330
ph:801-587-7707 ________________________________________ From:
ggpozo at us.es [1] [ggpozo at us.es [2]] Sent: Monday, October 07, 2013 2:49
AM To: Mark Yandell Subject: maker apollo error Dear Dr. Yandell, First,
thank you very much for provide us such a great tool as MAKER. I am
traying to install it in my Linux system, everything is ok, however when
I try to instal Apollo with ./Build apollo... Downloading apollo...
--2013-10-07 10:45:37--
http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar [3]
Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 302 Found Localizaci?n:
http://sourceforge.net/p/gmod/svn/ [4] [siguiendo] --2013-10-07
10:45:38-- http://sourceforge.net/p/gmod/svn/ [5] Resolviendo
sourceforge.net... 216.34.181.60 Connecting to
sourceforge.net|216.34.181.60|:80... conectado. Petici?n HTTP enviada,
esperando respuesta... 302 Found Localizaci?n:
http://sourceforge.net/p/gmod/svn/HEAD/tree/ [6] [siguiendo]
--2013-10-07 10:45:38-- http://sourceforge.net/p/gmod/svn/HEAD/tree/ [7]
Connecting to sourceforge.net|216.34.181.60|:80... conectado. Petici?n
HTTP enviada, esperando respuesta... 200 OK Longitud: 37730 (37K)
[text/html] Saving to: `/home/maker/src/../exe/apollo.tar.gz'
100%[=====================================================================
=============================================================>] 37.730
92,1K/s in 0,4s 2013-10-07 10:45:40 (92,1 KB/s) -
`/home/maker/src/../exe/apollo.tar.gz' saved [37730/37730] Unpacking
apollo tarball... gzip: stdin: not in gzip format tar: Child returned
status 1 tar: Error is not recoverable: exiting now ERROR: Failed
installing apollo, now cleaning installation path... You may need to
install apollo manually. It seems that the http direction in locations
file is wrong, Apollo has changed its version and now Apollo is
integrated in Apolloweb, may be this the problem. I would greatly
appreciate any help you can give me. Thank you very much. Dr. Gabriel
Gutierrez Department of Genetcis University of Seville Spain
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com [8]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
[9]
 

Links:
------
[1] mailto:ggpozo at us.es
[2] mailto:ggpozo at us.es
[3]
http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
[4]
http://sourceforge.net/p/gmod/svn/
[5]
http://sourceforge.net/p/gmod/svn/
[6]
http://sourceforge.net/p/gmod/svn/HEAD/tree/
[7]
http://sourceforge.net/p/gmod/svn/HEAD/tree/
[8]
mailto:maker-devel at box290.bluehost.com
[9]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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From felix.bemm at uni-wuerzburg.de  Sat Oct 12 09:06:52 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Sat, 12 Oct 2013 17:06:52 +0200
Subject: [maker-devel] Serious Start Codon Problem
Message-ID: <5259658C.4000102@uni-wuerzburg.de>

Hi,

I have a serious problems with maker annotations especially the start 
codon placement. It started happening with maker version 2.27! About 1/3 
of my genes are missing a proper start codon. When reviewing the GFF 
files gene predictors and est evidence standalone would predict the 
right gene structure including the start codon. I was thinking that this 
problem was somehow linked to my gene models but looking at their 
standalone prediction I discarded that theory. Just some stats about 
proteins with proper start codon (first column) and missing start codon 
(second column).

Maker		9268	4215
SNAP		16577	896
Genemark	18764	290

Numbers look the same when Augustus is used (currently retraining). 
Manually using EST's in Apollo often fixes the problems but I don't want 
to check > 4000 genes for this.

Do you have any idea what could cause such a problem? If you need some 
example gff files I can send you.

Best regards
Felix

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Sat Oct 12 09:48:29 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Sat, 12 Oct 2013 11:48:29 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <5259658C.4000102@uni-wuerzburg.de>
Message-ID: <CE7EE411.10C24%carsonhh@gmail.com>

This issue just came up this week on another e-mail as well.

One way to fix it, is to edit the Bio::Tools::CodonTable module from
BioPerl (use maker --debug to have maker print out the locations of all
modules it uses).  Such a hack should only be done as a temporary work
around.

You change line 256 from -->
---M---------------M---------------M----------------------------

To-->
-----------------------------------M----------------------------


Maker uses the BioPerl is_start_codon function to determine if the codon
used in a result it receives is acceptable or if it should look upstream
or downstream for a different one. Apparently there are actually 3
acceptable start codons in the standard codon table (2 rare ones and one
common), so making the edit removes the two rare ones from the list.

I'm also preparing a 2.30 release that exports a "strict" codon table to
the BioPerl module, that will be used by default and should fix the issue.

Thanks,
Carson



On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi,
>
>I have a serious problems with maker annotations especially the start
>codon placement. It started happening with maker version 2.27! About 1/3
>of my genes are missing a proper start codon. When reviewing the GFF
>files gene predictors and est evidence standalone would predict the
>right gene structure including the start codon. I was thinking that this
>problem was somehow linked to my gene models but looking at their
>standalone prediction I discarded that theory. Just some stats about
>proteins with proper start codon (first column) and missing start codon
>(second column).
>
>Maker		9268	4215
>SNAP		16577	896
>Genemark	18764	290
>
>Numbers look the same when Augustus is used (currently retraining).
>Manually using EST's in Apollo often fixes the problems but I don't want
>to check > 4000 genes for this.
>
>Do you have any idea what could cause such a problem? If you need some
>example gff files I can send you.
>
>Best regards
>Felix
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From felix.bemm at uni-wuerzburg.de  Sat Oct 12 10:16:06 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Sat, 12 Oct 2013 18:16:06 +0200
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE7EE411.10C24%carsonhh@gmail.com>
References: <CE7EE411.10C24%carsonhh@gmail.com>
Message-ID: <525975C6.4020403@uni-wuerzburg.de>

Thx Carson! Do you now when 2.30 will be available? Bests

On 12.10.2013 17:48, Carson Holt wrote:
> This issue just came up this week on another e-mail as well.
>
> One way to fix it, is to edit the Bio::Tools::CodonTable module from
> BioPerl (use maker --debug to have maker print out the locations of all
> modules it uses).  Such a hack should only be done as a temporary work
> around.
>
> You change line 256 from -->
> ---M---------------M---------------M----------------------------
>
> To-->
> -----------------------------------M----------------------------
>
>
> Maker uses the BioPerl is_start_codon function to determine if the codon
> used in a result it receives is acceptable or if it should look upstream
> or downstream for a different one. Apparently there are actually 3
> acceptable start codons in the standard codon table (2 rare ones and one
> common), so making the edit removes the two rare ones from the list.
>
> I'm also preparing a 2.30 release that exports a "strict" codon table to
> the BioPerl module, that will be used by default and should fix the issue.
>
> Thanks,
> Carson
>
>
>
> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>> Hi,
>>
>> I have a serious problems with maker annotations especially the start
>> codon placement. It started happening with maker version 2.27! About 1/3
>> of my genes are missing a proper start codon. When reviewing the GFF
>> files gene predictors and est evidence standalone would predict the
>> right gene structure including the start codon. I was thinking that this
>> problem was somehow linked to my gene models but looking at their
>> standalone prediction I discarded that theory. Just some stats about
>> proteins with proper start codon (first column) and missing start codon
>> (second column).
>>
>> Maker		9268	4215
>> SNAP		16577	896
>> Genemark	18764	290
>>
>> Numbers look the same when Augustus is used (currently retraining).
>> Manually using EST's in Apollo often fixes the problems but I don't want
>> to check > 4000 genes for this.
>>
>> Do you have any idea what could cause such a problem? If you need some
>> example gff files I can send you.
>>
>> Best regards
>> Felix
>>
>> --
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Sat Oct 12 23:26:17 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 13 Oct 2013 01:26:17 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <525975C6.4020403@uni-wuerzburg.de>
Message-ID: <CE7FA55D.10C4B%carsonhh@gmail.com>

Before Wednesday, because after that I'm on a 6 day road trip, so I have
to have it wrapped up before I leave.

--Carson




On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Thx Carson! Do you now when 2.30 will be available? Bests
>
>On 12.10.2013 17:48, Carson Holt wrote:
>> This issue just came up this week on another e-mail as well.
>>
>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>> BioPerl (use maker --debug to have maker print out the locations of all
>> modules it uses).  Such a hack should only be done as a temporary work
>> around.
>>
>> You change line 256 from -->
>> ---M---------------M---------------M----------------------------
>>
>> To-->
>> -----------------------------------M----------------------------
>>
>>
>> Maker uses the BioPerl is_start_codon function to determine if the codon
>> used in a result it receives is acceptable or if it should look upstream
>> or downstream for a different one. Apparently there are actually 3
>> acceptable start codons in the standard codon table (2 rare ones and one
>> common), so making the edit removes the two rare ones from the list.
>>
>> I'm also preparing a 2.30 release that exports a "strict" codon table to
>> the BioPerl module, that will be used by default and should fix the
>>issue.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Hi,
>>>
>>> I have a serious problems with maker annotations especially the start
>>> codon placement. It started happening with maker version 2.27! About
>>>1/3
>>> of my genes are missing a proper start codon. When reviewing the GFF
>>> files gene predictors and est evidence standalone would predict the
>>> right gene structure including the start codon. I was thinking that
>>>this
>>> problem was somehow linked to my gene models but looking at their
>>> standalone prediction I discarded that theory. Just some stats about
>>> proteins with proper start codon (first column) and missing start codon
>>> (second column).
>>>
>>> Maker		9268	4215
>>> SNAP		16577	896
>>> Genemark	18764	290
>>>
>>> Numbers look the same when Augustus is used (currently retraining).
>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>want
>>> to check > 4000 genes for this.
>>>
>>> Do you have any idea what could cause such a problem? If you need some
>>> example gff files I can send you.
>>>
>>> Best regards
>>> Felix
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de





From carsonhh at gmail.com  Mon Oct 14 08:45:25 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 14 Oct 2013 10:45:25 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <525975C6.4020403@uni-wuerzburg.de>
Message-ID: <CE817BB6.10C72%carsonhh@gmail.com>

Probably Tuesday or Wednesday.

--Carson


On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Thx Carson! Do you now when 2.30 will be available? Bests
>
>On 12.10.2013 17:48, Carson Holt wrote:
>> This issue just came up this week on another e-mail as well.
>>
>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>> BioPerl (use maker --debug to have maker print out the locations of all
>> modules it uses).  Such a hack should only be done as a temporary work
>> around.
>>
>> You change line 256 from -->
>> ---M---------------M---------------M----------------------------
>>
>> To-->
>> -----------------------------------M----------------------------
>>
>>
>> Maker uses the BioPerl is_start_codon function to determine if the codon
>> used in a result it receives is acceptable or if it should look upstream
>> or downstream for a different one. Apparently there are actually 3
>> acceptable start codons in the standard codon table (2 rare ones and one
>> common), so making the edit removes the two rare ones from the list.
>>
>> I'm also preparing a 2.30 release that exports a "strict" codon table to
>> the BioPerl module, that will be used by default and should fix the
>>issue.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Hi,
>>>
>>> I have a serious problems with maker annotations especially the start
>>> codon placement. It started happening with maker version 2.27! About
>>>1/3
>>> of my genes are missing a proper start codon. When reviewing the GFF
>>> files gene predictors and est evidence standalone would predict the
>>> right gene structure including the start codon. I was thinking that
>>>this
>>> problem was somehow linked to my gene models but looking at their
>>> standalone prediction I discarded that theory. Just some stats about
>>> proteins with proper start codon (first column) and missing start codon
>>> (second column).
>>>
>>> Maker		9268	4215
>>> SNAP		16577	896
>>> Genemark	18764	290
>>>
>>> Numbers look the same when Augustus is used (currently retraining).
>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>want
>>> to check > 4000 genes for this.
>>>
>>> Do you have any idea what could cause such a problem? If you need some
>>> example gff files I can send you.
>>>
>>> Best regards
>>> Felix
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de





From cjfields at illinois.edu  Mon Oct 14 09:07:43 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 14 Oct 2013 15:07:43 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE817BB6.10C72%carsonhh@gmail.com>
References: <CE817BB6.10C72%carsonhh@gmail.com>
Message-ID: <D51543B5-DCFB-4F2C-9BE5-3099B96E3317@illinois.edu>

Carson,

Regarding the CodonTable change below, should this be something that needs to be fixed, or made more flexible, in bioperl?  I could see this being a problem if using MAKER for bacterial annotation (where the alternative start codons are actually more common).

chris

On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Probably Tuesday or Wednesday.
> 
> --Carson
> 
> 
> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
> 
>> Thx Carson! Do you now when 2.30 will be available? Bests
>> 
>> On 12.10.2013 17:48, Carson Holt wrote:
>>> This issue just came up this week on another e-mail as well.
>>> 
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>> BioPerl (use maker --debug to have maker print out the locations of all
>>> modules it uses).  Such a hack should only be done as a temporary work
>>> around.
>>> 
>>> You change line 256 from -->
>>> ---M---------------M---------------M----------------------------
>>> 
>>> To-->
>>> -----------------------------------M----------------------------
>>> 
>>> 
>>> Maker uses the BioPerl is_start_codon function to determine if the codon
>>> used in a result it receives is acceptable or if it should look upstream
>>> or downstream for a different one. Apparently there are actually 3
>>> acceptable start codons in the standard codon table (2 rare ones and one
>>> common), so making the edit removes the two rare ones from the list.
>>> 
>>> I'm also preparing a 2.30 release that exports a "strict" codon table to
>>> the BioPerl module, that will be used by default and should fix the
>>> issue.
>>> 
>>> Thanks,
>>> Carson
>>> 
>>> 
>>> 
>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I have a serious problems with maker annotations especially the start
>>>> codon placement. It started happening with maker version 2.27! About
>>>> 1/3
>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>> files gene predictors and est evidence standalone would predict the
>>>> right gene structure including the start codon. I was thinking that
>>>> this
>>>> problem was somehow linked to my gene models but looking at their
>>>> standalone prediction I discarded that theory. Just some stats about
>>>> proteins with proper start codon (first column) and missing start codon
>>>> (second column).
>>>> 
>>>> Maker		9268	4215
>>>> SNAP		16577	896
>>>> Genemark	18764	290
>>>> 
>>>> Numbers look the same when Augustus is used (currently retraining).
>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>> want
>>>> to check > 4000 genes for this.
>>>> 
>>>> Do you have any idea what could cause such a problem? If you need some
>>>> example gff files I can send you.
>>>> 
>>>> Best regards
>>>> Felix
>>>> 
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> -- 
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Mon Oct 14 11:58:24 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 14 Oct 2013 13:58:24 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <D51543B5-DCFB-4F2C-9BE5-3099B96E3317@illinois.edu>
Message-ID: <CE81A824.10C7B%carsonhh@gmail.com>

I think adding one more codon table to the set of available tables would
be sufficient.  Call it the 'Strict' table or 'Canonical' table.  It
doesn't need to be the default, but should be a selectable option just as
the other codon tables are.  There is a way to export codon tables to the
module, which is what I've now added to MAKER, but I'm sure other BoiPerl
users would find a strictly canonical codon table useful as well.

Thanks,
Carson


On 10/14/13 11:07 AM, "Fields, Christopher J" <cjfields at illinois.edu>
wrote:

>Carson,
>
>Regarding the CodonTable change below, should this be something that
>needs to be fixed, or made more flexible, in bioperl?  I could see this
>being a problem if using MAKER for bacterial annotation (where the
>alternative start codons are actually more common).
>
>chris
>
>On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Probably Tuesday or Wednesday.
>> 
>> --Carson
>> 
>> 
>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>> 
>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>> 
>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>> This issue just came up this week on another e-mail as well.
>>>> 
>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>> BioPerl (use maker --debug to have maker print out the locations of
>>>>all
>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>> around.
>>>> 
>>>> You change line 256 from -->
>>>> ---M---------------M---------------M----------------------------
>>>> 
>>>> To-->
>>>> -----------------------------------M----------------------------
>>>> 
>>>> 
>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>codon
>>>> used in a result it receives is acceptable or if it should look
>>>>upstream
>>>> or downstream for a different one. Apparently there are actually 3
>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>one
>>>> common), so making the edit removes the two rare ones from the list.
>>>> 
>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>to
>>>> the BioPerl module, that will be used by default and should fix the
>>>> issue.
>>>> 
>>>> Thanks,
>>>> Carson
>>>> 
>>>> 
>>>> 
>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> I have a serious problems with maker annotations especially the start
>>>>> codon placement. It started happening with maker version 2.27! About
>>>>> 1/3
>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>> files gene predictors and est evidence standalone would predict the
>>>>> right gene structure including the start codon. I was thinking that
>>>>> this
>>>>> problem was somehow linked to my gene models but looking at their
>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>> proteins with proper start codon (first column) and missing start
>>>>>codon
>>>>> (second column).
>>>>> 
>>>>> Maker		9268	4215
>>>>> SNAP		16577	896
>>>>> Genemark	18764	290
>>>>> 
>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>> want
>>>>> to check > 4000 genes for this.
>>>>> 
>>>>> Do you have any idea what could cause such a problem? If you need
>>>>>some
>>>>> example gff files I can send you.
>>>>> 
>>>>> Best regards
>>>>> Felix
>>>>> 
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>> 
>>> -- 
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>> 
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>





From cjfields at illinois.edu  Mon Oct 14 12:51:28 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 14 Oct 2013 18:51:28 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE81A824.10C7B%carsonhh@gmail.com>
References: <CE81A824.10C7B%carsonhh@gmail.com>
Message-ID: <160BC401-0471-4285-8712-21440628A5DA@illinois.edu>

Done, with some added tests.  I labeled it 'Strict' ('Canonical' can be a bit of a loaded term).  It's currently set as ID 24.

I will likely push out a new 1.6 point release this week or next, I'll merge these in for that release.

chris

On Oct 14, 2013, at 12:58 PM, Carson Holt <carsonhh at gmail.com> wrote:

> I think adding one more codon table to the set of available tables would
> be sufficient.  Call it the 'Strict' table or 'Canonical' table.  It
> doesn't need to be the default, but should be a selectable option just as
> the other codon tables are.  There is a way to export codon tables to the
> module, which is what I've now added to MAKER, but I'm sure other BoiPerl
> users would find a strictly canonical codon table useful as well.
> 
> Thanks,
> Carson
> 
> 
> On 10/14/13 11:07 AM, "Fields, Christopher J" <cjfields at illinois.edu>
> wrote:
> 
>> Carson,
>> 
>> Regarding the CodonTable change below, should this be something that
>> needs to be fixed, or made more flexible, in bioperl?  I could see this
>> being a problem if using MAKER for bacterial annotation (where the
>> alternative start codons are actually more common).
>> 
>> chris
>> 
>> On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>>> Probably Tuesday or Wednesday.
>>> 
>>> --Carson
>>> 
>>> 
>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>> 
>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>> 
>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>> This issue just came up this week on another e-mail as well.
>>>>> 
>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>> BioPerl (use maker --debug to have maker print out the locations of
>>>>> all
>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>> around.
>>>>> 
>>>>> You change line 256 from -->
>>>>> ---M---------------M---------------M----------------------------
>>>>> 
>>>>> To-->
>>>>> -----------------------------------M----------------------------
>>>>> 
>>>>> 
>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>> codon
>>>>> used in a result it receives is acceptable or if it should look
>>>>> upstream
>>>>> or downstream for a different one. Apparently there are actually 3
>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>> one
>>>>> common), so making the edit removes the two rare ones from the list.
>>>>> 
>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>> to
>>>>> the BioPerl module, that will be used by default and should fix the
>>>>> issue.
>>>>> 
>>>>> Thanks,
>>>>> Carson
>>>>> 
>>>>> 
>>>>> 
>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>> wrote:
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I have a serious problems with maker annotations especially the start
>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>> 1/3
>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>> right gene structure including the start codon. I was thinking that
>>>>>> this
>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>> proteins with proper start codon (first column) and missing start
>>>>>> codon
>>>>>> (second column).
>>>>>> 
>>>>>> Maker		9268	4215
>>>>>> SNAP		16577	896
>>>>>> Genemark	18764	290
>>>>>> 
>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>> want
>>>>>> to check > 4000 genes for this.
>>>>>> 
>>>>>> Do you have any idea what could cause such a problem? If you need
>>>>>> some
>>>>>> example gff files I can send you.
>>>>>> 
>>>>>> Best regards
>>>>>> Felix
>>>>>> 
>>>>>> --
>>>>>> Felix Bemm
>>>>>> Department of Bioinformatics
>>>>>> University of W?rzburg, Germany
>>>>>> Tel: +49 931 - 31 83696
>>>>>> Fax: +49 931 - 31 84552
>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>> 
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> 
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>> 
>>>> -- 
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
> 
> 




From carsonhh at gmail.com  Mon Oct 14 18:59:45 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 14 Oct 2013 20:59:45 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <160BC401-0471-4285-8712-21440628A5DA@illinois.edu>
Message-ID: <CE820BA4.10C8F%carsonhh@gmail.com>

Thanks!!

--Carson


On 10/14/13 2:51 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

>Done, with some added tests.  I labeled it 'Strict' ('Canonical' can be a
>bit of a loaded term).  It's currently set as ID 24.
>
>I will likely push out a new 1.6 point release this week or next, I'll
>merge these in for that release.
>
>chris
>
>On Oct 14, 2013, at 12:58 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> I think adding one more codon table to the set of available tables would
>> be sufficient.  Call it the 'Strict' table or 'Canonical' table.  It
>> doesn't need to be the default, but should be a selectable option just
>>as
>> the other codon tables are.  There is a way to export codon tables to
>>the
>> module, which is what I've now added to MAKER, but I'm sure other
>>BoiPerl
>> users would find a strictly canonical codon table useful as well.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> On 10/14/13 11:07 AM, "Fields, Christopher J" <cjfields at illinois.edu>
>> wrote:
>> 
>>> Carson,
>>> 
>>> Regarding the CodonTable change below, should this be something that
>>> needs to be fixed, or made more flexible, in bioperl?  I could see this
>>> being a problem if using MAKER for bacterial annotation (where the
>>> alternative start codons are actually more common).
>>> 
>>> chris
>>> 
>>> On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> 
>>>> Probably Tuesday or Wednesday.
>>>> 
>>>> --Carson
>>>> 
>>>> 
>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>wrote:
>>>> 
>>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>>> 
>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>>> This issue just came up this week on another e-mail as well.
>>>>>> 
>>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>>> BioPerl (use maker --debug to have maker print out the locations of
>>>>>> all
>>>>>> modules it uses).  Such a hack should only be done as a temporary
>>>>>>work
>>>>>> around.
>>>>>> 
>>>>>> You change line 256 from -->
>>>>>> ---M---------------M---------------M----------------------------
>>>>>> 
>>>>>> To-->
>>>>>> -----------------------------------M----------------------------
>>>>>> 
>>>>>> 
>>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>>> codon
>>>>>> used in a result it receives is acceptable or if it should look
>>>>>> upstream
>>>>>> or downstream for a different one. Apparently there are actually 3
>>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>>> one
>>>>>> common), so making the edit removes the two rare ones from the list.
>>>>>> 
>>>>>> I'm also preparing a 2.30 release that exports a "strict" codon
>>>>>>table
>>>>>> to
>>>>>> the BioPerl module, that will be used by default and should fix the
>>>>>> issue.
>>>>>> 
>>>>>> Thanks,
>>>>>> Carson
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>>> wrote:
>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I have a serious problems with maker annotations especially the
>>>>>>>start
>>>>>>> codon placement. It started happening with maker version 2.27!
>>>>>>>About
>>>>>>> 1/3
>>>>>>> of my genes are missing a proper start codon. When reviewing the
>>>>>>>GFF
>>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>>> right gene structure including the start codon. I was thinking that
>>>>>>> this
>>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>>> standalone prediction I discarded that theory. Just some stats
>>>>>>>about
>>>>>>> proteins with proper start codon (first column) and missing start
>>>>>>> codon
>>>>>>> (second column).
>>>>>>> 
>>>>>>> Maker		9268	4215
>>>>>>> SNAP		16577	896
>>>>>>> Genemark	18764	290
>>>>>>> 
>>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>>> want
>>>>>>> to check > 4000 genes for this.
>>>>>>> 
>>>>>>> Do you have any idea what could cause such a problem? If you need
>>>>>>> some
>>>>>>> example gff files I can send you.
>>>>>>> 
>>>>>>> Best regards
>>>>>>> Felix
>>>>>>> 
>>>>>>> --
>>>>>>> Felix Bemm
>>>>>>> Department of Bioinformatics
>>>>>>> University of W?rzburg, Germany
>>>>>>> Tel: +49 931 - 31 83696
>>>>>>> Fax: +49 931 - 31 84552
>>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> 
>>>>>>> 
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>or
>>>>>>> g
>>>>> 
>>>>> -- 
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>> 
>> 
>





From jfierst at uoregon.edu  Mon Oct 21 11:40:06 2013
From: jfierst at uoregon.edu (Janna Fierst)
Date: Mon, 21 Oct 2013 10:40:06 -0700
Subject: [maker-devel] Fwd: exon/intron boundaries
In-Reply-To: <CE782A71.F621%carsonhh@gmail.com>
References: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
	<CE782A71.F621%carsonhh@gmail.com>
Message-ID: <CAGoyurZfiqRpEKg0C=__ou6muWD2PqCQh9b+S9y_+95-xsCfOQ@mail.gmail.com>

Hi,

thanks for your help- I have used Trinity to assemble the EST's but am
having a problem with the 2.29-beta release. Instead of starting and
finishing a set of scaffolds, it appears to re-start over and over again. I
am running it in parallel across 32 cores and I'm wondering if this is a
problem with the parallel implementation. I've gone through it several
times and not been able to find any errors or output that would suggest
what the problem is. Thanks -Janna


On Mon, Oct 7, 2013 at 6:20 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Hi Janna,
>
> There are a couple of things to do.  Download the maker-2.29p-beta from
> the lab website.  This includes some changes made to improve the
> performance of correct_est_fusion.  Whenever using the correct_est_fusion
> option, this also reduces the influence of ESTs on annotation.  So normally
> you would need to increase your protein dataset, but given that you have
> supplied 3 nematode species and all of UniProt already you should probably
> be fine. But there is one last thing you can do.  Instead of using
> cufflinks, try using trinity to assemble the ESTs.  There is a Jaccard clip
> option that reducing merging caused by overlapping UTR.  Between the
> trinity and correct_est_fusion you should be able to really reduce the
> effect of those ESTs.
>
> If those changes don't work there is one last option.  If you take the
> MAKER results and filter them for SNAP and Augustus ab initio results
> (match/match_part in the GFF3), then you can pass those in to the pred_gff
> options.  Then turn snaphmm and augustus_species off in the control files.
>  Basically what this will do is turn MAKER's hint based prediction off and
> force it to filter the ab intio results and select directly models from
> there.  Since the merging is being caused by bad hints (merged transcripts
> from mRNAseq) this would reduce that effect.  You will still need
> correct_est_fusion=1 though to trim UTR coming from the merged transcripts,
> because even though MAEKR can't process hints to rerun SNAP and Augustus
> this way, it will try and add UTR using the EST evidence.
>
> --Carson
>
>
> From: Janna Fierst <jfierst at uoregon.edu>
> Date: Friday, October 4, 2013 1:06 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Fwd: exon/intron boundaries
>
> Hi,
>
> thanks for your reply- I have been going through our annotations in detail
> and trying different parameter sets, and I think I have identified what is
> going on but I'm not sure how to set the MAKER2 parameters for our
> situation. We are working with a species of Caenorhabditid worm and there
> are long gene-dense blocks that are being incorrectly annotated as large
> single genes instead of several smaller closely spaced genes. The protein
> alignments (tblastx and protein2genome) show very clearly where the
> exon/intron boundaries are and in most cases agree with the augustus
> predictions. The assembled cufflinks output (through blastn, est2genome and
> est_gff:cufflinks) does not agree in some locations; I think this may be
> because in some cases the UTR nearly overlaps adjacent genes.
>
> I have included a screenshot of an annotated region viewed in apollo to
> try to show this. The large gene in the middle is actually 7 different
> genes that are extremely close together and MAKER2 is collapsing them into
> a single gene. I tried running without any RNASeq/cufflinks data and MAKER2
> annotates the region as two genes instead of one, but I can't get it to
> recognize the 7 as different genes. I have retrained SNAP but we have not
> been able to successfully train Augustus, we are currently using the
> default caenhorhabditis species model. I also included a species specific
> repeat library. I tried setting correct_est_fusion=1 and reducing
> pred_flank but these changes appear to really alter the annotations and we
> end up annotating almost nothing. I also tried setting est2genome=0 to
> decrease the influence of the cufflinks assembly but it didn't appear to
> help. There are some very large introns in these genes so I haven't tried
> yet decreasing the maximum intron size because I'm concerned this may
> generate too many split genes instead of our current merged gene problem.
> Thanks for your help, any advice is greatly appreciated! -Janna Fierst
>
>
> On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Are you getting gene fusions or just more exons?  Gene fusions can be
>> reduced by setting correct_est_fusion=1, or reducing pred_flank, although
>> reducing pred_flank can cause other issues (but those generally only appear
>> if setting the value below below 150).  Also if you have the maximum intron
>> size set to high (split_hit option), you may also be generating bridging
>> alignments that make evidence align across distant paralogous genes as well
>> (this can result in gene merging)
>>
>> You should also look at your results manually in a viewer like Apollo.
>>  Then see if the extra exons are supported by something such as protein
>> alignments from another species.  If this is the case, you may have a
>> poorly annotated protein set that is being used as evidence that is
>> carrying over it's erroneous exons into the species you are annotating.  If
>> the extra  exons are supported by EST evidence, then perhaps you should try
>> and rebuild the EST assembly (for example trinity has an option to use a
>> Jarccardian similarity coefficient to avoid fusing transcripts).
>>
>> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
>> produce any of the models itself (it is a pipeline not a predictor).  The
>> models are all generated using these other algorithms, MAKER just feeds
>> them hints based on protein and transcript alignments, so making sure
>> training is sufficient is important for those programs to produce their
>> best models.
>>
>> Finally make sure your repeat database is sufficient, you may need to
>> generate a species specific repeat library using something like
>> RepeatModeler.  Repeats can end up being included as extra exons in gene
>> models because they may contain reading frames the do code for proteins
>> (I.e. reverse transcriptases).
>>
>> If you have any questions on any of the above, just let us know.
>>
>> Thanks,
>> Carson
>>
>>
>> From: Janna Fierst <jfierst at uoregon.edu>
>> Date: Monday, August 26, 2013 2:54 PM
>> To: <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] exon/intron boundaries
>>
>> Hi,
>>
>> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
>> initial results appear fairly good but we seem to be be annotating too many
>> exons for multiple genes. I was wondering which parameters should be tuned
>> to change the threshold for exon/intron boundaries? Thanks for your help
>> -Janna Fierst
>> _______________________________________________ maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From graham.etherington at sainsbury-laboratory.ac.uk  Thu Oct 24 07:42:51 2013
From: graham.etherington at sainsbury-laboratory.ac.uk (graham etherington (TSL))
Date: Thu, 24 Oct 2013 13:42:51 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE7FA55D.10C4B%carsonhh@gmail.com>
Message-ID: <CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>

Hi,
I notice that the latest version of Maker available from
http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
2013). As we're also having the start codon problem we'd like to get hold
of v2.30. Do you know when this will be released?
Many thanks,
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:

>Before Wednesday, because after that I'm on a 6 day road trip, so I have
>to have it wrapped up before I leave.
>
>--Carson
>
>
>
>
>On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>>Thx Carson! Do you now when 2.30 will be available? Bests
>>
>>On 12.10.2013 17:48, Carson Holt wrote:
>>> This issue just came up this week on another e-mail as well.
>>>
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>> BioPerl (use maker --debug to have maker print out the locations of all
>>> modules it uses).  Such a hack should only be done as a temporary work
>>> around.
>>>
>>> You change line 256 from -->
>>> ---M---------------M---------------M----------------------------
>>>
>>> To-->
>>> -----------------------------------M----------------------------
>>>
>>>
>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>codon
>>> used in a result it receives is acceptable or if it should look
>>>upstream
>>> or downstream for a different one. Apparently there are actually 3
>>> acceptable start codons in the standard codon table (2 rare ones and
>>>one
>>> common), so making the edit removes the two rare ones from the list.
>>>
>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>to
>>> the BioPerl module, that will be used by default and should fix the
>>>issue.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a serious problems with maker annotations especially the start
>>>> codon placement. It started happening with maker version 2.27! About
>>>>1/3
>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>> files gene predictors and est evidence standalone would predict the
>>>> right gene structure including the start codon. I was thinking that
>>>>this
>>>> problem was somehow linked to my gene models but looking at their
>>>> standalone prediction I discarded that theory. Just some stats about
>>>> proteins with proper start codon (first column) and missing start
>>>>codon
>>>> (second column).
>>>>
>>>> Maker		9268	4215
>>>> SNAP		16577	896
>>>> Genemark	18764	290
>>>>
>>>> Numbers look the same when Augustus is used (currently retraining).
>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>want
>>>> to check > 4000 genes for this.
>>>>
>>>> Do you have any idea what could cause such a problem? If you need some
>>>> example gff files I can send you.
>>>>
>>>> Best regards
>>>> Felix
>>>>
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>-- 
>>Felix Bemm
>>Department of Bioinformatics
>>University of W?rzburg, Germany
>>Tel: +49 931 - 31 83696
>>Fax: +49 931 - 31 84552
>>felix.bemm at uni-wuerzburg.de
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From myandell at genetics.utah.edu  Thu Oct 24 07:55:05 2013
From: myandell at genetics.utah.edu (Mark Yandell)
Date: Thu, 24 Oct 2013 13:55:05 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>,
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
Message-ID: <7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>

Hi Graham,

 Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.


--mark


Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
Sent: Thursday, October 24, 2013 7:42 AM
To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
Cc: Kate Bailey (TSL)
Subject: Re: [maker-devel] Serious Start Codon Problem

Hi,
I notice that the latest version of Maker available from
http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
2013). As we're also having the start codon problem we'd like to get hold
of v2.30. Do you know when this will be released?
Many thanks,
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:

>Before Wednesday, because after that I'm on a 6 day road trip, so I have
>to have it wrapped up before I leave.
>
>--Carson
>
>
>
>
>On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>>Thx Carson! Do you now when 2.30 will be available? Bests
>>
>>On 12.10.2013 17:48, Carson Holt wrote:
>>> This issue just came up this week on another e-mail as well.
>>>
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>> BioPerl (use maker --debug to have maker print out the locations of all
>>> modules it uses).  Such a hack should only be done as a temporary work
>>> around.
>>>
>>> You change line 256 from -->
>>> ---M---------------M---------------M----------------------------
>>>
>>> To-->
>>> -----------------------------------M----------------------------
>>>
>>>
>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>codon
>>> used in a result it receives is acceptable or if it should look
>>>upstream
>>> or downstream for a different one. Apparently there are actually 3
>>> acceptable start codons in the standard codon table (2 rare ones and
>>>one
>>> common), so making the edit removes the two rare ones from the list.
>>>
>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>to
>>> the BioPerl module, that will be used by default and should fix the
>>>issue.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a serious problems with maker annotations especially the start
>>>> codon placement. It started happening with maker version 2.27! About
>>>>1/3
>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>> files gene predictors and est evidence standalone would predict the
>>>> right gene structure including the start codon. I was thinking that
>>>>this
>>>> problem was somehow linked to my gene models but looking at their
>>>> standalone prediction I discarded that theory. Just some stats about
>>>> proteins with proper start codon (first column) and missing start
>>>>codon
>>>> (second column).
>>>>
>>>> Maker              9268    4215
>>>> SNAP               16577   896
>>>> Genemark   18764   290
>>>>
>>>> Numbers look the same when Augustus is used (currently retraining).
>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>want
>>>> to check > 4000 genes for this.
>>>>
>>>> Do you have any idea what could cause such a problem? If you need some
>>>> example gff files I can send you.
>>>>
>>>> Best regards
>>>> Felix
>>>>
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>>
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>--
>>Felix Bemm
>>Department of Bioinformatics
>>University of W?rzburg, Germany
>>Tel: +49 931 - 31 83696
>>Fax: +49 931 - 31 84552
>>felix.bemm at uni-wuerzburg.de
>
>
>
>_______________________________________________
>maker-devel mailing list
>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
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


From felix.bemm at uni-wuerzburg.de  Thu Oct 24 08:03:27 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Thu, 24 Oct 2013 16:03:27 +0200
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>,
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
Message-ID: <526928AF.90108@uni-wuerzburg.de>

Hi,

I used the temporary fix of the Bio::Tools::CodonTable. It's working 
pretty nice. Almost every predicted proteins now start with a M ;)

Bests
Felix

On 24.10.2013 15:55, Mark Yandell wrote:
> Hi Graham,
>
>   Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>
>
> --mark
>
>
> Mark Yandell
> Professor of Human Genetics
> H.A. & Edna Benning Presidential Endowed Chair
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ph:801-587-7707
>
> ________________________________________
> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
> Sent: Thursday, October 24, 2013 7:42 AM
> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
> Cc: Kate Bailey (TSL)
> Subject: Re: [maker-devel] Serious Start Codon Problem
>
> Hi,
> I notice that the latest version of Maker available from
> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
> 2013). As we're also having the start codon problem we'd like to get hold
> of v2.30. Do you know when this will be released?
> Many thanks,
> Graham
>
>
> Dr. Graham Etherington
> Bioinformatics Support Officer,
> The Sainsbury Laboratory,
> Norwich Research Park,
> Norwich NR4 7UH.
> UK
> Tel: +44 (0)1603 450601
>
>
>
>
>
> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>
>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>> to have it wrapped up before I leave.
>>
>> --Carson
>>
>>
>>
>>
>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>
>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>> This issue just came up this week on another e-mail as well.
>>>>
>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>> around.
>>>>
>>>> You change line 256 from -->
>>>> ---M---------------M---------------M----------------------------
>>>>
>>>> To-->
>>>> -----------------------------------M----------------------------
>>>>
>>>>
>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>> codon
>>>> used in a result it receives is acceptable or if it should look
>>>> upstream
>>>> or downstream for a different one. Apparently there are actually 3
>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>> one
>>>> common), so making the edit removes the two rare ones from the list.
>>>>
>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>> to
>>>> the BioPerl module, that will be used by default and should fix the
>>>> issue.
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>>
>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I have a serious problems with maker annotations especially the start
>>>>> codon placement. It started happening with maker version 2.27! About
>>>>> 1/3
>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>> files gene predictors and est evidence standalone would predict the
>>>>> right gene structure including the start codon. I was thinking that
>>>>> this
>>>>> problem was somehow linked to my gene models but looking at their
>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>> proteins with proper start codon (first column) and missing start
>>>>> codon
>>>>> (second column).
>>>>>
>>>>> Maker              9268    4215
>>>>> SNAP               16577   896
>>>>> Genemark   18764   290
>>>>>
>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>> want
>>>>> to check > 4000 genes for this.
>>>>>
>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>> example gff files I can send you.
>>>>>
>>>>> Best regards
>>>>> Felix
>>>>>
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>>
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From jim.hu.biobio at gmail.com  Thu Oct 24 08:32:01 2013
From: jim.hu.biobio at gmail.com (JH Gmail)
Date: Thu, 24 Oct 2013 09:32:01 -0500
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
Message-ID: <69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>

Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 

Does maker handle ribosome profiling yet?

jim

Sent from my iPad

> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
> 
> Hi Graham,
> 
> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
> 
> 
> --mark
> 
> 
> Mark Yandell
> Professor of Human Genetics
> H.A. & Edna Benning Presidential Endowed Chair
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ph:801-587-7707
> 
> ________________________________________
> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
> Sent: Thursday, October 24, 2013 7:42 AM
> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
> Cc: Kate Bailey (TSL)
> Subject: Re: [maker-devel] Serious Start Codon Problem
> 
> Hi,
> I notice that the latest version of Maker available from
> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
> 2013). As we're also having the start codon problem we'd like to get hold
> of v2.30. Do you know when this will be released?
> Many thanks,
> Graham
> 
> 
> Dr. Graham Etherington
> Bioinformatics Support Officer,
> The Sainsbury Laboratory,
> Norwich Research Park,
> Norwich NR4 7UH.
> UK
> Tel: +44 (0)1603 450601
> 
> 
> 
> 
> 
>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>> 
>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>> to have it wrapped up before I leave.
>> 
>> --Carson
>> 
>> 
>> 
>> 
>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>> 
>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>> 
>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>> This issue just came up this week on another e-mail as well.
>>>> 
>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>> around.
>>>> 
>>>> You change line 256 from -->
>>>> ---M---------------M---------------M----------------------------
>>>> 
>>>> To-->
>>>> -----------------------------------M----------------------------
>>>> 
>>>> 
>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>> codon
>>>> used in a result it receives is acceptable or if it should look
>>>> upstream
>>>> or downstream for a different one. Apparently there are actually 3
>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>> one
>>>> common), so making the edit removes the two rare ones from the list.
>>>> 
>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>> to
>>>> the BioPerl module, that will be used by default and should fix the
>>>> issue.
>>>> 
>>>> Thanks,
>>>> Carson
>>>> 
>>>> 
>>>> 
>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> I have a serious problems with maker annotations especially the start
>>>>> codon placement. It started happening with maker version 2.27! About
>>>>> 1/3
>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>> files gene predictors and est evidence standalone would predict the
>>>>> right gene structure including the start codon. I was thinking that
>>>>> this
>>>>> problem was somehow linked to my gene models but looking at their
>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>> proteins with proper start codon (first column) and missing start
>>>>> codon
>>>>> (second column).
>>>>> 
>>>>> Maker              9268    4215
>>>>> SNAP               16577   896
>>>>> Genemark   18764   290
>>>>> 
>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>> want
>>>>> to check > 4000 genes for this.
>>>>> 
>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>> example gff files I can send you.
>>>>> 
>>>>> Best regards
>>>>> Felix
>>>>> 
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>> 
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



From amelia.ireland at gmod.org  Thu Oct 24 12:52:17 2013
From: amelia.ireland at gmod.org (Amelia Ireland)
Date: Thu, 24 Oct 2013 11:52:17 -0700
Subject: [maker-devel] GMOD 2014: San Diego
Message-ID: <CAALsq00kuy83m4_k_rcWLSpwFYwMCYm5LXEkUgwzqCOUGfryBw@mail.gmail.com>

Greetings GMOD community citizens!

Online registration is now open for the 2014 GMOD meeting, to be held at
the Best Western Seven Seas, San Diego, CA, on January 16-17, 2014 (after
PAG). The meeting is open to GMOD users, developers, and anyone interested
in the project and the software we provide.

Online registration is now open; please see the meeting page,
http://gmod.org/wiki/Jan_2014_GMOD_Meeting, for more information. Early
bird registration rates apply until Dec. 14th.

We have secured a discount on a block of rooms at the Best Western Seven
Seas; please see the wiki for more information on booking.

Please feel free to contact the GMOD helpdesk on help at gmod.org if you have
any questions. Thanks!

-- 
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject
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From barry.moore at genetics.utah.edu  Thu Oct 24 15:09:20 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Thu, 24 Oct 2013 15:09:20 -0600
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
	<69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
Message-ID: <1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>

Hi Jim,

You can and any kind of evidence you want to MAKER including ribosomal profiling data as long as you format it in GFF3 format.  You could pass in your GFF3 formatted ribosomal profiling data in maker_opt.ctl with the protein_gff option and it will be treated as protein evidence.  However if you are wondering if anyone has coded a specific addition to MAKER to accept ribosomal profiling data and treat it as a different kind of evidence then no, this hasn't been done.

B

On Oct 24, 2013, at 8:32 AM, JH Gmail wrote:

> Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 
> 
> Does maker handle ribosome profiling yet?
> 
> jim
> 
> Sent from my iPad
> 
>> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
>> 
>> Hi Graham,
>> 
>> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>> 
>> 
>> --mark
>> 
>> 
>> Mark Yandell
>> Professor of Human Genetics
>> H.A. & Edna Benning Presidential Endowed Chair
>> Eccles Institute of Human Genetics
>> University of Utah
>> 15 North 2030 East, Room 2100
>> Salt Lake City, UT 84112-5330
>> ph:801-587-7707
>> 
>> ________________________________________
>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
>> Sent: Thursday, October 24, 2013 7:42 AM
>> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
>> Cc: Kate Bailey (TSL)
>> Subject: Re: [maker-devel] Serious Start Codon Problem
>> 
>> Hi,
>> I notice that the latest version of Maker available from
>> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
>> 2013). As we're also having the start codon problem we'd like to get hold
>> of v2.30. Do you know when this will be released?
>> Many thanks,
>> Graham
>> 
>> 
>> Dr. Graham Etherington
>> Bioinformatics Support Officer,
>> The Sainsbury Laboratory,
>> Norwich Research Park,
>> Norwich NR4 7UH.
>> UK
>> Tel: +44 (0)1603 450601
>> 
>> 
>> 
>> 
>> 
>>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>>> 
>>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>>> to have it wrapped up before I leave.
>>> 
>>> --Carson
>>> 
>>> 
>>> 
>>> 
>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>> 
>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>> 
>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>> This issue just came up this week on another e-mail as well.
>>>>> 
>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>> around.
>>>>> 
>>>>> You change line 256 from -->
>>>>> ---M---------------M---------------M----------------------------
>>>>> 
>>>>> To-->
>>>>> -----------------------------------M----------------------------
>>>>> 
>>>>> 
>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>> codon
>>>>> used in a result it receives is acceptable or if it should look
>>>>> upstream
>>>>> or downstream for a different one. Apparently there are actually 3
>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>> one
>>>>> common), so making the edit removes the two rare ones from the list.
>>>>> 
>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>> to
>>>>> the BioPerl module, that will be used by default and should fix the
>>>>> issue.
>>>>> 
>>>>> Thanks,
>>>>> Carson
>>>>> 
>>>>> 
>>>>> 
>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I have a serious problems with maker annotations especially the start
>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>> 1/3
>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>> right gene structure including the start codon. I was thinking that
>>>>>> this
>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>> proteins with proper start codon (first column) and missing start
>>>>>> codon
>>>>>> (second column).
>>>>>> 
>>>>>> Maker              9268    4215
>>>>>> SNAP               16577   896
>>>>>> Genemark   18764   290
>>>>>> 
>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>> want
>>>>>> to check > 4000 genes for this.
>>>>>> 
>>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>>> example gff files I can send you.
>>>>>> 
>>>>>> Best regards
>>>>>> Felix
>>>>>> 
>>>>>> --
>>>>>> Felix Bemm
>>>>>> Department of Bioinformatics
>>>>>> University of W?rzburg, Germany
>>>>>> Tel: +49 931 - 31 83696
>>>>>> Fax: +49 931 - 31 84552
>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>> 
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> 
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> 
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> 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
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> _______________________________________________
>> maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From marc.hoeppner at imbim.uu.se  Fri Oct 25 08:20:04 2013
From: marc.hoeppner at imbim.uu.se (Marc P. Hoeppner)
Date: Fri, 25 Oct 2013 16:20:04 +0200
Subject: [maker-devel] Maker MPICH2 issue (Multiple MAKER processes have
 been started in the same directory)
Message-ID: <526A7E14.9010906@imbim.uu.se>

Dear list,

I know that MPICH2 related issues have been discussed previously, but 
the suggested solutions don't seem to work for me.
Briefly, I have set up a new cluster, with a fresh install of mpich2 (SL 
6.4, from the yum repos) and a newly compiled build of Maker 2.28.

When I start maker with mpiexec, I get spammed with
'WARNING: Multiple MAKER processes have been started in the same 
directory.'

Here is what I have tried so far - still getting the error :-< Any 
suggestions would be appreciated

--------
MPICH2
---------

which mpiexec:
/usr/lib64/mpich2/bin/mpiexec

Started the mpd ring as normal user across 5 nodes (bnode-01 to 
bnode-04, and the head node bhead)

mpdtrace:
bhead
bnode-02
bnode-03
bnode-04
bnode-01

mpdringtest:
time for 1 loops = 0.00128293037415 seconds

mpixec -n 32 -machinefile hostfile hostname:

<long list of host names, as ecpected>

I also ran the Skampi Mpi Benchmark, which ran through just fine.

-----------
MAKER
-----------

./Build status

PERL Dependencies:      VERIFIED
External Programs:      VERIFIED
External C Libraries:   VERIFIED
MPI SUPPORT:            ENABLED
MWAS Web Interface:     DISABLED
MAKER PACKAGE:          CONFIGURATION OK

During configuration/installation, Build.PL automatically detected all 
MPI data and never complained, so I have to assume that everything went 
fine there.

-- 
----------
Marc P. Hoeppner, PhD
Department of Microbiology and Medical Biochemistry
Uppsala University, Sweden
marc.hoeppner at imbim.uu.se




From jim.hu.biobio at gmail.com  Fri Oct 25 08:51:19 2013
From: jim.hu.biobio at gmail.com (JH Gmail)
Date: Fri, 25 Oct 2013 09:51:19 -0500
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
	<69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
	<1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>
Message-ID: <596400F6-3215-4F71-A896-AF52CEC8D77D@gmail.com>

Thanks Barry,

I'm thinking about this more theoretically, as we don't have immediate plans, but...

This would work for gff derived from ribosome profiling analysis, but it would be nice to be able to start with bam files of mapped reads, or coverage scores as bigwig or gff.  RNA-seq has similar issues, but IIRC Maker expects RNA-seq data to be assembled first.  It may not be possible to do de novo cds assembly from ribosome profiling because I think the nuclease step may kill the overlaps. I'd have to look at some of the available data. 

Jim

Sent from my iPad

> On Oct 24, 2013, at 4:09 PM, Barry Moore <barry.moore at genetics.utah.edu> wrote:
> 
> Hi Jim,
> 
> You can and any kind of evidence you want to MAKER including ribosomal profiling data as long as you format it in GFF3 format.  You could pass in your GFF3 formatted ribosomal profiling data in maker_opt.ctl with the protein_gff option and it will be treated as protein evidence.  However if you are wondering if anyone has coded a specific addition to MAKER to accept ribosomal profiling data and treat it as a different kind of evidence then no, this hasn't been done.
> 
> B
> 
>> On Oct 24, 2013, at 8:32 AM, JH Gmail wrote:
>> 
>> Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 
>> 
>> Does maker handle ribosome profiling yet?
>> 
>> jim
>> 
>> Sent from my iPad
>> 
>>> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
>>> 
>>> Hi Graham,
>>> 
>>> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>>> 
>>> 
>>> --mark
>>> 
>>> 
>>> Mark Yandell
>>> Professor of Human Genetics
>>> H.A. & Edna Benning Presidential Endowed Chair
>>> Eccles Institute of Human Genetics
>>> University of Utah
>>> 15 North 2030 East, Room 2100
>>> Salt Lake City, UT 84112-5330
>>> ph:801-587-7707
>>> 
>>> ________________________________________
>>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
>>> Sent: Thursday, October 24, 2013 7:42 AM
>>> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
>>> Cc: Kate Bailey (TSL)
>>> Subject: Re: [maker-devel] Serious Start Codon Problem
>>> 
>>> Hi,
>>> I notice that the latest version of Maker available from
>>> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
>>> 2013). As we're also having the start codon problem we'd like to get hold
>>> of v2.30. Do you know when this will be released?
>>> Many thanks,
>>> Graham
>>> 
>>> 
>>> Dr. Graham Etherington
>>> Bioinformatics Support Officer,
>>> The Sainsbury Laboratory,
>>> Norwich Research Park,
>>> Norwich NR4 7UH.
>>> UK
>>> Tel: +44 (0)1603 450601
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>>>> 
>>>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>>>> to have it wrapped up before I leave.
>>>> 
>>>> --Carson
>>>> 
>>>> 
>>>> 
>>>> 
>>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>> 
>>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>>> 
>>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>>> This issue just came up this week on another e-mail as well.
>>>>>> 
>>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>>> around.
>>>>>> 
>>>>>> You change line 256 from -->
>>>>>> ---M---------------M---------------M----------------------------
>>>>>> 
>>>>>> To-->
>>>>>> -----------------------------------M----------------------------
>>>>>> 
>>>>>> 
>>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>>> codon
>>>>>> used in a result it receives is acceptable or if it should look
>>>>>> upstream
>>>>>> or downstream for a different one. Apparently there are actually 3
>>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>>> one
>>>>>> common), so making the edit removes the two rare ones from the list.
>>>>>> 
>>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>>> to
>>>>>> the BioPerl module, that will be used by default and should fix the
>>>>>> issue.
>>>>>> 
>>>>>> Thanks,
>>>>>> Carson
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I have a serious problems with maker annotations especially the start
>>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>>> 1/3
>>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>>> right gene structure including the start codon. I was thinking that
>>>>>>> this
>>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>>> proteins with proper start codon (first column) and missing start
>>>>>>> codon
>>>>>>> (second column).
>>>>>>> 
>>>>>>> Maker              9268    4215
>>>>>>> SNAP               16577   896
>>>>>>> Genemark   18764   290
>>>>>>> 
>>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>>> want
>>>>>>> to check > 4000 genes for this.
>>>>>>> 
>>>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>>>> example gff files I can send you.
>>>>>>> 
>>>>>>> Best regards
>>>>>>> Felix
>>>>>>> 
>>>>>>> --
>>>>>>> Felix Bemm
>>>>>>> Department of Bioinformatics
>>>>>>> University of W?rzburg, Germany
>>>>>>> Tel: +49 931 - 31 83696
>>>>>>> Fax: +49 931 - 31 84552
>>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> 
>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>> 
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> 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
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> _______________________________________________
>>> maker-devel mailing list
>>> 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
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
> 
> 
> 
> 
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From barry.moore at genetics.utah.edu  Fri Oct 25 09:44:55 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Fri, 25 Oct 2013 09:44:55 -0600
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <596400F6-3215-4F71-A896-AF52CEC8D77D@gmail.com>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
	<69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
	<1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>
	<596400F6-3215-4F71-A896-AF52CEC8D77D@gmail.com>
Message-ID: <DA777487-D8DD-47E2-A852-DB123C3A1BB8@genetics.utah.edu>

Thanks Jim.

B

On Oct 25, 2013, at 8:51 AM, JH Gmail wrote:

> Thanks Barry,
> 
> I'm thinking about this more theoretically, as we don't have immediate plans, but...
> 
> This would work for gff derived from ribosome profiling analysis, but it would be nice to be able to start with bam files of mapped reads, or coverage scores as bigwig or gff.  RNA-seq has similar issues, but IIRC Maker expects RNA-seq data to be assembled first.  It may not be possible to do de novo cds assembly from ribosome profiling because I think the nuclease step may kill the overlaps. I'd have to look at some of the available data. 
> 
> Jim
> 
> Sent from my iPad
> 
> On Oct 24, 2013, at 4:09 PM, Barry Moore <barry.moore at genetics.utah.edu> wrote:
> 
>> Hi Jim,
>> 
>> You can and any kind of evidence you want to MAKER including ribosomal profiling data as long as you format it in GFF3 format.  You could pass in your GFF3 formatted ribosomal profiling data in maker_opt.ctl with the protein_gff option and it will be treated as protein evidence.  However if you are wondering if anyone has coded a specific addition to MAKER to accept ribosomal profiling data and treat it as a different kind of evidence then no, this hasn't been done.
>> 
>> B
>> 
>> On Oct 24, 2013, at 8:32 AM, JH Gmail wrote:
>> 
>>> Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 
>>> 
>>> Does maker handle ribosome profiling yet?
>>> 
>>> jim
>>> 
>>> Sent from my iPad
>>> 
>>>> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
>>>> 
>>>> Hi Graham,
>>>> 
>>>> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>>>> 
>>>> 
>>>> --mark
>>>> 
>>>> 
>>>> Mark Yandell
>>>> Professor of Human Genetics
>>>> H.A. & Edna Benning Presidential Endowed Chair
>>>> Eccles Institute of Human Genetics
>>>> University of Utah
>>>> 15 North 2030 East, Room 2100
>>>> Salt Lake City, UT 84112-5330
>>>> ph:801-587-7707
>>>> 
>>>> ________________________________________
>>>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
>>>> Sent: Thursday, October 24, 2013 7:42 AM
>>>> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
>>>> Cc: Kate Bailey (TSL)
>>>> Subject: Re: [maker-devel] Serious Start Codon Problem
>>>> 
>>>> Hi,
>>>> I notice that the latest version of Maker available from
>>>> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
>>>> 2013). As we're also having the start codon problem we'd like to get hold
>>>> of v2.30. Do you know when this will be released?
>>>> Many thanks,
>>>> Graham
>>>> 
>>>> 
>>>> Dr. Graham Etherington
>>>> Bioinformatics Support Officer,
>>>> The Sainsbury Laboratory,
>>>> Norwich Research Park,
>>>> Norwich NR4 7UH.
>>>> UK
>>>> Tel: +44 (0)1603 450601
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>>>>> 
>>>>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>>>>> to have it wrapped up before I leave.
>>>>> 
>>>>> --Carson
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>> 
>>>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>>>> 
>>>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>>>> This issue just came up this week on another e-mail as well.
>>>>>>> 
>>>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>>>> around.
>>>>>>> 
>>>>>>> You change line 256 from -->
>>>>>>> ---M---------------M---------------M----------------------------
>>>>>>> 
>>>>>>> To-->
>>>>>>> -----------------------------------M----------------------------
>>>>>>> 
>>>>>>> 
>>>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>>>> codon
>>>>>>> used in a result it receives is acceptable or if it should look
>>>>>>> upstream
>>>>>>> or downstream for a different one. Apparently there are actually 3
>>>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>>>> one
>>>>>>> common), so making the edit removes the two rare ones from the list.
>>>>>>> 
>>>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>>>> to
>>>>>>> the BioPerl module, that will be used by default and should fix the
>>>>>>> issue.
>>>>>>> 
>>>>>>> Thanks,
>>>>>>> Carson
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>>>> 
>>>>>>>> Hi,
>>>>>>>> 
>>>>>>>> I have a serious problems with maker annotations especially the start
>>>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>>>> 1/3
>>>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>>>> right gene structure including the start codon. I was thinking that
>>>>>>>> this
>>>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>>>> proteins with proper start codon (first column) and missing start
>>>>>>>> codon
>>>>>>>> (second column).
>>>>>>>> 
>>>>>>>> Maker              9268    4215
>>>>>>>> SNAP               16577   896
>>>>>>>> Genemark   18764   290
>>>>>>>> 
>>>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>>>> want
>>>>>>>> to check > 4000 genes for this.
>>>>>>>> 
>>>>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>>>>> example gff files I can send you.
>>>>>>>> 
>>>>>>>> Best regards
>>>>>>>> Felix
>>>>>>>> 
>>>>>>>> --
>>>>>>>> Felix Bemm
>>>>>>>> Department of Bioinformatics
>>>>>>>> University of W?rzburg, Germany
>>>>>>>> Tel: +49 931 - 31 83696
>>>>>>>> Fax: +49 931 - 31 84552
>>>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> maker-devel mailing list
>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>> 
>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>> 
>>>>>> --
>>>>>> Felix Bemm
>>>>>> Department of Bioinformatics
>>>>>> University of W?rzburg, Germany
>>>>>> Tel: +49 931 - 31 83696
>>>>>> Fax: +49 931 - 31 84552
>>>>>> felix.bemm at uni-wuerzburg.de
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> 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
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> 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
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> Barry Moore
>> Research Scientist
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT 84112
>> --------------------------------------------
>> (801) 585-3543
>> 
>> 
>> 
>> 

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From marc.hoeppner at imbim.uu.se  Sat Oct 26 05:54:07 2013
From: marc.hoeppner at imbim.uu.se (Marc P. Hoeppner)
Date: Sat, 26 Oct 2013 13:54:07 +0200
Subject: [maker-devel] Maker MPICH2 issue (Multiple MAKER processes have
 been started in the same directory)
In-Reply-To: <526A7E14.9010906@imbim.uu.se>
References: <526A7E14.9010906@imbim.uu.se>
Message-ID: <526BAD5F.2000800@imbim.uu.se>

Dear List,

after much more debugging, I found the solution myself. Here are the 
details:

The Maker installation instructions refer to 'mpich2' in multiple 
places, including weblinks (whchi are outdated btw). Some digging 
revealed that mpich2 has since been renamed and merged back into mpich. 
So the website is www.mpich.org and the current stable version is 
mpich-3.0.4.  Closely following the installation instruction yielded a 
working copy of mpiexec that Maker was willing to accept. Good news - 
but I suggest to update the documentation. Most importantly for either 
SL/CentOS users, mpich2 as packaged with e.g. Scientific Linux *does 
not* work with Maker. You will need to download the latest stable build 
and compile it yourself (the mpich2 version bundled with Maker doesn't 
work either btw).

Cheers,

Marc

> Dear list,
>
> I know that MPICH2 related issues have been discussed previously, but 
> the suggested solutions don't seem to work for me.
> Briefly, I have set up a new cluster, with a fresh install of mpich2 
> (SL 6.4, from the yum repos) and a newly compiled build of Maker 2.28.
>
> When I start maker with mpiexec, I get spammed with
> 'WARNING: Multiple MAKER processes have been started in the same 
> directory.'
>
> Here is what I have tried so far - still getting the error :-< Any 
> suggestions would be appreciated
>
> --------
> MPICH2
> ---------
>
> which mpiexec:
> /usr/lib64/mpich2/bin/mpiexec
>
> Started the mpd ring as normal user across 5 nodes (bnode-01 to 
> bnode-04, and the head node bhead)
>
> mpdtrace:
> bhead
> bnode-02
> bnode-03
> bnode-04
> bnode-01
>
> mpdringtest:
> time for 1 loops = 0.00128293037415 seconds
>
> mpixec -n 32 -machinefile hostfile hostname:
>
> <long list of host names, as ecpected>
>
> I also ran the Skampi Mpi Benchmark, which ran through just fine.
>
> -----------
> MAKER
> -----------
>
> ./Build status
>
> PERL Dependencies:      VERIFIED
> External Programs:      VERIFIED
> External C Libraries:   VERIFIED
> MPI SUPPORT:            ENABLED
> MWAS Web Interface:     DISABLED
> MAKER PACKAGE:          CONFIGURATION OK
>
> During configuration/installation, Build.PL automatically detected all 
> MPI data and never complained, so I have to assume that everything 
> went fine there.
>


-- 
----------
Marc P. Hoeppner, PhD
Department of Microbiology and Medical Biochemistry
Uppsala University, Sweden
marc.hoeppner at imbim.uu.se




From barry.utah at gmail.com  Sat Oct 26 08:41:24 2013
From: barry.utah at gmail.com (Barry Moore)
Date: Sat, 26 Oct 2013 08:41:24 -0600
Subject: [maker-devel] Maker MPICH2 issue (Multiple MAKER processes have
	been started in the same directory)
In-Reply-To: <526BAD5F.2000800@imbim.uu.se>
References: <526A7E14.9010906@imbim.uu.se> <526BAD5F.2000800@imbim.uu.se>
Message-ID: <DDEE11FF-9EE2-4359-9A50-3DA95770DDEC@genetics.utah.edu>

Hi Marc,

Thanks so much for sharing the results of all your hard work!  We will follow up on your feedback and incorporate the necessary updates to MAKER docs and installation procedures.

B

On Oct 26, 2013, at 5:54 AM, Marc P. Hoeppner wrote:

> Dear List,
> 
> after much more debugging, I found the solution myself. Here are the details:
> 
> The Maker installation instructions refer to 'mpich2' in multiple places, including weblinks (whchi are outdated btw). Some digging revealed that mpich2 has since been renamed and merged back into mpich. So the website is www.mpich.org and the current stable version is mpich-3.0.4.  Closely following the installation instruction yielded a working copy of mpiexec that Maker was willing to accept. Good news - but I suggest to update the documentation. Most importantly for either SL/CentOS users, mpich2 as packaged with e.g. Scientific Linux *does not* work with Maker. You will need to download the latest stable build and compile it yourself (the mpich2 version bundled with Maker doesn't work either btw).
> 
> Cheers,
> 
> Marc
> 
>> Dear list,
>> 
>> I know that MPICH2 related issues have been discussed previously, but the suggested solutions don't seem to work for me.
>> Briefly, I have set up a new cluster, with a fresh install of mpich2 (SL 6.4, from the yum repos) and a newly compiled build of Maker 2.28.
>> 
>> When I start maker with mpiexec, I get spammed with
>> 'WARNING: Multiple MAKER processes have been started in the same directory.'
>> 
>> Here is what I have tried so far - still getting the error :-< Any suggestions would be appreciated
>> 
>> --------
>> MPICH2
>> ---------
>> 
>> which mpiexec:
>> /usr/lib64/mpich2/bin/mpiexec
>> 
>> Started the mpd ring as normal user across 5 nodes (bnode-01 to bnode-04, and the head node bhead)
>> 
>> mpdtrace:
>> bhead
>> bnode-02
>> bnode-03
>> bnode-04
>> bnode-01
>> 
>> mpdringtest:
>> time for 1 loops = 0.00128293037415 seconds
>> 
>> mpixec -n 32 -machinefile hostfile hostname:
>> 
>> <long list of host names, as ecpected>
>> 
>> I also ran the Skampi Mpi Benchmark, which ran through just fine.
>> 
>> -----------
>> MAKER
>> -----------
>> 
>> ./Build status
>> 
>> PERL Dependencies:      VERIFIED
>> External Programs:      VERIFIED
>> External C Libraries:   VERIFIED
>> MPI SUPPORT:            ENABLED
>> MWAS Web Interface:     DISABLED
>> MAKER PACKAGE:          CONFIGURATION OK
>> 
>> During configuration/installation, Build.PL automatically detected all MPI data and never complained, so I have to assume that everything went fine there.
>> 
> 
> 
> -- 
> ----------
> Marc P. Hoeppner, PhD
> Department of Microbiology and Medical Biochemistry
> Uppsala University, Sweden
> marc.hoeppner at imbim.uu.se
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From wholtz at lygos.com  Wed Oct 30 12:21:52 2013
From: wholtz at lygos.com (William Holtz)
Date: Wed, 30 Oct 2013 11:21:52 -0700 (PDT)
Subject: [maker-devel] maker apollo error
Message-ID: <1383157312.95043.YahooMailNeo@web5706.biz.mail.ne1.yahoo.com>

Hi,

I'm attempting to reply to a thread on this list from before I was a member. My apologies if this gets messed up.

I've tried installing maker v2.28 and v2.29p-beta and both of them fail due to the URL of the apollo tar file being outdated as previously reported on this list.?The updated URL that Carson Holt posted,?http://sourceforge.net/code-snapshots/svn/g/gm/gmod/svn/gmod-svn-25291-apollo-trunk.zip,?is also no longer valid. I was able to find a copy of the apollo source at?http://downloads.sourceforge.net/project/gmod/Apollo/1.11.1/apollo-1.11.1.tgz. However my attempts to integrate this into the maker build process have been unsuccessful, but likely could be done by someone more skilled than I.?Any pointers on how to get past this hurdle would be appreciated.

Thanks in advance for your help.

-Will



From barry.utah at gmail.com  Wed Oct 30 16:31:58 2013
From: barry.utah at gmail.com (Barry Moore)
Date: Wed, 30 Oct 2013 16:31:58 -0600
Subject: [maker-devel] maker apollo error
In-Reply-To: <1383157312.95043.YahooMailNeo@web5706.biz.mail.ne1.yahoo.com>
References: <1383157312.95043.YahooMailNeo@web5706.biz.mail.ne1.yahoo.com>
Message-ID: <C6E0A4A7-10D2-43B4-AA77-CCF6BE62E927@genetics.utah.edu>

Hi Will,

You can edit these URLs in the following file:

maker/src/locations

In a section that looks like this:

    'apollo'       => {'Linux_x86_64'  => 'http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar',
                       'Linux_i386'    => 'http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar',
                       'Darwin_i386'   => 'http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz',
                       'Darwin_x86_64' => 'http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz',
                       'src_'          => 'http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz',
                   },

Carson may have more feedback for you as well, but he is right in the middle of a move, so there may be a few days before he can reply, so modifying this file should work for you in the mean time.

On any of the executables that are missing you can always install them manually and add them to your path and maker will find them.  Also, maker shouldn't be required for a base maker install, so you could ignore that dependency as well.

Thanks,

B




On Oct 30, 2013, at 12:21 PM, William Holtz wrote:

> Hi,
> 
> I'm attempting to reply to a thread on this list from before I was a member. My apologies if this gets messed up.
> 
> I've tried installing maker v2.28 and v2.29p-beta and both of them fail due to the URL of the apollo tar file being outdated as previously reported on this list. The updated URL that Carson Holt posted, http://sourceforge.net/code-snapshots/svn/g/gm/gmod/svn/gmod-svn-25291-apollo-trunk.zip, is also no longer valid. I was able to find a copy of the apollo source at http://downloads.sourceforge.net/project/gmod/Apollo/1.11.1/apollo-1.11.1.tgz. However my attempts to integrate this into the maker build process have been unsuccessful, but likely could be done by someone more skilled than I. Any pointers on how to get past this hurdle would be appreciated.
> 
> Thanks in advance for your help.
> 
> -Will
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From carsonhh at gmail.com  Wed Oct  2 08:14:44 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 02 Oct 2013 10:14:44 -0400
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
Message-ID: <CE709D72.EF15%carsonhh@gmail.com>

It still works, but it will be reduced.  Without ESTs you won't get any
UTR prediction, also you will be limited by how well the protein set
matches to the genes.  If you use the protein set of a close relative you
will capture most things.  You will probably capture 80-95% of what you
would by also including ESTs.  It all depending on how different the
species in the proteins evidence file are compared to the the species
being annotated.

--Carson

On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for your message and your kind help. Now conversion from
>match/match_part to gene/mRNA/exons/CDS works well after blanking out
>some options in control file.
>
>I have one more question about maker2. In case we don't have EST evidence
>(set of ESTs or assembled mRNA-seq in fasta format) for a genome, does
>maker2 function? If it does function, could you please let me know the
>performance of maker2 without providing EST evidence compared to the one
>with EST evidence?
>
>Thank you  again and I look forward to hearing from you.
>
>Best,
>Xia
>
>
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Wednesday, September 25, 2013 10:36 AM
>To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>If it is launching predictors then you have snap hmm or augustus_species
>set.  You ned to blank out all other options in the control files
>(including repeat masking options, proteins, ESTs, etc.) when trying to
>convert mathc/match_part to gene/mRNA/exons/CDS, or else those other
>programs will run.
>
>--Carson
>
>
>On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>
>>Hi Carson,
>>
>>Thank you for the message and your kind help. We tested maker2 by
>>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>But it seemed maker2 started to launch all predictors again and it took
>>long time to finish. I wonder if there is any way that we can directly
>>get gene/mRNA/exons/CDS gff file without re-running maker2 to convert
>>match/match_part features into gene/mRNA/exons/CDS.
>>
>>Thanks,
>>Xia
>>
>>-----Original Message-----
>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>Sent: Thursday, September 19, 2013 5:58 PM
>>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY;
>>maker-devel at yandell-lab.org
>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>
>>Hello Corban & Xia,
>>
>>Some scripts like gff3_preds2models are deprecated.  To get the same
>>result as was offered by gff3_preds2models, just give your
>>match/match_part features to pref_gff= in the maker_opts.ctl file, set
>>keep_preds=1, and run with all other options and predictors turned off.
>>The final MAKER result will be your match/match_part features converted
>>into gene/mRNA/exons/CDS.
>>
>>For functional annotation, you can use Interproscan, BLASTP against
>>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO
>>terms and proteins domains via the ipr_update_gff and iprscan2gff3
>>scripts.  Then add putative gene functions via BLASTP to UniProt and
>>maker_functional_fasta and maker_functional_gff scripts.
>>
>>Go ahead and take a look and that those tools and let me know if you
>>have any questions or need help you configuring them.
>>
>>Thanks,
>>Carson
>>
>>
>>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>
>>>Hi  Corban & Xia,
>>>
>>>
>>>I've forwarded your question along to the MAKER_dev list, were you can
>>>get speedy answers to your maker related questions. Thanks for using
>>>MAKER.
>>>
>>>--mark
>>>
>>>
>>>Mark Yandell
>>>Professor of Human Genetics
>>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of
>>>Human Genetics University of Utah
>>>15 North 2030 East, Room 2100
>>>Salt Lake City, UT 84112-5330
>>>ph:801-587-7707
>>>
>>>________________________________________
>>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>Sent: Thursday, September 19, 2013 11:49 AM
>>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>Subject: maker2 scripts for functional annotation
>>>
>>>Dr. Yandell,
>>>
>>>We were recently evaluating maker2 for annotation and going through
>>>the maker tutorial from 2012.
>>>
>>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>>
>>>The tutorial makes references to some scripts that we couldn?t find in
>>>the current release.  We were looking for scripts like
>>>gff3_preds2models to convert match/match_part format into annotations
>>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did
>>>not have the most up to date version.
>>>
>>>In addition to getting accurate gene annotations, I was looking for a
>>>solution to get functional assignments.  I see that there are some
>>>scripts like maker_functional_fasta that may help, but I was wondering
>>>what you would recommend.
>>>
>>>Thanks,
>>>
>>>Corban & Xia
>>>
>>>This communication is for use by the intended recipient and contains
>>>information that may be Privileged, confidential or copyrighted under
>>>applicable law. If you are not the intended recipient, you are hereby
>>>formally notified that any use, copying or distribution of this
>>>e-mail, in whole or in part, is strictly prohibited. Please notify the
>>>sender by return e-mail and delete this e-mail from your system.
>>>Unless explicitly and conspicuously designated as "E-Contract
>>>Intended", this e-mail does not constitute a contract offer, a
>>>contract amendment, or an acceptance of a contract offer. This e-mail
>>>does not constitute a consent to the use of sender's contact
>>>information for direct marketing purposes or for transfers of data to
>>>third parties.
>>>
>>>The dupont.com web address will continue in use for a transitional
>>>period for communications sent or received on behalf of DuPont
>>>Performance Coatings., which is not affiliated in any way with the
>>>DuPont Company.
>>>
>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>>Korean
>>>
>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>g
>>
>>
>>
>>This communication is for use by the intended recipient and contains
>>information that may be Privileged, confidential or copyrighted under
>>applicable law. If you are not the intended recipient, you are hereby
>>formally notified that any use, copying or distribution of this e-mail,
>>in whole or in part, is strictly prohibited. Please notify the sender
>>by return e-mail and delete this e-mail from your system. Unless
>>explicitly and conspicuously designated as "E-Contract Intended", this
>>e-mail does not constitute a contract offer, a contract amendment, or
>>an acceptance of a contract offer. This e-mail does not constitute a
>>consent to the use of sender's contact information for direct marketing
>>purposes or for transfers of data to third parties.
>>
>>The dupont.com<http://dupont.com/> web address will continue in use for
>>a transitional period for communications sent or received on behalf of
>>DuPont Performance Coatings., which is not affiliated in any way with
>>the DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>Korean
>>
>>           http://www.DuPont.com/corp/email_disclaimer.html
>>
>
>
>
>This communication is for use by the intended recipient and contains
>information that may be Privileged, confidential or copyrighted under
>applicable law. If you are not the intended recipient, you are hereby
>formally notified that any use, copying or distribution of this e-mail,
>in whole or in part, is strictly prohibited. Please notify the sender by
>return e-mail and delete this e-mail from your system. Unless explicitly
>and conspicuously designated as "E-Contract Intended", this e-mail does
>not constitute a contract offer, a contract amendment, or an acceptance
>of a contract offer. This e-mail does not constitute a consent to the
>use of sender's contact information for direct marketing purposes or for
>transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for a
>transitional period for communications sent or received on behalf of
>DuPont
>Performance Coatings., which is not affiliated in any way with the DuPont
>Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>





From Xia.Cao at dupont.com  Tue Oct  1 13:00:42 2013
From: Xia.Cao at dupont.com (Xia.Cao at dupont.com)
Date: Tue, 1 Oct 2013 19:00:42 +0000
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <CE686C71.ECAC%carsonhh@gmail.com>
References: <AAF36CDE29C45F45AE125A1D13F5D675ACE4B8@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE686C71.ECAC%carsonhh@gmail.com>
Message-ID: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>

Hi Carson,

Thank you for your message and your kind help. Now conversion from match/match_part to gene/mRNA/exons/CDS works well after blanking out some options in control file.  

I have one more question about maker2. In case we don't have EST evidence (set of ESTs or assembled mRNA-seq in fasta format) for a genome, does maker2 function? If it does function, could you please let me know the performance of maker2 without providing EST evidence compared to the one with EST evidence?

Thank you  again and I look forward to hearing from you.

Best,
Xia




-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Wednesday, September 25, 2013 10:36 AM
To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] maker2 scripts for functional annotation

If it is launching predictors then you have snap hmm or augustus_species set.  You ned to blank out all other options in the control files (including repeat masking options, proteins, ESTs, etc.) when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else those other programs will run.

--Carson


On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for the message and your kind help. We tested maker2 by 
>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun . 
>But it seemed maker2 started to launch all predictors again and it took 
>long time to finish. I wonder if there is any way that we can directly 
>get gene/mRNA/exons/CDS gff file without re-running maker2 to convert 
>match/match_part features into gene/mRNA/exons/CDS.
>
>Thanks,
>Xia
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Thursday, September 19, 2013 5:58 PM
>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; 
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>Hello Corban & Xia,
>
>Some scripts like gff3_preds2models are deprecated.  To get the same 
>result as was offered by gff3_preds2models, just give your 
>match/match_part features to pref_gff= in the maker_opts.ctl file, set 
>keep_preds=1, and run with all other options and predictors turned off.
>The final MAKER result will be your match/match_part features converted 
>into gene/mRNA/exons/CDS.
>
>For functional annotation, you can use Interproscan, BLASTP against 
>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO 
>terms and proteins domains via the ipr_update_gff and iprscan2gff3 
>scripts.  Then add putative gene functions via BLASTP to UniProt and 
>maker_functional_fasta and maker_functional_gff scripts.
>
>Go ahead and take a look and that those tools and let me know if you 
>have any questions or need help you configuring them.
>
>Thanks,
>Carson
>
>
>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>
>>Hi  Corban & Xia,
>>
>>
>>I've forwarded your question along to the MAKER_dev list, were you can 
>>get speedy answers to your maker related questions. Thanks for using 
>>MAKER.
>>
>>--mark
>>
>>
>>Mark Yandell
>>Professor of Human Genetics
>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of 
>>Human Genetics University of Utah
>>15 North 2030 East, Room 2100
>>Salt Lake City, UT 84112-5330
>>ph:801-587-7707
>>
>>________________________________________
>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>Sent: Thursday, September 19, 2013 11:49 AM
>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>Subject: maker2 scripts for functional annotation
>>
>>Dr. Yandell,
>>
>>We were recently evaluating maker2 for annotation and going through 
>>the maker tutorial from 2012.
>>
>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>
>>The tutorial makes references to some scripts that we couldn?t find in 
>>the current release.  We were looking for scripts like 
>>gff3_preds2models to convert match/match_part format into annotations 
>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did 
>>not have the most up to date version.
>>
>>In addition to getting accurate gene annotations, I was looking for a 
>>solution to get functional assignments.  I see that there are some 
>>scripts like maker_functional_fasta that may help, but I was wondering 
>>what you would recommend.
>>
>>Thanks,
>>
>>Corban & Xia
>>
>>This communication is for use by the intended recipient and contains 
>>information that may be Privileged, confidential or copyrighted under 
>>applicable law. If you are not the intended recipient, you are hereby 
>>formally notified that any use, copying or distribution of this 
>>e-mail, in whole or in part, is strictly prohibited. Please notify the 
>>sender by return e-mail and delete this e-mail from your system. 
>>Unless explicitly and conspicuously designated as "E-Contract 
>>Intended", this e-mail does not constitute a contract offer, a 
>>contract amendment, or an acceptance of a contract offer. This e-mail 
>>does not constitute a consent to the use of sender's contact 
>>information for direct marketing purposes or for transfers of data to third parties.
>>
>>The dupont.com web address will continue in use for a transitional 
>>period for communications sent or received on behalf of DuPont 
>>Performance Coatings., which is not affiliated in any way with the 
>>DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>Korean
>>
>>          http://www.DuPont.com/corp/email_disclaimer.html
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>g
>
>
>
>This communication is for use by the intended recipient and contains 
>information that may be Privileged, confidential or copyrighted under 
>applicable law. If you are not the intended recipient, you are hereby 
>formally notified that any use, copying or distribution of this e-mail, 
>in whole or in part, is strictly prohibited. Please notify the sender 
>by return e-mail and delete this e-mail from your system. Unless 
>explicitly and conspicuously designated as "E-Contract Intended", this 
>e-mail does not constitute a contract offer, a contract amendment, or 
>an acceptance of a contract offer. This e-mail does not constitute a 
>consent to the use of sender's contact information for direct marketing 
>purposes or for transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for 
>a transitional period for communications sent or received on behalf of 
>DuPont Performance Coatings., which is not affiliated in any way with 
>the DuPont Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  
>Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>



This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
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formally notified that any use, copying or distribution of this e-mail,
in whole or in part, is strictly prohibited. Please notify the sender by
return e-mail and delete this e-mail from your system. Unless explicitly
and conspicuously designated as "E-Contract Intended", this e-mail does
not constitute a contract offer, a contract amendment, or an acceptance
of a contract offer. This e-mail does not constitute a consent to the
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transfers of data to third parties.

The dupont.com<http://dupont.com/> web address will continue in use for a
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Performance Coatings., which is not affiliated in any way with the DuPont Company.

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From carsonhh at gmail.com  Wed Oct  2 08:43:29 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 02 Oct 2013 10:43:29 -0400
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
Message-ID: <CE71A8D4.F2AD%carsonhh@gmail.com>

That's ok.  If it is very closely related, provide it directly to the est=
option, otherwise provide it to the altest= option.  The difference
between the two options is how they are aligned.  The altest= alignments
takes about 10x longer than the est= alignments.

--Carson


On 10/2/13 10:40 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for your quick and kind reply. One more question here. If we
>don't have EST evidence for the strain we sequenced/assembled, will it be
>ok to provide some EST evidence that is from some other strains which are
>close to the one we are trying to annotate? Could you please let us know
>how this will affect performance of maker2?
>
>Thank you again.
>
>Best,
>Xia
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Wednesday, October 02, 2013 10:15 AM
>To: CAO, XIA
>Cc: myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>It still works, but it will be reduced.  Without ESTs you won't get any
>UTR prediction, also you will be limited by how well the protein set
>matches to the genes.  If you use the protein set of a close relative you
>will capture most things.  You will probably capture 80-95% of what you
>would by also including ESTs.  It all depending on how different the
>species in the proteins evidence file are compared to the the species
>being annotated.
>
>--Carson
>
>On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>
>>Hi Carson,
>>
>>Thank you for your message and your kind help. Now conversion from
>>match/match_part to gene/mRNA/exons/CDS works well after blanking out
>>some options in control file.
>>
>>I have one more question about maker2. In case we don't have EST
>>evidence (set of ESTs or assembled mRNA-seq in fasta format) for a
>>genome, does
>>maker2 function? If it does function, could you please let me know the
>>performance of maker2 without providing EST evidence compared to the
>>one with EST evidence?
>>
>>Thank you  again and I look forward to hearing from you.
>>
>>Best,
>>Xia
>>
>>
>>
>>
>>-----Original Message-----
>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>Sent: Wednesday, September 25, 2013 10:36 AM
>>To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>>maker-devel at yandell-lab.org
>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>
>>If it is launching predictors then you have snap hmm or
>>augustus_species set.  You ned to blank out all other options in the
>>control files (including repeat masking options, proteins, ESTs, etc.)
>>when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else
>>those other programs will run.
>>
>>--Carson
>>
>>
>>On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>>
>>>Hi Carson,
>>>
>>>Thank you for the message and your kind help. We tested maker2 by
>>>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>>But it seemed maker2 started to launch all predictors again and it
>>>took long time to finish. I wonder if there is any way that we can
>>>directly get gene/mRNA/exons/CDS gff file without re-running maker2 to
>>>convert match/match_part features into gene/mRNA/exons/CDS.
>>>
>>>Thanks,
>>>Xia
>>>
>>>-----Original Message-----
>>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>>Sent: Thursday, September 19, 2013 5:58 PM
>>>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY;
>>>maker-devel at yandell-lab.org
>>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>>
>>>Hello Corban & Xia,
>>>
>>>Some scripts like gff3_preds2models are deprecated.  To get the same
>>>result as was offered by gff3_preds2models, just give your
>>>match/match_part features to pref_gff= in the maker_opts.ctl file, set
>>>keep_preds=1, and run with all other options and predictors turned off.
>>>The final MAKER result will be your match/match_part features
>>>converted into gene/mRNA/exons/CDS.
>>>
>>>For functional annotation, you can use Interproscan, BLASTP against
>>>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO
>>>terms and proteins domains via the ipr_update_gff and iprscan2gff3
>>>scripts.  Then add putative gene functions via BLASTP to UniProt and
>>>maker_functional_fasta and maker_functional_gff scripts.
>>>
>>>Go ahead and take a look and that those tools and let me know if you
>>>have any questions or need help you configuring them.
>>>
>>>Thanks,
>>>Carson
>>>
>>>
>>>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>>
>>>>Hi  Corban & Xia,
>>>>
>>>>
>>>>I've forwarded your question along to the MAKER_dev list, were you
>>>>can get speedy answers to your maker related questions. Thanks for
>>>>using MAKER.
>>>>
>>>>--mark
>>>>
>>>>
>>>>Mark Yandell
>>>>Professor of Human Genetics
>>>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of
>>>>Human Genetics University of Utah
>>>>15 North 2030 East, Room 2100
>>>>Salt Lake City, UT 84112-5330
>>>>ph:801-587-7707
>>>>
>>>>________________________________________
>>>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>>Sent: Thursday, September 19, 2013 11:49 AM
>>>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>>Subject: maker2 scripts for functional annotation
>>>>
>>>>Dr. Yandell,
>>>>
>>>>We were recently evaluating maker2 for annotation and going through
>>>>the maker tutorial from 2012.
>>>>
>>>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>>>
>>>>The tutorial makes references to some scripts that we couldn?t find
>>>>in the current release.  We were looking for scripts like
>>>>gff3_preds2models to convert match/match_part format into annotations
>>>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did
>>>>not have the most up to date version.
>>>>
>>>>In addition to getting accurate gene annotations, I was looking for a
>>>>solution to get functional assignments.  I see that there are some
>>>>scripts like maker_functional_fasta that may help, but I was
>>>>wondering what you would recommend.
>>>>
>>>>Thanks,
>>>>
>>>>Corban & Xia
>>>>
>>>>This communication is for use by the intended recipient and contains
>>>>information that may be Privileged, confidential or copyrighted under
>>>>applicable law. If you are not the intended recipient, you are hereby
>>>>formally notified that any use, copying or distribution of this
>>>>e-mail, in whole or in part, is strictly prohibited. Please notify
>>>>the sender by return e-mail and delete this e-mail from your system.
>>>>Unless explicitly and conspicuously designated as "E-Contract
>>>>Intended", this e-mail does not constitute a contract offer, a
>>>>contract amendment, or an acceptance of a contract offer. This e-mail
>>>>does not constitute a consent to the use of sender's contact
>>>>information for direct marketing purposes or for transfers of data to
>>>>third parties.
>>>>
>>>>The dupont.com web address will continue in use for a transitional
>>>>period for communications sent or received on behalf of DuPont
>>>>Performance Coatings., which is not affiliated in any way with the
>>>>DuPont Company.
>>>>
>>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>>>Korean
>>>>
>>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>>>
>>>>_______________________________________________
>>>>maker-devel mailing list
>>>>maker-devel at box290.bluehost.com
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>>r
>>>>g
>>>
>>>
>>>
>>>This communication is for use by the intended recipient and contains
>>>information that may be Privileged, confidential or copyrighted under
>>>applicable law. If you are not the intended recipient, you are hereby
>>>formally notified that any use, copying or distribution of this
>>>e-mail, in whole or in part, is strictly prohibited. Please notify the
>>>sender by return e-mail and delete this e-mail from your system.
>>>Unless explicitly and conspicuously designated as "E-Contract
>>>Intended", this e-mail does not constitute a contract offer, a
>>>contract amendment, or an acceptance of a contract offer. This e-mail
>>>does not constitute a consent to the use of sender's contact
>>>information for direct marketing purposes or for transfers of data to
>>>third parties.
>>>
>>>The dupont.com<http://dupont.com/> web address will continue in use
>>>for a transitional period for communications sent or received on
>>>behalf of DuPont Performance Coatings., which is not affiliated in any
>>>way with the DuPont Company.
>>>
>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>>Korean
>>>
>>>           http://www.DuPont.com/corp/email_disclaimer.html
>>>
>>
>>
>>
>>This communication is for use by the intended recipient and contains
>>information that may be Privileged, confidential or copyrighted under
>>applicable law. If you are not the intended recipient, you are hereby
>>formally notified that any use, copying or distribution of this e-mail,
>>in whole or in part, is strictly prohibited. Please notify the sender
>>by return e-mail and delete this e-mail from your system. Unless
>>explicitly and conspicuously designated as "E-Contract Intended", this
>>e-mail does not constitute a contract offer, a contract amendment, or
>>an acceptance of a contract offer. This e-mail does not constitute a
>>consent to the use of sender's contact information for direct marketing
>>purposes or for transfers of data to third parties.
>>
>>The dupont.com<http://dupont.com/> web address will continue in use for
>>a transitional period for communications sent or received on behalf of
>>DuPont Performance Coatings., which is not affiliated in any way with
>>the DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>Korean
>>
>>           http://www.DuPont.com/corp/email_disclaimer.html
>>
>
>
>
>This communication is for use by the intended recipient and contains
>information that may be Privileged, confidential or copyrighted under
>applicable law. If you are not the intended recipient, you are hereby
>formally notified that any use, copying or distribution of this e-mail,
>in whole or in part, is strictly prohibited. Please notify the sender by
>return e-mail and delete this e-mail from your system. Unless explicitly
>and conspicuously designated as "E-Contract Intended", this e-mail does
>not constitute a contract offer, a contract amendment, or an acceptance
>of a contract offer. This e-mail does not constitute a consent to the
>use of sender's contact information for direct marketing purposes or for
>transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for a
>transitional period for communications sent or received on behalf of
>DuPont
>Performance Coatings., which is not affiliated in any way with the DuPont
>Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>





From Carson.Holt at oicr.on.ca  Wed Oct  2 09:24:42 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Wed, 2 Oct 2013 15:24:42 +0000
Subject: [maker-devel] Incorrect gene model, antisense transcripts
In-Reply-To: <A21F03FBB429334EB4D450CC75E8CBF37F0454C6@CH1PRD0210MB384.namprd02.prod.outlook.com>
Message-ID: <CE71B238.F2B7%carson.holt@oicr.on.ca>

SNAP appears to be making small ab initio calls all over the place.  You may need to retrain it, or just drop it completely from your analysis and just use augustus.

Try running with protein2genome and then training SNAP off of those results.  Also make sure your repeat masking is sufficient.  You may be getting too many SANP predictions if that is the case.

Thanks,
Carson



From: Sivaranjani Namasivayam <ranjani at uga.edu<mailto:ranjani at uga.edu>>
Date: Tuesday, October 1, 2013 5:01 PM
To: "maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>" <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>>
Subject: Incorrect gene model, antisense transcripts

Hello,

I am working on annotating a genome. I have RNAseq data assembled with Cufflinks and Trinity. I am using to predict gene models. Below is the procedure I used

- For the first round of prediction I provided the following : EST evidence: assembled RNAseq, Protein evidence: proteins from related organism, Gene predictor: augustus trained on a related organism.
- The number of genes I got was much less than expected (Expect atleast 10K genes, got ~4K genes)
- Used the gene models from the first round of annotations to train SNAP (default parameters) and provided the HMM for the second round of annotation (used augustus also). All other data I passed as such in the gff3, except the gene models.I also included the some manually curated genes in the EST evidence.

- The number of genes were much higher, ~11k, but many seemed incorrect and appear to have been generated from the SNAP models. I am attaching a screen shot from Apollo showing this.

Would you have any suggestions on why this might be happening and how I can fix?
I am essentially looking for gene models for my assembled RNAseq, can I achieve this by setting est2genome to 1? Would I be losing/misrepresenting any data if I do this.

Also, I recently noticed my RNAseq data has assembled antisense transcripts. MAKER seems to be predicting a coding region for these antisense transcripts in some cases, (although the coding region predicted is much smaller than that of the sense gene model.) Is there a way to tell MAKER not to predict gene models on both strands at the same loci.

Appreciate your help.

Thanks,
Ranjani





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From Xia.Cao at dupont.com  Wed Oct  2 08:40:12 2013
From: Xia.Cao at dupont.com (Xia.Cao at dupont.com)
Date: Wed, 2 Oct 2013 14:40:12 +0000
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <CE709D72.EF15%carsonhh@gmail.com>
References: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE709D72.EF15%carsonhh@gmail.com>
Message-ID: <AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>

Hi Carson,

Thank you for your quick and kind reply. One more question here. If we don't have EST evidence for the strain we sequenced/assembled, will it be ok to provide some EST evidence that is from some other strains which are close to the one we are trying to annotate? Could you please let us know how this will affect performance of maker2?

Thank you again.

Best,
Xia

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Wednesday, October 02, 2013 10:15 AM
To: CAO, XIA
Cc: myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] maker2 scripts for functional annotation

It still works, but it will be reduced.  Without ESTs you won't get any UTR prediction, also you will be limited by how well the protein set matches to the genes.  If you use the protein set of a close relative you will capture most things.  You will probably capture 80-95% of what you would by also including ESTs.  It all depending on how different the species in the proteins evidence file are compared to the the species being annotated.

--Carson

On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>Thank you for your message and your kind help. Now conversion from 
>match/match_part to gene/mRNA/exons/CDS works well after blanking out 
>some options in control file.
>
>I have one more question about maker2. In case we don't have EST 
>evidence (set of ESTs or assembled mRNA-seq in fasta format) for a 
>genome, does
>maker2 function? If it does function, could you please let me know the 
>performance of maker2 without providing EST evidence compared to the 
>one with EST evidence?
>
>Thank you  again and I look forward to hearing from you.
>
>Best,
>Xia
>
>
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Wednesday, September 25, 2013 10:36 AM
>To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; 
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>If it is launching predictors then you have snap hmm or 
>augustus_species set.  You ned to blank out all other options in the 
>control files (including repeat masking options, proteins, ESTs, etc.) 
>when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else 
>those other programs will run.
>
>--Carson
>
>
>On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>
>>Hi Carson,
>>
>>Thank you for the message and your kind help. We tested maker2 by 
>>setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>But it seemed maker2 started to launch all predictors again and it 
>>took long time to finish. I wonder if there is any way that we can 
>>directly get gene/mRNA/exons/CDS gff file without re-running maker2 to 
>>convert match/match_part features into gene/mRNA/exons/CDS.
>>
>>Thanks,
>>Xia
>>
>>-----Original Message-----
>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>Sent: Thursday, September 19, 2013 5:58 PM
>>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; 
>>maker-devel at yandell-lab.org
>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>
>>Hello Corban & Xia,
>>
>>Some scripts like gff3_preds2models are deprecated.  To get the same 
>>result as was offered by gff3_preds2models, just give your 
>>match/match_part features to pref_gff= in the maker_opts.ctl file, set 
>>keep_preds=1, and run with all other options and predictors turned off.
>>The final MAKER result will be your match/match_part features 
>>converted into gene/mRNA/exons/CDS.
>>
>>For functional annotation, you can use Interproscan, BLASTP against 
>>UniProt, or BALST2GO.  My preference is to use InterProScan to add GO 
>>terms and proteins domains via the ipr_update_gff and iprscan2gff3 
>>scripts.  Then add putative gene functions via BLASTP to UniProt and 
>>maker_functional_fasta and maker_functional_gff scripts.
>>
>>Go ahead and take a look and that those tools and let me know if you 
>>have any questions or need help you configuring them.
>>
>>Thanks,
>>Carson
>>
>>
>>On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>
>>>Hi  Corban & Xia,
>>>
>>>
>>>I've forwarded your question along to the MAKER_dev list, were you 
>>>can get speedy answers to your maker related questions. Thanks for 
>>>using MAKER.
>>>
>>>--mark
>>>
>>>
>>>Mark Yandell
>>>Professor of Human Genetics
>>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of 
>>>Human Genetics University of Utah
>>>15 North 2030 East, Room 2100
>>>Salt Lake City, UT 84112-5330
>>>ph:801-587-7707
>>>
>>>________________________________________
>>>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>Sent: Thursday, September 19, 2013 11:49 AM
>>>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>Subject: maker2 scripts for functional annotation
>>>
>>>Dr. Yandell,
>>>
>>>We were recently evaluating maker2 for annotation and going through 
>>>the maker tutorial from 2012.
>>>
>>>http://gmod.org/wiki/MAKER_Tutorial_2012
>>>
>>>The tutorial makes references to some scripts that we couldn?t find 
>>>in the current release.  We were looking for scripts like 
>>>gff3_preds2models to convert match/match_part format into annotations 
>>>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did 
>>>not have the most up to date version.
>>>
>>>In addition to getting accurate gene annotations, I was looking for a 
>>>solution to get functional assignments.  I see that there are some 
>>>scripts like maker_functional_fasta that may help, but I was 
>>>wondering what you would recommend.
>>>
>>>Thanks,
>>>
>>>Corban & Xia
>>>
>>>This communication is for use by the intended recipient and contains 
>>>information that may be Privileged, confidential or copyrighted under 
>>>applicable law. If you are not the intended recipient, you are hereby 
>>>formally notified that any use, copying or distribution of this 
>>>e-mail, in whole or in part, is strictly prohibited. Please notify 
>>>the sender by return e-mail and delete this e-mail from your system.
>>>Unless explicitly and conspicuously designated as "E-Contract 
>>>Intended", this e-mail does not constitute a contract offer, a 
>>>contract amendment, or an acceptance of a contract offer. This e-mail 
>>>does not constitute a consent to the use of sender's contact 
>>>information for direct marketing purposes or for transfers of data to 
>>>third parties.
>>>
>>>The dupont.com web address will continue in use for a transitional 
>>>period for communications sent or received on behalf of DuPont 
>>>Performance Coatings., which is not affiliated in any way with the 
>>>DuPont Company.
>>>
>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>>Korean
>>>
>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>r
>>>g
>>
>>
>>
>>This communication is for use by the intended recipient and contains 
>>information that may be Privileged, confidential or copyrighted under 
>>applicable law. If you are not the intended recipient, you are hereby 
>>formally notified that any use, copying or distribution of this 
>>e-mail, in whole or in part, is strictly prohibited. Please notify the 
>>sender by return e-mail and delete this e-mail from your system. 
>>Unless explicitly and conspicuously designated as "E-Contract 
>>Intended", this e-mail does not constitute a contract offer, a 
>>contract amendment, or an acceptance of a contract offer. This e-mail 
>>does not constitute a consent to the use of sender's contact 
>>information for direct marketing purposes or for transfers of data to third parties.
>>
>>The dupont.com<http://dupont.com/> web address will continue in use 
>>for a transitional period for communications sent or received on 
>>behalf of DuPont Performance Coatings., which is not affiliated in any 
>>way with the DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>Korean
>>
>>           http://www.DuPont.com/corp/email_disclaimer.html
>>
>
>
>
>This communication is for use by the intended recipient and contains 
>information that may be Privileged, confidential or copyrighted under 
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>e-mail does not constitute a contract offer, a contract amendment, or 
>an acceptance of a contract offer. This e-mail does not constitute a 
>consent to the use of sender's contact information for direct marketing 
>purposes or for transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for 
>a transitional period for communications sent or received on behalf of 
>DuPont Performance Coatings., which is not affiliated in any way with 
>the DuPont Company.
>
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>Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>



This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
applicable law. If you are not the intended recipient, you are hereby
formally notified that any use, copying or distribution of this e-mail,
in whole or in part, is strictly prohibited. Please notify the sender by
return e-mail and delete this e-mail from your system. Unless explicitly
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use of sender's contact information for direct marketing purposes or for
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The dupont.com<http://dupont.com/> web address will continue in use for a
transitional period for communications sent or received on behalf of DuPont
Performance Coatings., which is not affiliated in any way with the DuPont Company.

Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean

           http://www.DuPont.com/corp/email_disclaimer.html




From markwiz at us.ibm.com  Wed Oct  2 10:52:55 2013
From: markwiz at us.ibm.com (Mark Wisner)
Date: Wed, 2 Oct 2013 12:52:55 -0400
Subject: [maker-devel] Maker2 on IBM PowerLinux?
Message-ID: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>

IBMs PowerLinux is tuned for Big Data workloads. We have had queries for 
Maker2 on PowerLinux.
How do we work with Maker2 development to create a PowerLinux port.
Thanks,

Mark K. Wisner
Linux On Power ISV PM
IBM
3039 Cornwallis Rd
RTP, NC 27709
Cell 919-649-5813
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From barry.moore at genetics.utah.edu  Wed Oct  2 11:29:36 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Wed, 2 Oct 2013 11:29:36 -0600
Subject: [maker-devel] Maker2 on IBM PowerLinux?
In-Reply-To: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>
References: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>
Message-ID: <E59BC7E8-B562-4AD6-B4CF-C793329B688B@genetics.utah.edu>

Hi Mark,

Carson Holt is the primary Maker developer, but others of us may be able to help as well.  I've added e-mails for Carson, Michael Campbell, Mark Yandell and myself who are currently developers on the project.   You can feel free to contact this mailing list - or if the conversation is getting too far afield for general interest you can contact us off list and we will do whatever we can to help.  If you feel like you need to do some modification of MAKER code to optimize it for PowerLinux I'm happy to give you a branch on the subversion repo to work with and then we can work with you to merge these changes back to the trunk when you feel like you have some improvements that benefit PowerLinux (and all other) users.

Thanks very much for your interest in MAKER - your participation in the community is most welcome!

Barry

On Oct 2, 2013, at 10:52 AM, Mark Wisner wrote:

> IBMs PowerLinux is tuned for Big Data workloads. We have had queries for Maker2 on PowerLinux. 
> How do we work with Maker2 development to create a PowerLinux port. 
> Thanks,
> 
> Mark K. Wisner
> Linux On Power ISV PM
> IBM
> 3039 Cornwallis Rd
> RTP, NC 27709
> Cell 919-649-5813
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From carsonhh at gmail.com  Wed Oct  2 11:29:50 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 02 Oct 2013 13:29:50 -0400
Subject: [maker-devel] Maker2 on IBM PowerLinux?
In-Reply-To: <OF886CA575.8F4B0E2E-ON87257BF8.005C5F17-85257BF8.005CBC6A@us.ibm.com>
Message-ID: <CE71CD2E.F2D8%carsonhh@gmail.com>

MAKER is written in perl, so it can work pretty much anywhere you have perl.
It is more an issue of the tools MAKER uses.  If you can get SNAP, BLAST,
exonerate, etc. to run then MAKER should be no problem.

You can let MAKER try and install and configure any missing perl libraries
as well as external tools for you (this is by far the easiest way).  You
will need an internet connection.

cd ?/maker/src/
perl Build.PL               #say 'Y' to local installation of libraries and
'N' to MPI for now
./Build installdeps     #grabs missing perl libraries from the ether, and
installs them in  the .../maker/perl/ directory
./Build installers        #grabs missing tools from the ether, installs, and
configures them in the .../maker/exe/ directory
./Build install              #just installs maker


If you want to run via MPI, I'd recommend OpenMPI, and you will need to
rerun the 'perl Build.PL' and './Build install' steps (say yes to MPI this
time around).

Here are some variables you will likly have to add to your .bash_profile to
get openmpi to run with MAKER (you must add these and source the profile
before attempting to install with OpenMPI), otherwise compilation will not
work correctly (OpenMPI shared library issue).

#you need to set $OMPIHOME to OpenMPI's location here -->
export LD_PRELOAD=$OMPIHOME/lib/libmpi.so:$LD_PRELOAD


#this one just suppresses a warning -->
export OMPI_MCA_mpi_warn_on_fork=0


And on some systems you have to add this  ' -mca btl ^openib' to the mpiexec
command when I run maker.
Example-->
mpiexec -mca btl ^openib -n 20 maker

Thanks,
Carson


From:  Mark Wisner <markwiz at us.ibm.com>
Date:  Wednesday, October 2, 2013 12:52 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker2 on IBM PowerLinux?

IBMs PowerLinux is tuned for Big Data workloads. We have had queries for
Maker2 on PowerLinux.
How do we work with Maker2 development to create a PowerLinux port.
Thanks,

Mark K. Wisner
Linux On Power ISV PM
IBM
3039 Cornwallis Rd
RTP, NC 27709
Cell 919-649-5813
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From barry.moore at genetics.utah.edu  Wed Oct  2 11:21:29 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Wed, 2 Oct 2013 11:21:29 -0600
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
References: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE709D72.EF15%carsonhh@gmail.com>
	<AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
Message-ID: <E9DC8DC1-8E1F-42E7-94CC-5D58EF0A1F21@genetics.utah.edu>

Hi Xia,

You can use EST evidence from other strains/species.  The considerations are as follows:  When you pass EST (or mRNASeq based transcripts) evidence MAKER uses blastn to align those with alignment parameters that assume they sequences will align easily with almost perfect identity - this is fast.  If you use EST/mRNA evidence from another species MAKER uses tblastx to compare the RNA evidence to the assembly, both translated into protein space - this works fine, but it is slow and often doesn't get you much more evidence than you could have gotten from proteins as evidence.  If you believe that you're other strain should have very little divergence in sequence at the nt level then you could experiment with passing EST/mRNA evidence as est in the control file.  Consider this an experiment, do it on a few contigs and examine the results carefully and skeptically.  If it works well, that would be the way to go because you've get better UTRs, but if it doesn't you'll see that you get little support for models because sequence divergence was too much for good alignment.  In that case you'll need to use alt_est and this will be slower and you'll likely get little in the way of support for UTRs - in this case as well, do a few contigs and examine the output carefully to see if the additional alignment time with tblastx is worth it in your case.

Barry


On Oct 2, 2013, at 8:40 AM, <Xia.Cao at dupont.com>
 wrote:

> Hi Carson,
> 
> Thank you for your quick and kind reply. One more question here. If we don't have EST evidence for the strain we sequenced/assembled, will it be ok to provide some EST evidence that is from some other strains which are close to the one we are trying to annotate? Could you please let us know how this will affect performance of maker2?
> 
> Thank you again.
> 
> Best,
> Xia
> 
> -----Original Message-----
> From: Carson Holt [mailto:carsonhh at gmail.com] 
> Sent: Wednesday, October 02, 2013 10:15 AM
> To: CAO, XIA
> Cc: myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org
> Subject: Re: [maker-devel] maker2 scripts for functional annotation
> 
> It still works, but it will be reduced.  Without ESTs you won't get any UTR prediction, also you will be limited by how well the protein set matches to the genes.  If you use the protein set of a close relative you will capture most things.  You will probably capture 80-95% of what you would by also including ESTs.  It all depending on how different the species in the proteins evidence file are compared to the the species being annotated.
> 
> --Carson
> 
> On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
> 
>> Hi Carson,
>> 
>> Thank you for your message and your kind help. Now conversion from 
>> match/match_part to gene/mRNA/exons/CDS works well after blanking out 
>> some options in control file.
>> 
>> I have one more question about maker2. In case we don't have EST 
>> evidence (set of ESTs or assembled mRNA-seq in fasta format) for a 
>> genome, does
>> maker2 function? If it does function, could you please let me know the 
>> performance of maker2 without providing EST evidence compared to the 
>> one with EST evidence?
>> 
>> Thank you  again and I look forward to hearing from you.
>> 
>> Best,
>> Xia
>> 
>> 
>> 
>> 
>> -----Original Message-----
>> From: Carson Holt [mailto:carsonhh at gmail.com]
>> Sent: Wednesday, September 25, 2013 10:36 AM
>> To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY; 
>> maker-devel at yandell-lab.org
>> Subject: Re: [maker-devel] maker2 scripts for functional annotation
>> 
>> If it is launching predictors then you have snap hmm or 
>> augustus_species set.  You ned to blank out all other options in the 
>> control files (including repeat masking options, proteins, ESTs, etc.) 
>> when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else 
>> those other programs will run.
>> 
>> --Carson
>> 
>> 
>> On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>> 
>>> Hi Carson,
>>> 
>>> Thank you for the message and your kind help. We tested maker2 by 
>>> setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
>>> But it seemed maker2 started to launch all predictors again and it 
>>> took long time to finish. I wonder if there is any way that we can 
>>> directly get gene/mRNA/exons/CDS gff file without re-running maker2 to 
>>> convert match/match_part features into gene/mRNA/exons/CDS.
>>> 
>>> Thanks,
>>> Xia
>>> 
>>> -----Original Message-----
>>> From: Carson Holt [mailto:carsonhh at gmail.com]
>>> Sent: Thursday, September 19, 2013 5:58 PM
>>> To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; 
>>> maker-devel at yandell-lab.org
>>> Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>> 
>>> Hello Corban & Xia,
>>> 
>>> Some scripts like gff3_preds2models are deprecated.  To get the same 
>>> result as was offered by gff3_preds2models, just give your 
>>> match/match_part features to pref_gff= in the maker_opts.ctl file, set 
>>> keep_preds=1, and run with all other options and predictors turned off.
>>> The final MAKER result will be your match/match_part features 
>>> converted into gene/mRNA/exons/CDS.
>>> 
>>> For functional annotation, you can use Interproscan, BLASTP against 
>>> UniProt, or BALST2GO.  My preference is to use InterProScan to add GO 
>>> terms and proteins domains via the ipr_update_gff and iprscan2gff3 
>>> scripts.  Then add putative gene functions via BLASTP to UniProt and 
>>> maker_functional_fasta and maker_functional_gff scripts.
>>> 
>>> Go ahead and take a look and that those tools and let me know if you 
>>> have any questions or need help you configuring them.
>>> 
>>> Thanks,
>>> Carson
>>> 
>>> 
>>> On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>>> 
>>>> Hi  Corban & Xia,
>>>> 
>>>> 
>>>> I've forwarded your question along to the MAKER_dev list, were you 
>>>> can get speedy answers to your maker related questions. Thanks for 
>>>> using MAKER.
>>>> 
>>>> --mark
>>>> 
>>>> 
>>>> Mark Yandell
>>>> Professor of Human Genetics
>>>> H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of 
>>>> Human Genetics University of Utah
>>>> 15 North 2030 East, Room 2100
>>>> Salt Lake City, UT 84112-5330
>>>> ph:801-587-7707
>>>> 
>>>> ________________________________________
>>>> From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>>>> Sent: Thursday, September 19, 2013 11:49 AM
>>>> To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>>>> Subject: maker2 scripts for functional annotation
>>>> 
>>>> Dr. Yandell,
>>>> 
>>>> We were recently evaluating maker2 for annotation and going through 
>>>> the maker tutorial from 2012.
>>>> 
>>>> http://gmod.org/wiki/MAKER_Tutorial_2012
>>>> 
>>>> The tutorial makes references to some scripts that we couldn?t find 
>>>> in the current release.  We were looking for scripts like 
>>>> gff3_preds2models to convert match/match_part format into annotations 
>>>> with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did 
>>>> not have the most up to date version.
>>>> 
>>>> In addition to getting accurate gene annotations, I was looking for a 
>>>> solution to get functional assignments.  I see that there are some 
>>>> scripts like maker_functional_fasta that may help, but I was 
>>>> wondering what you would recommend.
>>>> 
>>>> Thanks,
>>>> 
>>>> Corban & Xia
>>>> 
>>>> This communication is for use by the intended recipient and contains 
>>>> information that may be Privileged, confidential or copyrighted under 
>>>> applicable law. If you are not the intended recipient, you are hereby 
>>>> formally notified that any use, copying or distribution of this 
>>>> e-mail, in whole or in part, is strictly prohibited. Please notify 
>>>> the sender by return e-mail and delete this e-mail from your system.
>>>> Unless explicitly and conspicuously designated as "E-Contract 
>>>> Intended", this e-mail does not constitute a contract offer, a 
>>>> contract amendment, or an acceptance of a contract offer. This e-mail 
>>>> does not constitute a consent to the use of sender's contact 
>>>> information for direct marketing purposes or for transfers of data to 
>>>> third parties.
>>>> 
>>>> The dupont.com web address will continue in use for a transitional 
>>>> period for communications sent or received on behalf of DuPont 
>>>> Performance Coatings., which is not affiliated in any way with the 
>>>> DuPont Company.
>>>> 
>>>> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>>> Korean
>>>> 
>>>>         http://www.DuPont.com/corp/email_disclaimer.html
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>> r
>>>> g
>>> 
>>> 
>>> 
>>> This communication is for use by the intended recipient and contains 
>>> information that may be Privileged, confidential or copyrighted under 
>>> applicable law. If you are not the intended recipient, you are hereby 
>>> formally notified that any use, copying or distribution of this 
>>> e-mail, in whole or in part, is strictly prohibited. Please notify the 
>>> sender by return e-mail and delete this e-mail from your system. 
>>> Unless explicitly and conspicuously designated as "E-Contract 
>>> Intended", this e-mail does not constitute a contract offer, a 
>>> contract amendment, or an acceptance of a contract offer. This e-mail 
>>> does not constitute a consent to the use of sender's contact 
>>> information for direct marketing purposes or for transfers of data to third parties.
>>> 
>>> The dupont.com<http://dupont.com/> web address will continue in use 
>>> for a transitional period for communications sent or received on 
>>> behalf of DuPont Performance Coatings., which is not affiliated in any 
>>> way with the DuPont Company.
>>> 
>>> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese 
>>> Korean
>>> 
>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>> 
>> 
>> 
>> 
>> This communication is for use by the intended recipient and contains 
>> information that may be Privileged, confidential or copyrighted under 
>> applicable law. If you are not the intended recipient, you are hereby 
>> formally notified that any use, copying or distribution of this e-mail, 
>> in whole or in part, is strictly prohibited. Please notify the sender 
>> by return e-mail and delete this e-mail from your system. Unless 
>> explicitly and conspicuously designated as "E-Contract Intended", this 
>> e-mail does not constitute a contract offer, a contract amendment, or 
>> an acceptance of a contract offer. This e-mail does not constitute a 
>> consent to the use of sender's contact information for direct marketing 
>> purposes or for transfers of data to third parties.
>> 
>> The dupont.com<http://dupont.com/> web address will continue in use for 
>> a transitional period for communications sent or received on behalf of 
>> DuPont Performance Coatings., which is not affiliated in any way with 
>> the DuPont Company.
>> 
>> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  
>> Korean
>> 
>>          http://www.DuPont.com/corp/email_disclaimer.html
>> 
> 
> 
> 
> This communication is for use by the intended recipient and contains
> information that may be Privileged, confidential or copyrighted under
> applicable law. If you are not the intended recipient, you are hereby
> formally notified that any use, copying or distribution of this e-mail,
> in whole or in part, is strictly prohibited. Please notify the sender by
> return e-mail and delete this e-mail from your system. Unless explicitly
> and conspicuously designated as "E-Contract Intended", this e-mail does
> not constitute a contract offer, a contract amendment, or an acceptance
> of a contract offer. This e-mail does not constitute a consent to the
> use of sender's contact information for direct marketing purposes or for
> transfers of data to third parties.
> 
> The dupont.com<http://dupont.com/> web address will continue in use for a
> transitional period for communications sent or received on behalf of DuPont
> Performance Coatings., which is not affiliated in any way with the DuPont Company.
> 
> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean
> 
>           http://www.DuPont.com/corp/email_disclaimer.html
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From Xia.Cao at dupont.com  Wed Oct  2 11:51:26 2013
From: Xia.Cao at dupont.com (Xia.Cao at dupont.com)
Date: Wed, 2 Oct 2013 17:51:26 +0000
Subject: [maker-devel] maker2 scripts for functional annotation
In-Reply-To: <E9DC8DC1-8E1F-42E7-94CC-5D58EF0A1F21@genetics.utah.edu>
References: <AAF36CDE29C45F45AE125A1D13F5D675ADFFC0@033-CH1MPN2-063.033d.mgd.msft.net>
	<CE709D72.EF15%carsonhh@gmail.com>
	<AAF36CDE29C45F45AE125A1D13F5D675AE20C9@033-CH1MPN2-063.033d.mgd.msft.net>
	<E9DC8DC1-8E1F-42E7-94CC-5D58EF0A1F21@genetics.utah.edu>
Message-ID: <AAF36CDE29C45F45AE125A1D13F5D675AE2175@033-CH1MPN2-063.033d.mgd.msft.net>

Hi Barry,

Thank you very much for the message and suggestions. It's really helpful to us.  We will do some tests to see how we can take advantage of Maker2  to produce high-quality gene models from our assembled genome.

Thank you again,
Xia


From: Barry Moore [mailto:barry.moore at genetics.utah.edu]
Sent: Wednesday, October 02, 2013 1:21 PM
To: CAO, XIA
Cc: carsonhh at gmail.com; maker-devel at yandell-lab.org; RIVERA, CORBAN GREGORY
Subject: Re: [maker-devel] maker2 scripts for functional annotation

Hi Xia,

You can use EST evidence from other strains/species.  The considerations are as follows:  When you pass EST (or mRNASeq based transcripts) evidence MAKER uses blastn to align those with alignment parameters that assume they sequences will align easily with almost perfect identity - this is fast.  If you use EST/mRNA evidence from another species MAKER uses tblastx to compare the RNA evidence to the assembly, both translated into protein space - this works fine, but it is slow and often doesn't get you much more evidence than you could have gotten from proteins as evidence.  If you believe that you're other strain should have very little divergence in sequence at the nt level then you could experiment with passing EST/mRNA evidence as est in the control file.  Consider this an experiment, do it on a few contigs and examine the results carefully and skeptically.  If it works well, that would be the way to go because you've get better UTRs, but if it doesn't you'll see that you get little support for models because sequence divergence was too much for good alignment.  In that case you'll need to use alt_est and this will be slower and you'll likely get little in the way of support for UTRs - in this case as well, do a few contigs and examine the output carefully to see if the additional alignment time with tblastx is worth it in your case.

Barry


On Oct 2, 2013, at 8:40 AM, <Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>>
 wrote:


Hi Carson,

Thank you for your quick and kind reply. One more question here. If we don't have EST evidence for the strain we sequenced/assembled, will it be ok to provide some EST evidence that is from some other strains which are close to the one we are trying to annotate? Could you please let us know how this will affect performance of maker2?

Thank you again.

Best,
Xia

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Wednesday, October 02, 2013 10:15 AM
To: CAO, XIA
Cc: myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker2 scripts for functional annotation

It still works, but it will be reduced.  Without ESTs you won't get any UTR prediction, also you will be limited by how well the protein set matches to the genes.  If you use the protein set of a close relative you will capture most things.  You will probably capture 80-95% of what you would by also including ESTs.  It all depending on how different the species in the proteins evidence file are compared to the the species being annotated.

--Carson

On 10/1/13 3:00 PM, "Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>" <Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>> wrote:


Hi Carson,

Thank you for your message and your kind help. Now conversion from
match/match_part to gene/mRNA/exons/CDS works well after blanking out
some options in control file.

I have one more question about maker2. In case we don't have EST
evidence (set of ESTs or assembled mRNA-seq in fasta format) for a
genome, does
maker2 function? If it does function, could you please let me know the
performance of maker2 without providing EST evidence compared to the
one with EST evidence?

Thank you  again and I look forward to hearing from you.

Best,
Xia




-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Wednesday, September 25, 2013 10:36 AM
To: CAO, XIA; myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>; RIVERA, CORBAN GREGORY;
maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker2 scripts for functional annotation

If it is launching predictors then you have snap hmm or
augustus_species set.  You ned to blank out all other options in the
control files (including repeat masking options, proteins, ESTs, etc.)
when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else
those other programs will run.

--Carson


On 9/25/13 10:31 AM, "Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>" <Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>> wrote:

Hi Carson,

Thank you for the message and your kind help. We tested maker2 by
setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .
But it seemed maker2 started to launch all predictors again and it
took long time to finish. I wonder if there is any way that we can
directly get gene/mRNA/exons/CDS gff file without re-running maker2 to
convert match/match_part features into gene/mRNA/exons/CDS.

Thanks,
Xia

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Thursday, September 19, 2013 5:58 PM
To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY;
maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker2 scripts for functional annotation

Hello Corban & Xia,

Some scripts like gff3_preds2models are deprecated.  To get the same
result as was offered by gff3_preds2models, just give your
match/match_part features to pref_gff= in the maker_opts.ctl file, set
keep_preds=1, and run with all other options and predictors turned off.
The final MAKER result will be your match/match_part features
converted into gene/mRNA/exons/CDS.

For functional annotation, you can use Interproscan, BLASTP against
UniProt, or BALST2GO.  My preference is to use InterProScan to add GO
terms and proteins domains via the ipr_update_gff and iprscan2gff3
scripts.  Then add putative gene functions via BLASTP to UniProt and
maker_functional_fasta and maker_functional_gff scripts.

Go ahead and take a look and that those tools and let me know if you
have any questions or need help you configuring them.

Thanks,
Carson


On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>> wrote:

Hi  Corban & Xia,


I've forwarded your question along to the MAKER_dev list, were you
can get speedy answers to your maker related questions. Thanks for
using MAKER.

--mark


Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of
Human Genetics University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com> [Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>]
Sent: Thursday, September 19, 2013 11:49 AM
To: Mark Yandell; Corban-Gregory.Rivera at dupont.com<mailto:Corban-Gregory.Rivera at dupont.com>
Subject: maker2 scripts for functional annotation

Dr. Yandell,

We were recently evaluating maker2 for annotation and going through
the maker tutorial from 2012.

http://gmod.org/wiki/MAKER_Tutorial_2012

The tutorial makes references to some scripts that we couldn?t find
in the current release.  We were looking for scripts like
gff3_preds2models to convert match/match_part format into annotations
with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did
not have the most up to date version.

In addition to getting accurate gene annotations, I was looking for a
solution to get functional assignments.  I see that there are some
scripts like maker_functional_fasta that may help, but I was
wondering what you would recommend.

Thanks,

Corban & Xia

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--------------------------------------------
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From cjfields at illinois.edu  Thu Oct  3 12:44:07 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 3 Oct 2013 18:44:07 +0000
Subject: [maker-devel] NFSLock problem
Message-ID: <B9943BBA-BEFF-4B23-A6B8-7581247F3C95@illinois.edu>

I have a MAKER job running that seems to be stalled on a failed scaffold.  It's running via MPI (MAKER v2.28, openMPI 1.6.3), that appears to have worked successfully for the most part.  This is a run that only uses transcriptome and protein information in order to get a decent dseat of 

The failed scaffold seems to be holding the job from completion.  There does seem to be changes, but mainly they are on the NFSLock files:

./.NFSLock.gi_lock.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.282.start.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.281.end.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.281.end.blastn.holdover.NFSLock.STACK

Everything else seems to have completed.  

I have seen a few issues re: NFS locking problems, would this be related?  Should I stop the job?  

We're running GPFS for our NFS.  Here's 'mount':

-system-specific-4.1$ mount
/dev/sda5 on / type ext4 (rw)
proc on /proc type proc (rw)
sysfs on /sys type sysfs (rw)
devpts on /dev/pts type devpts (rw,gid=5,mode=620)
tmpfs on /dev/shm type tmpfs (rw)
/dev/sda1 on /boot type ext4 (rw)
/dev/sdb1 on /export type ext4 (rw)
/dev/sda2 on /var type ext4 (rw)
tmpfs on /var/lib/ganglia/rrds type tmpfs (rw,size=6180842000,gid=99,uid=99)
none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
nfsd on /proc/fs/nfsd type nfsd (rw)
/dev/IGBHOME0 on /home type gpfs (rw,mtime,dev=IGBHOME0)
128.174.124.79:/shares/group on /archive/group type nfs (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,proto=tcp,mountproto=tcp,addr=128.174.124.79)
128.174.124.79:/shares/CBC on /archive/CBC type nfs (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,proto=tcp,mountproto=tcp,addr=128.174.124.79)

chris


From carsonhh at gmail.com  Thu Oct  3 12:45:37 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 03 Oct 2013 14:45:37 -0400
Subject: [maker-devel] NFSLock problem
In-Reply-To: <B9943BBA-BEFF-4B23-A6B8-7581247F3C95@illinois.edu>
Message-ID: <CE73336F.F347%carsonhh@gmail.com>

Stop the job and restart it.  No need to delete anything.  Just restart it.

Thanks,
Carson


On 10/3/13 2:44 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

>I have a MAKER job running that seems to be stalled on a failed scaffold.
> It's running via MPI (MAKER v2.28, openMPI 1.6.3), that appears to have
>worked successfully for the most part.  This is a run that only uses
>transcriptome and protein information in order to get a decent dseat of
>
>The failed scaffold seems to be holding the job from completion.  There
>does seem to be changes, but mainly they are on the NFSLock files:
>
>./.NFSLock.gi_lock.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.282.start.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.end.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.end.blastn.holdover.NFSLock.STACK
>
>Everything else seems to have completed.
>
>I have seen a few issues re: NFS locking problems, would this be related?
> Should I stop the job?
>
>We're running GPFS for our NFS.  Here's 'mount':
>
>-system-specific-4.1$ mount
>/dev/sda5 on / type ext4 (rw)
>proc on /proc type proc (rw)
>sysfs on /sys type sysfs (rw)
>devpts on /dev/pts type devpts (rw,gid=5,mode=620)
>tmpfs on /dev/shm type tmpfs (rw)
>/dev/sda1 on /boot type ext4 (rw)
>/dev/sdb1 on /export type ext4 (rw)
>/dev/sda2 on /var type ext4 (rw)
>tmpfs on /var/lib/ganglia/rrds type tmpfs
>(rw,size=6180842000,gid=99,uid=99)
>none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
>sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
>nfsd on /proc/fs/nfsd type nfsd (rw)
>/dev/IGBHOME0 on /home type gpfs (rw,mtime,dev=IGBHOME0)
>128.174.124.79:/shares/group on /archive/group type nfs
>(rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>roto=tcp,mountproto=tcp,addr=128.174.124.79)
>128.174.124.79:/shares/CBC on /archive/CBC type nfs
>(rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>roto=tcp,mountproto=tcp,addr=128.174.124.79)
>
>chris
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From cjfields at illinois.edu  Thu Oct  3 20:45:29 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 4 Oct 2013 02:45:29 +0000
Subject: [maker-devel] NFSLock problem
In-Reply-To: <CE73336F.F347%carsonhh@gmail.com>
References: <CE73336F.F347%carsonhh@gmail.com>
Message-ID: <EB3895BA-F1EF-4F14-813F-233D1B4269AB@illinois.edu>

Carson,

Took a couple of restarts but finally processed through.  I saw a prior email on the mail list where you mentioned this could be due to failed jobs hanging things up; I may set up my next job to allow one processor for logging into the nodes in case there is a similar problem, maybe try to track this down.

chris

On Oct 3, 2013, at 1:45 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Stop the job and restart it.  No need to delete anything.  Just restart it.
> 
> Thanks,
> Carson
> 
> 
> On 10/3/13 2:44 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> 
>> I have a MAKER job running that seems to be stalled on a failed scaffold.
>> It's running via MPI (MAKER v2.28, openMPI 1.6.3), that appears to have
>> worked successfully for the most part.  This is a run that only uses
>> transcriptome and protein information in order to get a decent dseat of
>> 
>> The failed scaffold seems to be holding the job from completion.  There
>> does seem to be changes, but mainly they are on the NFSLock files:
>> 
>> ./.NFSLock.gi_lock.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.282.start.blastn.holdover.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.281.end.blastn.holdover.NFSLock
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
>> ./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>> ck.KB913038%2E1.281.end.blastn.holdover.NFSLock.STACK
>> 
>> Everything else seems to have completed.
>> 
>> I have seen a few issues re: NFS locking problems, would this be related?
>> Should I stop the job?
>> 
>> We're running GPFS for our NFS.  Here's 'mount':
>> 
>> -system-specific-4.1$ mount
>> /dev/sda5 on / type ext4 (rw)
>> proc on /proc type proc (rw)
>> sysfs on /sys type sysfs (rw)
>> devpts on /dev/pts type devpts (rw,gid=5,mode=620)
>> tmpfs on /dev/shm type tmpfs (rw)
>> /dev/sda1 on /boot type ext4 (rw)
>> /dev/sdb1 on /export type ext4 (rw)
>> /dev/sda2 on /var type ext4 (rw)
>> tmpfs on /var/lib/ganglia/rrds type tmpfs
>> (rw,size=6180842000,gid=99,uid=99)
>> none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
>> sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
>> nfsd on /proc/fs/nfsd type nfsd (rw)
>> /dev/IGBHOME0 on /home type gpfs (rw,mtime,dev=IGBHOME0)
>> 128.174.124.79:/shares/group on /archive/group type nfs
>> (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>> roto=tcp,mountproto=tcp,addr=128.174.124.79)
>> 128.174.124.79:/shares/CBC on /archive/CBC type nfs
>> (rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>> roto=tcp,mountproto=tcp,addr=128.174.124.79)
>> 
>> chris
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 




From felix.bemm at uni-wuerzburg.de  Fri Oct  4 01:10:08 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Fri, 04 Oct 2013 09:10:08 +0200
Subject: [maker-devel] Contigs failing - could not make datastore directory
Message-ID: <524E69D0.1090905@uni-wuerzburg.de>

Hi,

I have a problem with Contigs failing like this:

examining contents of the fasta file and run log
ERROR: could not make datastore directory
--> rank=11, hostname=r5n04
ERROR: Failed while examining contents of the fasta file and run log
ERROR: Chunk failed at level:0, tier_type:0
FAILED CONTIG:MA_gen_v8.05_c31675

There is enough space available on both the storage device and the tmp 
device that is being used. The datastore log files looks like this:

MA_gen_v8.05_c1149              FAILED
MA_gen_v8.05_c1153              FAILED
MA_gen_v8.05_c1154              FAILED
MA_gen_v8.05_c1155              FAILED
MA_gen_v8.05_c1156              FAILED

Since there is no datastore for this contigs, I can not provide any more 
informationen. Approx. 1/3 of the contigs were annotated, after that 
maker started to fail. It kept running for a while and finishing some of 
the contigs in the second or third try like this:

MA_gen_v8.05_c4443		FAILED
MA_gen_v8.05_c4443		FAILED
MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	STARTED
MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/ 
FINISHED

Any ideas what can cause this problems?

Best regards
Felix

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Fri Oct  4 12:15:35 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 04 Oct 2013 14:15:35 -0400
Subject: [maker-devel] Contigs failing - could not make datastore
 directory
In-Reply-To: <524E69D0.1090905@uni-wuerzburg.de>
Message-ID: <CE747D9A.F599%carsonhh@gmail.com>

Let me know what you find.  With some failures it's hard to identify the
problem especially with long running processes, which is why I made MAKER
restartable, so you can at least get completion by just launching again.

--Carson


On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi,
>
>I have a problem with Contigs failing like this:
>
>examining contents of the fasta file and run log
>ERROR: could not make datastore directory
>--> rank=11, hostname=r5n04
>ERROR: Failed while examining contents of the fasta file and run log
>ERROR: Chunk failed at level:0, tier_type:0
>FAILED CONTIG:MA_gen_v8.05_c31675
>
>There is enough space available on both the storage device and the tmp
>device that is being used. The datastore log files looks like this:
>
>MA_gen_v8.05_c1149              FAILED
>MA_gen_v8.05_c1153              FAILED
>MA_gen_v8.05_c1154              FAILED
>MA_gen_v8.05_c1155              FAILED
>MA_gen_v8.05_c1156              FAILED
>
>Since there is no datastore for this contigs, I can not provide any more
>informationen. Approx. 1/3 of the contigs were annotated, after that
>maker started to fail. It kept running for a while and finishing some of
>the contigs in the second or third try like this:
>
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	START
>ED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>FINISHED
>
>Any ideas what can cause this problems?
>
>Best regards
>Felix
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Fri Oct  4 12:21:42 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 04 Oct 2013 14:21:42 -0400
Subject: [maker-devel] Contigs failing - could not make datastore
 directory
In-Reply-To: <524E69D0.1090905@uni-wuerzburg.de>
Message-ID: <CE743B26.F369%carsonhh@gmail.com>

Hi Felix,

There are other potential issues as well, for example a file quota limit
set by your administrator or full local /tmp which will be unique to each
node and cannot be queried directly from the root node on a cluster.  On a
cluster one node may also not have the NFS location mounted.  Or it could
be system related, for example on ibrix NFS mounted systems you can get a
weird filesystem issue with ghost files and directories when using MAKER
that can neither be created nor deleted.  Try running the failed contigs
in a different directory (even if it's on the same disk).  Also what
version of MAKER are you using?

--Carson



On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi,
>
>I have a problem with Contigs failing like this:
>
>examining contents of the fasta file and run log
>ERROR: could not make datastore directory
>--> rank=11, hostname=r5n04
>ERROR: Failed while examining contents of the fasta file and run log
>ERROR: Chunk failed at level:0, tier_type:0
>FAILED CONTIG:MA_gen_v8.05_c31675
>
>There is enough space available on both the storage device and the tmp
>device that is being used. The datastore log files looks like this:
>
>MA_gen_v8.05_c1149              FAILED
>MA_gen_v8.05_c1153              FAILED
>MA_gen_v8.05_c1154              FAILED
>MA_gen_v8.05_c1155              FAILED
>MA_gen_v8.05_c1156              FAILED
>
>Since there is no datastore for this contigs, I can not provide any more
>informationen. Approx. 1/3 of the contigs were annotated, after that
>maker started to fail. It kept running for a while and finishing some of
>the contigs in the second or third try like this:
>
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443		FAILED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	START
>ED
>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>FINISHED
>
>Any ideas what can cause this problems?
>
>Best regards
>Felix
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From felix.bemm at uni-wuerzburg.de  Sat Oct  5 08:09:15 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Sat, 05 Oct 2013 16:09:15 +0200
Subject: [maker-devel] Contigs failing - could not make datastore
	directory
In-Reply-To: <CE743B26.F369%carsonhh@gmail.com>
References: <CE743B26.F369%carsonhh@gmail.com>
Message-ID: <52501D8B.2060301@uni-wuerzburg.de>

Hi Carson,

there is definitely no quota neither a full local tmp device. I changed 
to another tmp device, which is unfortunately residing on nfs but now it 
seems to work. I am using the latest version of maker (2.28). The 
complete job is running on a single machine with 32 mpi threads.

Bests
Felix

Am 04.10.2013 20:21, schrieb Carson Holt:
> Hi Felix,
>
> There are other potential issues as well, for example a file quota limit
> set by your administrator or full local /tmp which will be unique to each
> node and cannot be queried directly from the root node on a cluster.  On a
> cluster one node may also not have the NFS location mounted.  Or it could
> be system related, for example on ibrix NFS mounted systems you can get a
> weird filesystem issue with ghost files and directories when using MAKER
> that can neither be created nor deleted.  Try running the failed contigs
> in a different directory (even if it's on the same disk).  Also what
> version of MAKER are you using?
>
> --Carson
>
>
>
> On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>> Hi,
>>
>> I have a problem with Contigs failing like this:
>>
>> examining contents of the fasta file and run log
>> ERROR: could not make datastore directory
>> --> rank=11, hostname=r5n04
>> ERROR: Failed while examining contents of the fasta file and run log
>> ERROR: Chunk failed at level:0, tier_type:0
>> FAILED CONTIG:MA_gen_v8.05_c31675
>>
>> There is enough space available on both the storage device and the tmp
>> device that is being used. The datastore log files looks like this:
>>
>> MA_gen_v8.05_c1149              FAILED
>> MA_gen_v8.05_c1153              FAILED
>> MA_gen_v8.05_c1154              FAILED
>> MA_gen_v8.05_c1155              FAILED
>> MA_gen_v8.05_c1156              FAILED
>>
>> Since there is no datastore for this contigs, I can not provide any more
>> informationen. Approx. 1/3 of the contigs were annotated, after that
>> maker started to fail. It kept running for a while and finishing some of
>> the contigs in the second or third try like this:
>>
>> MA_gen_v8.05_c4443		FAILED
>> MA_gen_v8.05_c4443		FAILED
>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	START
>> ED
>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>> FINISHED
>>
>> Any ideas what can cause this problems?
>>
>> Best regards
>> Felix
>>
>> --
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From jfierst at uoregon.edu  Fri Oct  4 11:06:36 2013
From: jfierst at uoregon.edu (Janna Fierst)
Date: Fri, 4 Oct 2013 10:06:36 -0700
Subject: [maker-devel] Fwd:  exon/intron boundaries
In-Reply-To: <CAGoyurYe_c3Cd6KK-z0t0WqYmGGh5VQsSZXo9_=Lt9MGMSz=kA@mail.gmail.com>
References: <CAGoyuraVoRp94vbk_mb1qLzELeXSbeybGwkvgFx-6smEVt_DcQ@mail.gmail.com>
	<CE411E31.998A%carsonhh@gmail.com>
	<CAGoyurYe_c3Cd6KK-z0t0WqYmGGh5VQsSZXo9_=Lt9MGMSz=kA@mail.gmail.com>
Message-ID: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>

Hi,

thanks for your reply- I have been going through our annotations in detail
and trying different parameter sets, and I think I have identified what is
going on but I'm not sure how to set the MAKER2 parameters for our
situation. We are working with a species of Caenorhabditid worm and there
are long gene-dense blocks that are being incorrectly annotated as large
single genes instead of several smaller closely spaced genes. The protein
alignments (tblastx and protein2genome) show very clearly where the
exon/intron boundaries are and in most cases agree with the augustus
predictions. The assembled cufflinks output (through blastn, est2genome and
est_gff:cufflinks) does not agree in some locations; I think this may be
because in some cases the UTR nearly overlaps adjacent genes.

I have included a screenshot of an annotated region viewed in apollo to try
to show this. The large gene in the middle is actually 7 different genes
that are extremely close together and MAKER2 is collapsing them into a
single gene. I tried running without any RNASeq/cufflinks data and MAKER2
annotates the region as two genes instead of one, but I can't get it to
recognize the 7 as different genes. I have retrained SNAP but we have not
been able to successfully train Augustus, we are currently using the
default caenhorhabditis species model. I also included a species specific
repeat library. I tried setting correct_est_fusion=1 and reducing
pred_flank but these changes appear to really alter the annotations and we
end up annotating almost nothing. I also tried setting est2genome=0 to
decrease the influence of the cufflinks assembly but it didn't appear to
help. There are some very large introns in these genes so I haven't tried
yet decreasing the maximum intron size because I'm concerned this may
generate too many split genes instead of our current merged gene problem.
Thanks for your help, any advice is greatly appreciated! -Janna Fierst


On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Are you getting gene fusions or just more exons?  Gene fusions can be
> reduced by setting correct_est_fusion=1, or reducing pred_flank, although
> reducing pred_flank can cause other issues (but those generally only appear
> if setting the value below below 150).  Also if you have the maximum intron
> size set to high (split_hit option), you may also be generating bridging
> alignments that make evidence align across distant paralogous genes as well
> (this can result in gene merging)
>
> You should also look at your results manually in a viewer like Apollo.
>  Then see if the extra exons are supported by something such as protein
> alignments from another species.  If this is the case, you may have a
> poorly annotated protein set that is being used as evidence that is
> carrying over it's erroneous exons into the species you are annotating.  If
> the extra  exons are supported by EST evidence, then perhaps you should try
> and rebuild the EST assembly (for example trinity has an option to use a
> Jarccardian similarity coefficient to avoid fusing transcripts).
>
> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
> produce any of the models itself (it is a pipeline not a predictor).  The
> models are all generated using these other algorithms, MAKER just feeds
> them hints based on protein and transcript alignments, so making sure
> training is sufficient is important for those programs to produce their
> best models.
>
> Finally make sure your repeat database is sufficient, you may need to
> generate a species specific repeat library using something like
> RepeatModeler.  Repeats can end up being included as extra exons in gene
> models because they may contain reading frames the do code for proteins
> (I.e. reverse transcriptases).
>
> If you have any questions on any of the above, just let us know.
>
> Thanks,
> Carson
>
>
> From: Janna Fierst <jfierst at uoregon.edu>
> Date: Monday, August 26, 2013 2:54 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] exon/intron boundaries
>
> Hi,
>
> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
> initial results appear fairly good but we seem to be be annotating too many
> exons for multiple genes. I was wondering which parameters should be tuned
> to change the threshold for exon/intron boundaries? Thanks for your help
> -Janna Fierst
>  _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From jfierst at uoregon.edu  Sat Oct  5 16:18:52 2013
From: jfierst at uoregon.edu (Janna Fierst)
Date: Sat, 5 Oct 2013 15:18:52 -0700
Subject: [maker-devel] Fwd:  exon/intron boundaries
In-Reply-To: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
References: <CAGoyuraVoRp94vbk_mb1qLzELeXSbeybGwkvgFx-6smEVt_DcQ@mail.gmail.com>
	<CE411E31.998A%carsonhh@gmail.com>
	<CAGoyurYe_c3Cd6KK-z0t0WqYmGGh5VQsSZXo9_=Lt9MGMSz=kA@mail.gmail.com>
	<CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
Message-ID: <CAGoyurYHu9ir90T2-xhBxDyv_xVY5=AGFHJJL3Fu0o2fxtvqOg@mail.gmail.com>

Hi,

thanks for your reply- I have been going through our annotations in detail
and trying different parameter sets, and I think I have identified what is
going on but I'm not sure how to set the MAKER2 parameters for our
situation. We are working with a species of Caenorhabditid worm and there
are long gene-dense blocks that are being incorrectly annotated as large
single genes instead of several smaller closely spaced genes. The protein
alignments (tblastx and protein2genome) show very clearly where the
exon/intron boundaries are and in most cases agree with the augustus
predictions. The assembled cufflinks output (through blastn, est2genome and
est_gff:cufflinks) does not agree in some locations; I think this may be
because in some cases the UTR nearly overlaps adjacent genes.

I have included a screenshot of an annotated region viewed in apollo to try
to show this. The large gene in the middle is actually 7 different genes
that are extremely close together and MAKER2 is collapsing them into a
single gene. I tried running without any RNASeq/cufflinks data and MAKER2
annotates the region as two genes instead of one, but I can't get it to
recognize the 7 as different genes. I have retrained SNAP but we have not
been able to successfully train Augustus, we are currently using the
default caenhorhabditis species model. I also included a species specific
repeat library. I tried setting correct_est_fusion=1 and reducing
pred_flank but these changes appear to really alter the annotations and we
end up annotating almost nothing. I also tried setting est2genome=0 to
decrease the influence of the cufflinks assembly but it didn't appear to
help. There are some very large introns in these genes so I haven't tried
yet decreasing the maximum intron size because I'm concerned this may
generate too many split genes instead of our current merged gene problem.
Thanks for your help, any advice is greatly appreciated! -Janna Fierst


On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Are you getting gene fusions or just more exons?  Gene fusions can be
> reduced by setting correct_est_fusion=1, or reducing pred_flank, although
> reducing pred_flank can cause other issues (but those generally only appear
> if setting the value below below 150).  Also if you have the maximum intron
> size set to high (split_hit option), you may also be generating bridging
> alignments that make evidence align across distant paralogous genes as well
> (this can result in gene merging)
>
> You should also look at your results manually in a viewer like Apollo.
>  Then see if the extra exons are supported by something such as protein
> alignments from another species.  If this is the case, you may have a
> poorly annotated protein set that is being used as evidence that is
> carrying over it's erroneous exons into the species you are annotating.  If
> the extra  exons are supported by EST evidence, then perhaps you should try
> and rebuild the EST assembly (for example trinity has an option to use a
> Jarccardian similarity coefficient to avoid fusing transcripts).
>
> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
> produce any of the models itself (it is a pipeline not a predictor).  The
> models are all generated using these other algorithms, MAKER just feeds
> them hints based on protein and transcript alignments, so making sure
> training is sufficient is important for those programs to produce their
> best models.
>
> Finally make sure your repeat database is sufficient, you may need to
> generate a species specific repeat library using something like
> RepeatModeler.  Repeats can end up being included as extra exons in gene
> models because they may contain reading frames the do code for proteins
> (I.e. reverse transcriptases).
>
> If you have any questions on any of the above, just let us know.
>
> Thanks,
> Carson
>
>
> From: Janna Fierst <jfierst at uoregon.edu>
> Date: Monday, August 26, 2013 2:54 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] exon/intron boundaries
>
> Hi,
>
> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
> initial results appear fairly good but we seem to be be annotating too many
> exons for multiple genes. I was wondering which parameters should be tuned
> to change the threshold for exon/intron boundaries? Thanks for your help
> -Janna Fierst
>  _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From myandell at genetics.utah.edu  Mon Oct  7 05:36:53 2013
From: myandell at genetics.utah.edu (Mark Yandell)
Date: Mon, 7 Oct 2013 11:36:53 +0000
Subject: [maker-devel] maker apollo error
In-Reply-To: <8687323557146056ef885dd8a1bf2ea4@buzonweb.us.es>
References: <8687323557146056ef885dd8a1bf2ea4@buzonweb.us.es>
Message-ID: <7A60AB257EFF2B48B1F4C814817EA05365E66B3C@mxb2.hg.genetics.utah.edu>


Hi Gabriel,

I've forwarded your request on to the MAKER email list...

cheers,

--mark

Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: ggpozo at us.es [ggpozo at us.es]
Sent: Monday, October 07, 2013 2:49 AM
To: Mark Yandell
Subject: maker apollo error

Dear Dr. Yandell,

First, thank you very much for provide us such a great tool as MAKER. I am traying to install it in my Linux system, everything is ok, however when I try to instal Apollo with ./Build apollo...

Downloading apollo...
--2013-10-07 10:45:37--  http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 302 Found
Localizaci?n: http://sourceforge.net/p/gmod/svn/ [siguiendo]
--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/
Resolviendo sourceforge.net... 216.34.181.60
Connecting to sourceforge.net|216.34.181.60|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 302 Found
Localizaci?n: http://sourceforge.net/p/gmod/svn/HEAD/tree/ [siguiendo]
--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/HEAD/tree/
Connecting to sourceforge.net|216.34.181.60|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 200 OK
Longitud: 37730 (37K) [text/html]
Saving to: `/home/maker/src/../exe/apollo.tar.gz'

100%[==================================================================================================================================>] 37.730      92,1K/s   in 0,4s

2013-10-07 10:45:40 (92,1 KB/s) - `/home/maker/src/../exe/apollo.tar.gz' saved [37730/37730]

Unpacking apollo tarball...

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now


ERROR: Failed installing apollo, now cleaning installation path...
You may need to install apollo manually.



It seems that the http direction  in locations file is wrong, Apollo has changed its version and now Apollo is integrated in Apolloweb, may be this the problem.



I would greatly appreciate any help you can give me.

Thank you very much.



Dr. Gabriel Gutierrez

Department of Genetcis

University of Seville

Spain




From carsonhh at gmail.com  Mon Oct  7 07:20:17 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 09:20:17 -0400
Subject: [maker-devel] Fwd:  exon/intron boundaries
In-Reply-To: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
Message-ID: <CE782A71.F621%carsonhh@gmail.com>

Hi Janna,

There are a couple of things to do.  Download the maker-2.29p-beta from the
lab website.  This includes some changes made to improve the performance of
correct_est_fusion.  Whenever using the correct_est_fusion option, this also
reduces the influence of ESTs on annotation.  So normally you would need to
increase your protein dataset, but given that you have supplied 3 nematode
species and all of UniProt already you should probably be fine. But there is
one last thing you can do.  Instead of using cufflinks, try using trinity to
assemble the ESTs.  There is a Jaccard clip option that reducing merging
caused by overlapping UTR.  Between the trinity and correct_est_fusion you
should be able to really reduce the effect of those ESTs.

If those changes don't work there is one last option.  If you take the MAKER
results and filter them for SNAP and Augustus ab initio results
(match/match_part in the GFF3), then you can pass those in to the pred_gff
options.  Then turn snaphmm and augustus_species off in the control files.
Basically what this will do is turn MAKER's hint based prediction off and
force it to filter the ab intio results and select directly models from
there.  Since the merging is being caused by bad hints (merged transcripts
from mRNAseq) this would reduce that effect.  You will still need
correct_est_fusion=1 though to trim UTR coming from the merged transcripts,
because even though MAEKR can't process hints to rerun SNAP and Augustus
this way, it will try and add UTR using the EST evidence.

--Carson


From:  Janna Fierst <jfierst at uoregon.edu>
Date:  Friday, October 4, 2013 1:06 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Fwd:  exon/intron boundaries

Hi,

thanks for your reply- I have been going through our annotations in detail
and trying different parameter sets, and I think I have identified what is
going on but I'm not sure how to set the MAKER2 parameters for our
situation. We are working with a species of Caenorhabditid worm and there
are long gene-dense blocks that are being incorrectly annotated as large
single genes instead of several smaller closely spaced genes. The protein
alignments (tblastx and protein2genome) show very clearly where the
exon/intron boundaries are and in most cases agree with the augustus
predictions. The assembled cufflinks output (through blastn, est2genome and
est_gff:cufflinks) does not agree in some locations; I think this may be
because in some cases the UTR nearly overlaps adjacent genes.

I have included a screenshot of an annotated region viewed in apollo to try
to show this. The large gene in the middle is actually 7 different genes
that are extremely close together and MAKER2 is collapsing them into a
single gene. I tried running without any RNASeq/cufflinks data and MAKER2
annotates the region as two genes instead of one, but I can't get it to
recognize the 7 as different genes. I have retrained SNAP but we have not
been able to successfully train Augustus, we are currently using the default
caenhorhabditis species model. I also included a species specific repeat
library. I tried setting correct_est_fusion=1 and reducing pred_flank but
these changes appear to really alter the annotations and we end up
annotating almost nothing. I also tried setting est2genome=0 to decrease the
influence of the cufflinks assembly but it didn't appear to help. There are
some very large introns in these genes so I haven't tried yet decreasing the
maximum intron size because I'm concerned this may generate too many split
genes instead of our current merged gene problem. Thanks for your help, any
advice is greatly appreciated! -Janna Fierst


On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:
> Are you getting gene fusions or just more exons?  Gene fusions can be reduced
> by setting correct_est_fusion=1, or reducing pred_flank, although reducing
> pred_flank can cause other issues (but those generally only appear if setting
> the value below below 150).  Also if you have the maximum intron size set to
> high (split_hit option), you may also be generating bridging alignments that
> make evidence align across distant paralogous genes as well (this can result
> in gene merging)
> 
> You should also look at your results manually in a viewer like Apollo.  Then
> see if the extra exons are supported by something such as protein alignments
> from another species.  If this is the case, you may have a poorly annotated
> protein set that is being used as evidence that is carrying over it's
> erroneous exons into the species you are annotating.  If the extra  exons are
> supported by EST evidence, then perhaps you should try and rebuild the EST
> assembly (for example trinity has an option to use a Jarccardian similarity
> coefficient to avoid fusing transcripts).
> 
> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
> produce any of the models itself (it is a pipeline not a predictor).  The
> models are all generated using these other algorithms, MAKER just feeds them
> hints based on protein and transcript alignments, so making sure training is
> sufficient is important for those programs to produce their best models.
> 
> Finally make sure your repeat database is sufficient, you may need to generate
> a species specific repeat library using something like RepeatModeler.  Repeats
> can end up being included as extra exons in gene models because they may
> contain reading frames the do code for proteins (I.e. reverse transcriptases).
> 
> If you have any questions on any of the above, just let us know.
> 
> Thanks,
> Carson
> 
> 
> From:  Janna Fierst <jfierst at uoregon.edu>
> Date:  Monday, August 26, 2013 2:54 PM
> To:  <maker-devel at yandell-lab.org>
> Subject:  [maker-devel] exon/intron boundaries
> 
> Hi,
> 
> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
> initial results appear fairly good but we seem to be be annotating too many
> exons for multiple genes. I was wondering which parameters should be tuned to
> change the threshold for exon/intron boundaries? Thanks for your help -Janna
> Fierst
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak
> er-devel_yandell-lab.org


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

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From carsonhh at gmail.com  Mon Oct  7 08:12:24 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 10:12:24 -0400
Subject: [maker-devel] maker apollo error
In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05365E66B3C@mxb2.hg.genetics.utah.edu>
Message-ID: <CE783792.F640%carsonhh@gmail.com>

This was a location from GMOD for the older Apollo.  It looks like they've
dropped it, so it now points to nothing. Perhaps there is another location
that still has the old code I can get from Ed.

--Carson



On 10/7/13 7:36 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:

>
>Hi Gabriel,
>
>I've forwarded your request on to the MAKER email list...
>
>cheers,
>
>--mark
>
>Mark Yandell
>Professor of Human Genetics
>H.A. & Edna Benning Presidential Endowed Chair
>Eccles Institute of Human Genetics
>University of Utah
>15 North 2030 East, Room 2100
>Salt Lake City, UT 84112-5330
>ph:801-587-7707
>
>________________________________________
>From: ggpozo at us.es [ggpozo at us.es]
>Sent: Monday, October 07, 2013 2:49 AM
>To: Mark Yandell
>Subject: maker apollo error
>
>Dear Dr. Yandell,
>
>First, thank you very much for provide us such a great tool as MAKER. I
>am traying to install it in my Linux system, everything is ok, however
>when I try to instal Apollo with ./Build apollo...
>
>Downloading apollo...
>--2013-10-07 10:45:37--
>http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
>Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
>Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
>Petici?n HTTP enviada, esperando respuesta... 302 Found
>Localizaci?n: http://sourceforge.net/p/gmod/svn/ [siguiendo]
>--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/
>Resolviendo sourceforge.net... 216.34.181.60
>Connecting to sourceforge.net|216.34.181.60|:80... conectado.
>Petici?n HTTP enviada, esperando respuesta... 302 Found
>Localizaci?n: http://sourceforge.net/p/gmod/svn/HEAD/tree/ [siguiendo]
>--2013-10-07 10:45:38--  http://sourceforge.net/p/gmod/svn/HEAD/tree/
>Connecting to sourceforge.net|216.34.181.60|:80... conectado.
>Petici?n HTTP enviada, esperando respuesta... 200 OK
>Longitud: 37730 (37K) [text/html]
>Saving to: `/home/maker/src/../exe/apollo.tar.gz'
>
>100%[=====================================================================
>=============================================================>] 37.730
>  92,1K/s   in 0,4s
>
>2013-10-07 10:45:40 (92,1 KB/s) - `/home/maker/src/../exe/apollo.tar.gz'
>saved [37730/37730]
>
>Unpacking apollo tarball...
>
>gzip: stdin: not in gzip format
>tar: Child returned status 1
>tar: Error is not recoverable: exiting now
>
>
>ERROR: Failed installing apollo, now cleaning installation path...
>You may need to install apollo manually.
>
>
>
>It seems that the http direction  in locations file is wrong, Apollo has
>changed its version and now Apollo is integrated in Apolloweb, may be
>this the problem.
>
>
>
>I would greatly appreciate any help you can give me.
>
>Thank you very much.
>
>
>
>Dr. Gabriel Gutierrez
>
>Department of Genetcis
>
>University of Seville
>
>Spain
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Mon Oct  7 08:33:44 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 10:33:44 -0400
Subject: [maker-devel] Contigs failing - could not make datastore
 directory
In-Reply-To: <52501D8B.2060301@uni-wuerzburg.de>
Message-ID: <CE783CF2.F65A%carsonhh@gmail.com>

You can also try the 2.29 beta if you want (on the website).  Also when
MAKER exits, it tries to delete anything left behind in temporary folders,
so is it possible that it is creating space on exit after filling up /tmp?

Given that the issue seems to go away when you switch to another
directory, it suggests that this might be the kind of thing that is
specific to something about the current state of your your system.

Thanks,
Carson


On 10/5/13 10:09 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi Carson,
>
>there is definitely no quota neither a full local tmp device. I changed
>to another tmp device, which is unfortunately residing on nfs but now it
>seems to work. I am using the latest version of maker (2.28). The
>complete job is running on a single machine with 32 mpi threads.
>
>Bests
>Felix
>
>Am 04.10.2013 20:21, schrieb Carson Holt:
>> Hi Felix,
>>
>> There are other potential issues as well, for example a file quota limit
>> set by your administrator or full local /tmp which will be unique to
>>each
>> node and cannot be queried directly from the root node on a cluster.
>>On a
>> cluster one node may also not have the NFS location mounted.  Or it
>>could
>> be system related, for example on ibrix NFS mounted systems you can get
>>a
>> weird filesystem issue with ghost files and directories when using MAKER
>> that can neither be created nor deleted.  Try running the failed contigs
>> in a different directory (even if it's on the same disk).  Also what
>> version of MAKER are you using?
>>
>> --Carson
>>
>>
>>
>> On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Hi,
>>>
>>> I have a problem with Contigs failing like this:
>>>
>>> examining contents of the fasta file and run log
>>> ERROR: could not make datastore directory
>>> --> rank=11, hostname=r5n04
>>> ERROR: Failed while examining contents of the fasta file and run log
>>> ERROR: Chunk failed at level:0, tier_type:0
>>> FAILED CONTIG:MA_gen_v8.05_c31675
>>>
>>> There is enough space available on both the storage device and the tmp
>>> device that is being used. The datastore log files looks like this:
>>>
>>> MA_gen_v8.05_c1149              FAILED
>>> MA_gen_v8.05_c1153              FAILED
>>> MA_gen_v8.05_c1154              FAILED
>>> MA_gen_v8.05_c1155              FAILED
>>> MA_gen_v8.05_c1156              FAILED
>>>
>>> Since there is no datastore for this contigs, I can not provide any
>>>more
>>> informationen. Approx. 1/3 of the contigs were annotated, after that
>>> maker started to fail. It kept running for a while and finishing some
>>>of
>>> the contigs in the second or third try like this:
>>>
>>> MA_gen_v8.05_c4443		FAILED
>>> MA_gen_v8.05_c4443		FAILED
>>> 
>>>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	STA
>>>RT
>>> ED
>>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>>> FINISHED
>>>
>>> Any ideas what can cause this problems?
>>>
>>> Best regards
>>> Felix
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de





From felix.bemm at uni-wuerzburg.de  Mon Oct  7 10:40:12 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Mon, 07 Oct 2013 18:40:12 +0200
Subject: [maker-devel] Contigs failing - could not make datastore
	directory
In-Reply-To: <CE783CF2.F65A%carsonhh@gmail.com>
References: <CE783CF2.F65A%carsonhh@gmail.com>
Message-ID: <5252E3EC.6050908@uni-wuerzburg.de>

Do you have a changelog for 2.29b?

On 07.10.2013 16:33, Carson Holt wrote:
> You can also try the 2.29 beta if you want (on the website).  Also when
> MAKER exits, it tries to delete anything left behind in temporary folders,
> so is it possible that it is creating space on exit after filling up /tmp?

I will try to monitor that!

> Given that the issue seems to go away when you switch to another
> directory, it suggests that this might be the kind of thing that is
> specific to something about the current state of your your system.

I agree with that. Interestingly it happens with the only directory 
where I would not expect that.

> Thanks,
> Carson
>
>
> On 10/5/13 10:09 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>> Hi Carson,
>>
>> there is definitely no quota neither a full local tmp device. I changed
>> to another tmp device, which is unfortunately residing on nfs but now it
>> seems to work. I am using the latest version of maker (2.28). The
>> complete job is running on a single machine with 32 mpi threads.
>>
>> Bests
>> Felix
>>
>> Am 04.10.2013 20:21, schrieb Carson Holt:
>>> Hi Felix,
>>>
>>> There are other potential issues as well, for example a file quota limit
>>> set by your administrator or full local /tmp which will be unique to
>>> each
>>> node and cannot be queried directly from the root node on a cluster.
>>> On a
>>> cluster one node may also not have the NFS location mounted.  Or it
>>> could
>>> be system related, for example on ibrix NFS mounted systems you can get
>>> a
>>> weird filesystem issue with ghost files and directories when using MAKER
>>> that can neither be created nor deleted.  Try running the failed contigs
>>> in a different directory (even if it's on the same disk).  Also what
>>> version of MAKER are you using?
>>>
>>> --Carson
>>>
>>>
>>>
>>> On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a problem with Contigs failing like this:
>>>>
>>>> examining contents of the fasta file and run log
>>>> ERROR: could not make datastore directory
>>>> --> rank=11, hostname=r5n04
>>>> ERROR: Failed while examining contents of the fasta file and run log
>>>> ERROR: Chunk failed at level:0, tier_type:0
>>>> FAILED CONTIG:MA_gen_v8.05_c31675
>>>>
>>>> There is enough space available on both the storage device and the tmp
>>>> device that is being used. The datastore log files looks like this:
>>>>
>>>> MA_gen_v8.05_c1149              FAILED
>>>> MA_gen_v8.05_c1153              FAILED
>>>> MA_gen_v8.05_c1154              FAILED
>>>> MA_gen_v8.05_c1155              FAILED
>>>> MA_gen_v8.05_c1156              FAILED
>>>>
>>>> Since there is no datastore for this contigs, I can not provide any
>>>> more
>>>> informationen. Approx. 1/3 of the contigs were annotated, after that
>>>> maker started to fail. It kept running for a while and finishing some
>>>> of
>>>> the contigs in the second or third try like this:
>>>>
>>>> MA_gen_v8.05_c4443		FAILED
>>>> MA_gen_v8.05_c4443		FAILED
>>>>
>>>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	STA
>>>> RT
>>>> ED
>>>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>>>> FINISHED
>>>>
>>>> Any ideas what can cause this problems?
>>>>
>>>> Best regards
>>>> Felix
>>>>
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> --
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Mon Oct  7 11:25:34 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 07 Oct 2013 13:25:34 -0400
Subject: [maker-devel] maker apollo error
In-Reply-To: <14a642f3dc9cb615f048b70228bad3be@buzonweb.us.es>
Message-ID: <CE78668C.F68A%carsonhh@gmail.com>

Here is a new location for the source -->
http://sourceforge.net/code-snapshots/svn/g/gm/gmod/svn/gmod-svn-25291-apoll
o-trunk.zip

--Carson


From:  <ggpozo at us.es>
Date:  Monday, October 7, 2013 12:47 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Mark Yandell <myandell at genetics.utah.edu>,
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] maker apollo error

Thanks, I have modified the locations file pointing to a personal server
where I downloaded an old version of Apollo but it did not work, but if you
can get a new one I would try it again.

Thanks

Gabriel

 
El 07/10/2013 16:12, Carson Holt escribi?:
> This was a location from GMOD for the older Apollo.  It looks like they've
> dropped it, so it now points to nothing. Perhaps there is another location
> that still has the old code I can get from Ed.
> 
> --Carson
> 
> 
> 
> On 10/7/13 7:36 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
>> Hi Gabriel, I've forwarded your request on to the MAKER email list... cheers,
>> --mark Mark Yandell Professor of Human Genetics H.A. & Edna Benning
>> Presidential Endowed Chair Eccles Institute of Human Genetics University of
>> Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330
>> ph:801-587-7707 ________________________________________ From: ggpozo at us.es
>> [ggpozo at us.es] Sent: Monday, October 07, 2013 2:49 AM To: Mark Yandell
>> Subject: maker apollo error Dear Dr. Yandell, First, thank you very much for
>> provide us such a great tool as MAKER. I am traying to install it in my Linux
>> system, everything is ok, however when I try to instal Apollo with ./Build
>> apollo... Downloading apollo... --2013-10-07 10:45:37--
>> http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
>> Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
>> Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
>> Petici?n HTTP enviada, esperando respuesta... 302 Found Localizaci?n:
>> http://sourceforge.net/p/gmod/svn/ [siguiendo] --2013-10-07 10:45:38--
>> http://sourceforge.net/p/gmod/svn/ Resolviendo sourceforge.net...
>> 216.34.181.60 Connecting to sourceforge.net|216.34.181.60|:80... conectado.
>> Petici?n HTTP enviada, esperando respuesta... 302 Found Localizaci?n:
>> http://sourceforge.net/p/gmod/svn/HEAD/tree/ [siguiendo] --2013-10-07
>> 10:45:38-- http://sourceforge.net/p/gmod/svn/HEAD/tree/ Connecting to
>> sourceforge.net|216.34.181.60|:80... conectado. Petici?n HTTP enviada,
>> esperando respuesta... 200 OK Longitud: 37730 (37K) [text/html] Saving to:
>> `/home/maker/src/../exe/apollo.tar.gz'
>> 100%[=====================================================================
>> =============================================================>] 37.730
>> 92,1K/s in 0,4s 2013-10-07 10:45:40 (92,1 KB/s) -
>> `/home/maker/src/../exe/apollo.tar.gz' saved [37730/37730] Unpacking apollo
>> tarball... gzip: stdin: not in gzip format tar: Child returned status 1 tar:
>> Error is not recoverable: exiting now ERROR: Failed installing apollo, now
>> cleaning installation path... You may need to install apollo manually. It
>> seems that the http direction in locations file is wrong, Apollo has changed
>> its version and now Apollo is integrated in Apolloweb, may be this the
>> problem. I would greatly appreciate any help you can give me. Thank you very
>> much. Dr. Gabriel Gutierrez Department of Genetcis University of Seville
>> Spain _______________________________________________ maker-devel mailing
>> list maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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From ggpozo at us.es  Mon Oct  7 10:47:13 2013
From: ggpozo at us.es (ggpozo at us.es)
Date: Mon, 07 Oct 2013 18:47:13 +0200
Subject: [maker-devel] maker apollo error
In-Reply-To: <CE783792.F640%carsonhh@gmail.com>
References: <CE783792.F640%carsonhh@gmail.com>
Message-ID: <14a642f3dc9cb615f048b70228bad3be@buzonweb.us.es>

 

Thanks, I have modified the locations file pointing to a personal
server where I downloaded an old version of Apollo but it did not work,
but if you can get a new one I would try it again. 

Thanks 

Gabriel


El 07/10/2013 16:12, Carson Holt escribi?: 

> This was a location
from GMOD for the older Apollo. It looks like they've
> dropped it, so
it now points to nothing. Perhaps there is another location
> that still
has the old code I can get from Ed.
> 
> --Carson
> 
> On 10/7/13 7:36
AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:
> 
>> Hi Gabriel,
I've forwarded your request on to the MAKER email list... cheers, --mark
Mark Yandell Professor of Human Genetics H.A. & Edna Benning
Presidential Endowed Chair Eccles Institute of Human Genetics University
of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330
ph:801-587-7707 ________________________________________ From:
ggpozo at us.es [1] [ggpozo at us.es [2]] Sent: Monday, October 07, 2013 2:49
AM To: Mark Yandell Subject: maker apollo error Dear Dr. Yandell, First,
thank you very much for provide us such a great tool as MAKER. I am
traying to install it in my Linux system, everything is ok, however when
I try to instal Apollo with ./Build apollo... Downloading apollo...
--2013-10-07 10:45:37--
http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar [3]
Resolviendo gmod.svn.sourceforge.net... 216.34.181.65, 216.34.181.177
Connecting to gmod.svn.sourceforge.net|216.34.181.65|:80... conectado.
Petici?n HTTP enviada, esperando respuesta... 302 Found Localizaci?n:
http://sourceforge.net/p/gmod/svn/ [4] [siguiendo] --2013-10-07
10:45:38-- http://sourceforge.net/p/gmod/svn/ [5] Resolviendo
sourceforge.net... 216.34.181.60 Connecting to
sourceforge.net|216.34.181.60|:80... conectado. Petici?n HTTP enviada,
esperando respuesta... 302 Found Localizaci?n:
http://sourceforge.net/p/gmod/svn/HEAD/tree/ [6] [siguiendo]
--2013-10-07 10:45:38-- http://sourceforge.net/p/gmod/svn/HEAD/tree/ [7]
Connecting to sourceforge.net|216.34.181.60|:80... conectado. Petici?n
HTTP enviada, esperando respuesta... 200 OK Longitud: 37730 (37K)
[text/html] Saving to: `/home/maker/src/../exe/apollo.tar.gz'
100%[=====================================================================
=============================================================>] 37.730
92,1K/s in 0,4s 2013-10-07 10:45:40 (92,1 KB/s) -
`/home/maker/src/../exe/apollo.tar.gz' saved [37730/37730] Unpacking
apollo tarball... gzip: stdin: not in gzip format tar: Child returned
status 1 tar: Error is not recoverable: exiting now ERROR: Failed
installing apollo, now cleaning installation path... You may need to
install apollo manually. It seems that the http direction in locations
file is wrong, Apollo has changed its version and now Apollo is
integrated in Apolloweb, may be this the problem. I would greatly
appreciate any help you can give me. Thank you very much. Dr. Gabriel
Gutierrez Department of Genetcis University of Seville Spain
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com [8]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
[9]
 

Links:
------
[1] mailto:ggpozo at us.es
[2] mailto:ggpozo at us.es
[3]
http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar
[4]
http://sourceforge.net/p/gmod/svn/
[5]
http://sourceforge.net/p/gmod/svn/
[6]
http://sourceforge.net/p/gmod/svn/HEAD/tree/
[7]
http://sourceforge.net/p/gmod/svn/HEAD/tree/
[8]
mailto:maker-devel at box290.bluehost.com
[9]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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From felix.bemm at uni-wuerzburg.de  Sat Oct 12 09:06:52 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Sat, 12 Oct 2013 17:06:52 +0200
Subject: [maker-devel] Serious Start Codon Problem
Message-ID: <5259658C.4000102@uni-wuerzburg.de>

Hi,

I have a serious problems with maker annotations especially the start 
codon placement. It started happening with maker version 2.27! About 1/3 
of my genes are missing a proper start codon. When reviewing the GFF 
files gene predictors and est evidence standalone would predict the 
right gene structure including the start codon. I was thinking that this 
problem was somehow linked to my gene models but looking at their 
standalone prediction I discarded that theory. Just some stats about 
proteins with proper start codon (first column) and missing start codon 
(second column).

Maker		9268	4215
SNAP		16577	896
Genemark	18764	290

Numbers look the same when Augustus is used (currently retraining). 
Manually using EST's in Apollo often fixes the problems but I don't want 
to check > 4000 genes for this.

Do you have any idea what could cause such a problem? If you need some 
example gff files I can send you.

Best regards
Felix

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Sat Oct 12 09:48:29 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Sat, 12 Oct 2013 11:48:29 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <5259658C.4000102@uni-wuerzburg.de>
Message-ID: <CE7EE411.10C24%carsonhh@gmail.com>

This issue just came up this week on another e-mail as well.

One way to fix it, is to edit the Bio::Tools::CodonTable module from
BioPerl (use maker --debug to have maker print out the locations of all
modules it uses).  Such a hack should only be done as a temporary work
around.

You change line 256 from -->
---M---------------M---------------M----------------------------

To-->
-----------------------------------M----------------------------


Maker uses the BioPerl is_start_codon function to determine if the codon
used in a result it receives is acceptable or if it should look upstream
or downstream for a different one. Apparently there are actually 3
acceptable start codons in the standard codon table (2 rare ones and one
common), so making the edit removes the two rare ones from the list.

I'm also preparing a 2.30 release that exports a "strict" codon table to
the BioPerl module, that will be used by default and should fix the issue.

Thanks,
Carson



On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi,
>
>I have a serious problems with maker annotations especially the start
>codon placement. It started happening with maker version 2.27! About 1/3
>of my genes are missing a proper start codon. When reviewing the GFF
>files gene predictors and est evidence standalone would predict the
>right gene structure including the start codon. I was thinking that this
>problem was somehow linked to my gene models but looking at their
>standalone prediction I discarded that theory. Just some stats about
>proteins with proper start codon (first column) and missing start codon
>(second column).
>
>Maker		9268	4215
>SNAP		16577	896
>Genemark	18764	290
>
>Numbers look the same when Augustus is used (currently retraining).
>Manually using EST's in Apollo often fixes the problems but I don't want
>to check > 4000 genes for this.
>
>Do you have any idea what could cause such a problem? If you need some
>example gff files I can send you.
>
>Best regards
>Felix
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From felix.bemm at uni-wuerzburg.de  Sat Oct 12 10:16:06 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Sat, 12 Oct 2013 18:16:06 +0200
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE7EE411.10C24%carsonhh@gmail.com>
References: <CE7EE411.10C24%carsonhh@gmail.com>
Message-ID: <525975C6.4020403@uni-wuerzburg.de>

Thx Carson! Do you now when 2.30 will be available? Bests

On 12.10.2013 17:48, Carson Holt wrote:
> This issue just came up this week on another e-mail as well.
>
> One way to fix it, is to edit the Bio::Tools::CodonTable module from
> BioPerl (use maker --debug to have maker print out the locations of all
> modules it uses).  Such a hack should only be done as a temporary work
> around.
>
> You change line 256 from -->
> ---M---------------M---------------M----------------------------
>
> To-->
> -----------------------------------M----------------------------
>
>
> Maker uses the BioPerl is_start_codon function to determine if the codon
> used in a result it receives is acceptable or if it should look upstream
> or downstream for a different one. Apparently there are actually 3
> acceptable start codons in the standard codon table (2 rare ones and one
> common), so making the edit removes the two rare ones from the list.
>
> I'm also preparing a 2.30 release that exports a "strict" codon table to
> the BioPerl module, that will be used by default and should fix the issue.
>
> Thanks,
> Carson
>
>
>
> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>> Hi,
>>
>> I have a serious problems with maker annotations especially the start
>> codon placement. It started happening with maker version 2.27! About 1/3
>> of my genes are missing a proper start codon. When reviewing the GFF
>> files gene predictors and est evidence standalone would predict the
>> right gene structure including the start codon. I was thinking that this
>> problem was somehow linked to my gene models but looking at their
>> standalone prediction I discarded that theory. Just some stats about
>> proteins with proper start codon (first column) and missing start codon
>> (second column).
>>
>> Maker		9268	4215
>> SNAP		16577	896
>> Genemark	18764	290
>>
>> Numbers look the same when Augustus is used (currently retraining).
>> Manually using EST's in Apollo often fixes the problems but I don't want
>> to check > 4000 genes for this.
>>
>> Do you have any idea what could cause such a problem? If you need some
>> example gff files I can send you.
>>
>> Best regards
>> Felix
>>
>> --
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From carsonhh at gmail.com  Sat Oct 12 23:26:17 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 13 Oct 2013 01:26:17 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <525975C6.4020403@uni-wuerzburg.de>
Message-ID: <CE7FA55D.10C4B%carsonhh@gmail.com>

Before Wednesday, because after that I'm on a 6 day road trip, so I have
to have it wrapped up before I leave.

--Carson




On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Thx Carson! Do you now when 2.30 will be available? Bests
>
>On 12.10.2013 17:48, Carson Holt wrote:
>> This issue just came up this week on another e-mail as well.
>>
>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>> BioPerl (use maker --debug to have maker print out the locations of all
>> modules it uses).  Such a hack should only be done as a temporary work
>> around.
>>
>> You change line 256 from -->
>> ---M---------------M---------------M----------------------------
>>
>> To-->
>> -----------------------------------M----------------------------
>>
>>
>> Maker uses the BioPerl is_start_codon function to determine if the codon
>> used in a result it receives is acceptable or if it should look upstream
>> or downstream for a different one. Apparently there are actually 3
>> acceptable start codons in the standard codon table (2 rare ones and one
>> common), so making the edit removes the two rare ones from the list.
>>
>> I'm also preparing a 2.30 release that exports a "strict" codon table to
>> the BioPerl module, that will be used by default and should fix the
>>issue.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Hi,
>>>
>>> I have a serious problems with maker annotations especially the start
>>> codon placement. It started happening with maker version 2.27! About
>>>1/3
>>> of my genes are missing a proper start codon. When reviewing the GFF
>>> files gene predictors and est evidence standalone would predict the
>>> right gene structure including the start codon. I was thinking that
>>>this
>>> problem was somehow linked to my gene models but looking at their
>>> standalone prediction I discarded that theory. Just some stats about
>>> proteins with proper start codon (first column) and missing start codon
>>> (second column).
>>>
>>> Maker		9268	4215
>>> SNAP		16577	896
>>> Genemark	18764	290
>>>
>>> Numbers look the same when Augustus is used (currently retraining).
>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>want
>>> to check > 4000 genes for this.
>>>
>>> Do you have any idea what could cause such a problem? If you need some
>>> example gff files I can send you.
>>>
>>> Best regards
>>> Felix
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de





From carsonhh at gmail.com  Mon Oct 14 08:45:25 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 14 Oct 2013 10:45:25 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <525975C6.4020403@uni-wuerzburg.de>
Message-ID: <CE817BB6.10C72%carsonhh@gmail.com>

Probably Tuesday or Wednesday.

--Carson


On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Thx Carson! Do you now when 2.30 will be available? Bests
>
>On 12.10.2013 17:48, Carson Holt wrote:
>> This issue just came up this week on another e-mail as well.
>>
>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>> BioPerl (use maker --debug to have maker print out the locations of all
>> modules it uses).  Such a hack should only be done as a temporary work
>> around.
>>
>> You change line 256 from -->
>> ---M---------------M---------------M----------------------------
>>
>> To-->
>> -----------------------------------M----------------------------
>>
>>
>> Maker uses the BioPerl is_start_codon function to determine if the codon
>> used in a result it receives is acceptable or if it should look upstream
>> or downstream for a different one. Apparently there are actually 3
>> acceptable start codons in the standard codon table (2 rare ones and one
>> common), so making the edit removes the two rare ones from the list.
>>
>> I'm also preparing a 2.30 release that exports a "strict" codon table to
>> the BioPerl module, that will be used by default and should fix the
>>issue.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Hi,
>>>
>>> I have a serious problems with maker annotations especially the start
>>> codon placement. It started happening with maker version 2.27! About
>>>1/3
>>> of my genes are missing a proper start codon. When reviewing the GFF
>>> files gene predictors and est evidence standalone would predict the
>>> right gene structure including the start codon. I was thinking that
>>>this
>>> problem was somehow linked to my gene models but looking at their
>>> standalone prediction I discarded that theory. Just some stats about
>>> proteins with proper start codon (first column) and missing start codon
>>> (second column).
>>>
>>> Maker		9268	4215
>>> SNAP		16577	896
>>> Genemark	18764	290
>>>
>>> Numbers look the same when Augustus is used (currently retraining).
>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>want
>>> to check > 4000 genes for this.
>>>
>>> Do you have any idea what could cause such a problem? If you need some
>>> example gff files I can send you.
>>>
>>> Best regards
>>> Felix
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of W?rzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de





From cjfields at illinois.edu  Mon Oct 14 09:07:43 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 14 Oct 2013 15:07:43 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE817BB6.10C72%carsonhh@gmail.com>
References: <CE817BB6.10C72%carsonhh@gmail.com>
Message-ID: <D51543B5-DCFB-4F2C-9BE5-3099B96E3317@illinois.edu>

Carson,

Regarding the CodonTable change below, should this be something that needs to be fixed, or made more flexible, in bioperl?  I could see this being a problem if using MAKER for bacterial annotation (where the alternative start codons are actually more common).

chris

On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Probably Tuesday or Wednesday.
> 
> --Carson
> 
> 
> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
> 
>> Thx Carson! Do you now when 2.30 will be available? Bests
>> 
>> On 12.10.2013 17:48, Carson Holt wrote:
>>> This issue just came up this week on another e-mail as well.
>>> 
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>> BioPerl (use maker --debug to have maker print out the locations of all
>>> modules it uses).  Such a hack should only be done as a temporary work
>>> around.
>>> 
>>> You change line 256 from -->
>>> ---M---------------M---------------M----------------------------
>>> 
>>> To-->
>>> -----------------------------------M----------------------------
>>> 
>>> 
>>> Maker uses the BioPerl is_start_codon function to determine if the codon
>>> used in a result it receives is acceptable or if it should look upstream
>>> or downstream for a different one. Apparently there are actually 3
>>> acceptable start codons in the standard codon table (2 rare ones and one
>>> common), so making the edit removes the two rare ones from the list.
>>> 
>>> I'm also preparing a 2.30 release that exports a "strict" codon table to
>>> the BioPerl module, that will be used by default and should fix the
>>> issue.
>>> 
>>> Thanks,
>>> Carson
>>> 
>>> 
>>> 
>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I have a serious problems with maker annotations especially the start
>>>> codon placement. It started happening with maker version 2.27! About
>>>> 1/3
>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>> files gene predictors and est evidence standalone would predict the
>>>> right gene structure including the start codon. I was thinking that
>>>> this
>>>> problem was somehow linked to my gene models but looking at their
>>>> standalone prediction I discarded that theory. Just some stats about
>>>> proteins with proper start codon (first column) and missing start codon
>>>> (second column).
>>>> 
>>>> Maker		9268	4215
>>>> SNAP		16577	896
>>>> Genemark	18764	290
>>>> 
>>>> Numbers look the same when Augustus is used (currently retraining).
>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>> want
>>>> to check > 4000 genes for this.
>>>> 
>>>> Do you have any idea what could cause such a problem? If you need some
>>>> example gff files I can send you.
>>>> 
>>>> Best regards
>>>> Felix
>>>> 
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> -- 
>> Felix Bemm
>> Department of Bioinformatics
>> University of W?rzburg, Germany
>> Tel: +49 931 - 31 83696
>> Fax: +49 931 - 31 84552
>> felix.bemm at uni-wuerzburg.de
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Mon Oct 14 11:58:24 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 14 Oct 2013 13:58:24 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <D51543B5-DCFB-4F2C-9BE5-3099B96E3317@illinois.edu>
Message-ID: <CE81A824.10C7B%carsonhh@gmail.com>

I think adding one more codon table to the set of available tables would
be sufficient.  Call it the 'Strict' table or 'Canonical' table.  It
doesn't need to be the default, but should be a selectable option just as
the other codon tables are.  There is a way to export codon tables to the
module, which is what I've now added to MAKER, but I'm sure other BoiPerl
users would find a strictly canonical codon table useful as well.

Thanks,
Carson


On 10/14/13 11:07 AM, "Fields, Christopher J" <cjfields at illinois.edu>
wrote:

>Carson,
>
>Regarding the CodonTable change below, should this be something that
>needs to be fixed, or made more flexible, in bioperl?  I could see this
>being a problem if using MAKER for bacterial annotation (where the
>alternative start codons are actually more common).
>
>chris
>
>On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Probably Tuesday or Wednesday.
>> 
>> --Carson
>> 
>> 
>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>> 
>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>> 
>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>> This issue just came up this week on another e-mail as well.
>>>> 
>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>> BioPerl (use maker --debug to have maker print out the locations of
>>>>all
>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>> around.
>>>> 
>>>> You change line 256 from -->
>>>> ---M---------------M---------------M----------------------------
>>>> 
>>>> To-->
>>>> -----------------------------------M----------------------------
>>>> 
>>>> 
>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>codon
>>>> used in a result it receives is acceptable or if it should look
>>>>upstream
>>>> or downstream for a different one. Apparently there are actually 3
>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>one
>>>> common), so making the edit removes the two rare ones from the list.
>>>> 
>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>to
>>>> the BioPerl module, that will be used by default and should fix the
>>>> issue.
>>>> 
>>>> Thanks,
>>>> Carson
>>>> 
>>>> 
>>>> 
>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> I have a serious problems with maker annotations especially the start
>>>>> codon placement. It started happening with maker version 2.27! About
>>>>> 1/3
>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>> files gene predictors and est evidence standalone would predict the
>>>>> right gene structure including the start codon. I was thinking that
>>>>> this
>>>>> problem was somehow linked to my gene models but looking at their
>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>> proteins with proper start codon (first column) and missing start
>>>>>codon
>>>>> (second column).
>>>>> 
>>>>> Maker		9268	4215
>>>>> SNAP		16577	896
>>>>> Genemark	18764	290
>>>>> 
>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>> want
>>>>> to check > 4000 genes for this.
>>>>> 
>>>>> Do you have any idea what could cause such a problem? If you need
>>>>>some
>>>>> example gff files I can send you.
>>>>> 
>>>>> Best regards
>>>>> Felix
>>>>> 
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>> 
>>> -- 
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>> 
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>





From cjfields at illinois.edu  Mon Oct 14 12:51:28 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 14 Oct 2013 18:51:28 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE81A824.10C7B%carsonhh@gmail.com>
References: <CE81A824.10C7B%carsonhh@gmail.com>
Message-ID: <160BC401-0471-4285-8712-21440628A5DA@illinois.edu>

Done, with some added tests.  I labeled it 'Strict' ('Canonical' can be a bit of a loaded term).  It's currently set as ID 24.

I will likely push out a new 1.6 point release this week or next, I'll merge these in for that release.

chris

On Oct 14, 2013, at 12:58 PM, Carson Holt <carsonhh at gmail.com> wrote:

> I think adding one more codon table to the set of available tables would
> be sufficient.  Call it the 'Strict' table or 'Canonical' table.  It
> doesn't need to be the default, but should be a selectable option just as
> the other codon tables are.  There is a way to export codon tables to the
> module, which is what I've now added to MAKER, but I'm sure other BoiPerl
> users would find a strictly canonical codon table useful as well.
> 
> Thanks,
> Carson
> 
> 
> On 10/14/13 11:07 AM, "Fields, Christopher J" <cjfields at illinois.edu>
> wrote:
> 
>> Carson,
>> 
>> Regarding the CodonTable change below, should this be something that
>> needs to be fixed, or made more flexible, in bioperl?  I could see this
>> being a problem if using MAKER for bacterial annotation (where the
>> alternative start codons are actually more common).
>> 
>> chris
>> 
>> On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>>> Probably Tuesday or Wednesday.
>>> 
>>> --Carson
>>> 
>>> 
>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>> 
>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>> 
>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>> This issue just came up this week on another e-mail as well.
>>>>> 
>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>> BioPerl (use maker --debug to have maker print out the locations of
>>>>> all
>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>> around.
>>>>> 
>>>>> You change line 256 from -->
>>>>> ---M---------------M---------------M----------------------------
>>>>> 
>>>>> To-->
>>>>> -----------------------------------M----------------------------
>>>>> 
>>>>> 
>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>> codon
>>>>> used in a result it receives is acceptable or if it should look
>>>>> upstream
>>>>> or downstream for a different one. Apparently there are actually 3
>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>> one
>>>>> common), so making the edit removes the two rare ones from the list.
>>>>> 
>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>> to
>>>>> the BioPerl module, that will be used by default and should fix the
>>>>> issue.
>>>>> 
>>>>> Thanks,
>>>>> Carson
>>>>> 
>>>>> 
>>>>> 
>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>> wrote:
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I have a serious problems with maker annotations especially the start
>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>> 1/3
>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>> right gene structure including the start codon. I was thinking that
>>>>>> this
>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>> proteins with proper start codon (first column) and missing start
>>>>>> codon
>>>>>> (second column).
>>>>>> 
>>>>>> Maker		9268	4215
>>>>>> SNAP		16577	896
>>>>>> Genemark	18764	290
>>>>>> 
>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>> want
>>>>>> to check > 4000 genes for this.
>>>>>> 
>>>>>> Do you have any idea what could cause such a problem? If you need
>>>>>> some
>>>>>> example gff files I can send you.
>>>>>> 
>>>>>> Best regards
>>>>>> Felix
>>>>>> 
>>>>>> --
>>>>>> Felix Bemm
>>>>>> Department of Bioinformatics
>>>>>> University of W?rzburg, Germany
>>>>>> Tel: +49 931 - 31 83696
>>>>>> Fax: +49 931 - 31 84552
>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>> 
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> 
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>> 
>>>> -- 
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
> 
> 




From carsonhh at gmail.com  Mon Oct 14 18:59:45 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 14 Oct 2013 20:59:45 -0400
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <160BC401-0471-4285-8712-21440628A5DA@illinois.edu>
Message-ID: <CE820BA4.10C8F%carsonhh@gmail.com>

Thanks!!

--Carson


On 10/14/13 2:51 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

>Done, with some added tests.  I labeled it 'Strict' ('Canonical' can be a
>bit of a loaded term).  It's currently set as ID 24.
>
>I will likely push out a new 1.6 point release this week or next, I'll
>merge these in for that release.
>
>chris
>
>On Oct 14, 2013, at 12:58 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> I think adding one more codon table to the set of available tables would
>> be sufficient.  Call it the 'Strict' table or 'Canonical' table.  It
>> doesn't need to be the default, but should be a selectable option just
>>as
>> the other codon tables are.  There is a way to export codon tables to
>>the
>> module, which is what I've now added to MAKER, but I'm sure other
>>BoiPerl
>> users would find a strictly canonical codon table useful as well.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> On 10/14/13 11:07 AM, "Fields, Christopher J" <cjfields at illinois.edu>
>> wrote:
>> 
>>> Carson,
>>> 
>>> Regarding the CodonTable change below, should this be something that
>>> needs to be fixed, or made more flexible, in bioperl?  I could see this
>>> being a problem if using MAKER for bacterial annotation (where the
>>> alternative start codons are actually more common).
>>> 
>>> chris
>>> 
>>> On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> 
>>>> Probably Tuesday or Wednesday.
>>>> 
>>>> --Carson
>>>> 
>>>> 
>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>wrote:
>>>> 
>>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>>> 
>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>>> This issue just came up this week on another e-mail as well.
>>>>>> 
>>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>>> BioPerl (use maker --debug to have maker print out the locations of
>>>>>> all
>>>>>> modules it uses).  Such a hack should only be done as a temporary
>>>>>>work
>>>>>> around.
>>>>>> 
>>>>>> You change line 256 from -->
>>>>>> ---M---------------M---------------M----------------------------
>>>>>> 
>>>>>> To-->
>>>>>> -----------------------------------M----------------------------
>>>>>> 
>>>>>> 
>>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>>> codon
>>>>>> used in a result it receives is acceptable or if it should look
>>>>>> upstream
>>>>>> or downstream for a different one. Apparently there are actually 3
>>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>>> one
>>>>>> common), so making the edit removes the two rare ones from the list.
>>>>>> 
>>>>>> I'm also preparing a 2.30 release that exports a "strict" codon
>>>>>>table
>>>>>> to
>>>>>> the BioPerl module, that will be used by default and should fix the
>>>>>> issue.
>>>>>> 
>>>>>> Thanks,
>>>>>> Carson
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de>
>>>>>> wrote:
>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I have a serious problems with maker annotations especially the
>>>>>>>start
>>>>>>> codon placement. It started happening with maker version 2.27!
>>>>>>>About
>>>>>>> 1/3
>>>>>>> of my genes are missing a proper start codon. When reviewing the
>>>>>>>GFF
>>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>>> right gene structure including the start codon. I was thinking that
>>>>>>> this
>>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>>> standalone prediction I discarded that theory. Just some stats
>>>>>>>about
>>>>>>> proteins with proper start codon (first column) and missing start
>>>>>>> codon
>>>>>>> (second column).
>>>>>>> 
>>>>>>> Maker		9268	4215
>>>>>>> SNAP		16577	896
>>>>>>> Genemark	18764	290
>>>>>>> 
>>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>>> want
>>>>>>> to check > 4000 genes for this.
>>>>>>> 
>>>>>>> Do you have any idea what could cause such a problem? If you need
>>>>>>> some
>>>>>>> example gff files I can send you.
>>>>>>> 
>>>>>>> Best regards
>>>>>>> Felix
>>>>>>> 
>>>>>>> --
>>>>>>> Felix Bemm
>>>>>>> Department of Bioinformatics
>>>>>>> University of W?rzburg, Germany
>>>>>>> Tel: +49 931 - 31 83696
>>>>>>> Fax: +49 931 - 31 84552
>>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> 
>>>>>>> 
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>or
>>>>>>> g
>>>>> 
>>>>> -- 
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>> 
>> 
>





From jfierst at uoregon.edu  Mon Oct 21 11:40:06 2013
From: jfierst at uoregon.edu (Janna Fierst)
Date: Mon, 21 Oct 2013 10:40:06 -0700
Subject: [maker-devel] Fwd: exon/intron boundaries
In-Reply-To: <CE782A71.F621%carsonhh@gmail.com>
References: <CAGoyurbCe-g7Vx5VSkBzj7+YNhgd6PwC+JBTDem7Uadv0Fhw5Q@mail.gmail.com>
	<CE782A71.F621%carsonhh@gmail.com>
Message-ID: <CAGoyurZfiqRpEKg0C=__ou6muWD2PqCQh9b+S9y_+95-xsCfOQ@mail.gmail.com>

Hi,

thanks for your help- I have used Trinity to assemble the EST's but am
having a problem with the 2.29-beta release. Instead of starting and
finishing a set of scaffolds, it appears to re-start over and over again. I
am running it in parallel across 32 cores and I'm wondering if this is a
problem with the parallel implementation. I've gone through it several
times and not been able to find any errors or output that would suggest
what the problem is. Thanks -Janna


On Mon, Oct 7, 2013 at 6:20 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Hi Janna,
>
> There are a couple of things to do.  Download the maker-2.29p-beta from
> the lab website.  This includes some changes made to improve the
> performance of correct_est_fusion.  Whenever using the correct_est_fusion
> option, this also reduces the influence of ESTs on annotation.  So normally
> you would need to increase your protein dataset, but given that you have
> supplied 3 nematode species and all of UniProt already you should probably
> be fine. But there is one last thing you can do.  Instead of using
> cufflinks, try using trinity to assemble the ESTs.  There is a Jaccard clip
> option that reducing merging caused by overlapping UTR.  Between the
> trinity and correct_est_fusion you should be able to really reduce the
> effect of those ESTs.
>
> If those changes don't work there is one last option.  If you take the
> MAKER results and filter them for SNAP and Augustus ab initio results
> (match/match_part in the GFF3), then you can pass those in to the pred_gff
> options.  Then turn snaphmm and augustus_species off in the control files.
>  Basically what this will do is turn MAKER's hint based prediction off and
> force it to filter the ab intio results and select directly models from
> there.  Since the merging is being caused by bad hints (merged transcripts
> from mRNAseq) this would reduce that effect.  You will still need
> correct_est_fusion=1 though to trim UTR coming from the merged transcripts,
> because even though MAEKR can't process hints to rerun SNAP and Augustus
> this way, it will try and add UTR using the EST evidence.
>
> --Carson
>
>
> From: Janna Fierst <jfierst at uoregon.edu>
> Date: Friday, October 4, 2013 1:06 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Fwd: exon/intron boundaries
>
> Hi,
>
> thanks for your reply- I have been going through our annotations in detail
> and trying different parameter sets, and I think I have identified what is
> going on but I'm not sure how to set the MAKER2 parameters for our
> situation. We are working with a species of Caenorhabditid worm and there
> are long gene-dense blocks that are being incorrectly annotated as large
> single genes instead of several smaller closely spaced genes. The protein
> alignments (tblastx and protein2genome) show very clearly where the
> exon/intron boundaries are and in most cases agree with the augustus
> predictions. The assembled cufflinks output (through blastn, est2genome and
> est_gff:cufflinks) does not agree in some locations; I think this may be
> because in some cases the UTR nearly overlaps adjacent genes.
>
> I have included a screenshot of an annotated region viewed in apollo to
> try to show this. The large gene in the middle is actually 7 different
> genes that are extremely close together and MAKER2 is collapsing them into
> a single gene. I tried running without any RNASeq/cufflinks data and MAKER2
> annotates the region as two genes instead of one, but I can't get it to
> recognize the 7 as different genes. I have retrained SNAP but we have not
> been able to successfully train Augustus, we are currently using the
> default caenhorhabditis species model. I also included a species specific
> repeat library. I tried setting correct_est_fusion=1 and reducing
> pred_flank but these changes appear to really alter the annotations and we
> end up annotating almost nothing. I also tried setting est2genome=0 to
> decrease the influence of the cufflinks assembly but it didn't appear to
> help. There are some very large introns in these genes so I haven't tried
> yet decreasing the maximum intron size because I'm concerned this may
> generate too many split genes instead of our current merged gene problem.
> Thanks for your help, any advice is greatly appreciated! -Janna Fierst
>
>
> On Mon, Aug 26, 2013 at 12:21 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Are you getting gene fusions or just more exons?  Gene fusions can be
>> reduced by setting correct_est_fusion=1, or reducing pred_flank, although
>> reducing pred_flank can cause other issues (but those generally only appear
>> if setting the value below below 150).  Also if you have the maximum intron
>> size set to high (split_hit option), you may also be generating bridging
>> alignments that make evidence align across distant paralogous genes as well
>> (this can result in gene merging)
>>
>> You should also look at your results manually in a viewer like Apollo.
>>  Then see if the extra exons are supported by something such as protein
>> alignments from another species.  If this is the case, you may have a
>> poorly annotated protein set that is being used as evidence that is
>> carrying over it's erroneous exons into the species you are annotating.  If
>> the extra  exons are supported by EST evidence, then perhaps you should try
>> and rebuild the EST assembly (for example trinity has an option to use a
>> Jarccardian similarity coefficient to avoid fusing transcripts).
>>
>> Another option, is to retrain SNAP or Augustus.  MAKER does not actually
>> produce any of the models itself (it is a pipeline not a predictor).  The
>> models are all generated using these other algorithms, MAKER just feeds
>> them hints based on protein and transcript alignments, so making sure
>> training is sufficient is important for those programs to produce their
>> best models.
>>
>> Finally make sure your repeat database is sufficient, you may need to
>> generate a species specific repeat library using something like
>> RepeatModeler.  Repeats can end up being included as extra exons in gene
>> models because they may contain reading frames the do code for proteins
>> (I.e. reverse transcriptases).
>>
>> If you have any questions on any of the above, just let us know.
>>
>> Thanks,
>> Carson
>>
>>
>> From: Janna Fierst <jfierst at uoregon.edu>
>> Date: Monday, August 26, 2013 2:54 PM
>> To: <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] exon/intron boundaries
>>
>> Hi,
>>
>> I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the
>> initial results appear fairly good but we seem to be be annotating too many
>> exons for multiple genes. I was wondering which parameters should be tuned
>> to change the threshold for exon/intron boundaries? Thanks for your help
>> -Janna Fierst
>> _______________________________________________ maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From graham.etherington at sainsbury-laboratory.ac.uk  Thu Oct 24 07:42:51 2013
From: graham.etherington at sainsbury-laboratory.ac.uk (graham etherington (TSL))
Date: Thu, 24 Oct 2013 13:42:51 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE7FA55D.10C4B%carsonhh@gmail.com>
Message-ID: <CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>

Hi,
I notice that the latest version of Maker available from
http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
2013). As we're also having the start codon problem we'd like to get hold
of v2.30. Do you know when this will be released?
Many thanks,
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:

>Before Wednesday, because after that I'm on a 6 day road trip, so I have
>to have it wrapped up before I leave.
>
>--Carson
>
>
>
>
>On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>>Thx Carson! Do you now when 2.30 will be available? Bests
>>
>>On 12.10.2013 17:48, Carson Holt wrote:
>>> This issue just came up this week on another e-mail as well.
>>>
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>> BioPerl (use maker --debug to have maker print out the locations of all
>>> modules it uses).  Such a hack should only be done as a temporary work
>>> around.
>>>
>>> You change line 256 from -->
>>> ---M---------------M---------------M----------------------------
>>>
>>> To-->
>>> -----------------------------------M----------------------------
>>>
>>>
>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>codon
>>> used in a result it receives is acceptable or if it should look
>>>upstream
>>> or downstream for a different one. Apparently there are actually 3
>>> acceptable start codons in the standard codon table (2 rare ones and
>>>one
>>> common), so making the edit removes the two rare ones from the list.
>>>
>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>to
>>> the BioPerl module, that will be used by default and should fix the
>>>issue.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a serious problems with maker annotations especially the start
>>>> codon placement. It started happening with maker version 2.27! About
>>>>1/3
>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>> files gene predictors and est evidence standalone would predict the
>>>> right gene structure including the start codon. I was thinking that
>>>>this
>>>> problem was somehow linked to my gene models but looking at their
>>>> standalone prediction I discarded that theory. Just some stats about
>>>> proteins with proper start codon (first column) and missing start
>>>>codon
>>>> (second column).
>>>>
>>>> Maker		9268	4215
>>>> SNAP		16577	896
>>>> Genemark	18764	290
>>>>
>>>> Numbers look the same when Augustus is used (currently retraining).
>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>want
>>>> to check > 4000 genes for this.
>>>>
>>>> Do you have any idea what could cause such a problem? If you need some
>>>> example gff files I can send you.
>>>>
>>>> Best regards
>>>> Felix
>>>>
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>-- 
>>Felix Bemm
>>Department of Bioinformatics
>>University of W?rzburg, Germany
>>Tel: +49 931 - 31 83696
>>Fax: +49 931 - 31 84552
>>felix.bemm at uni-wuerzburg.de
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From myandell at genetics.utah.edu  Thu Oct 24 07:55:05 2013
From: myandell at genetics.utah.edu (Mark Yandell)
Date: Thu, 24 Oct 2013 13:55:05 +0000
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>,
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
Message-ID: <7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>

Hi Graham,

 Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.


--mark


Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
Sent: Thursday, October 24, 2013 7:42 AM
To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
Cc: Kate Bailey (TSL)
Subject: Re: [maker-devel] Serious Start Codon Problem

Hi,
I notice that the latest version of Maker available from
http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
2013). As we're also having the start codon problem we'd like to get hold
of v2.30. Do you know when this will be released?
Many thanks,
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:

>Before Wednesday, because after that I'm on a 6 day road trip, so I have
>to have it wrapped up before I leave.
>
>--Carson
>
>
>
>
>On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>>Thx Carson! Do you now when 2.30 will be available? Bests
>>
>>On 12.10.2013 17:48, Carson Holt wrote:
>>> This issue just came up this week on another e-mail as well.
>>>
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>> BioPerl (use maker --debug to have maker print out the locations of all
>>> modules it uses).  Such a hack should only be done as a temporary work
>>> around.
>>>
>>> You change line 256 from -->
>>> ---M---------------M---------------M----------------------------
>>>
>>> To-->
>>> -----------------------------------M----------------------------
>>>
>>>
>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>codon
>>> used in a result it receives is acceptable or if it should look
>>>upstream
>>> or downstream for a different one. Apparently there are actually 3
>>> acceptable start codons in the standard codon table (2 rare ones and
>>>one
>>> common), so making the edit removes the two rare ones from the list.
>>>
>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>to
>>> the BioPerl module, that will be used by default and should fix the
>>>issue.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a serious problems with maker annotations especially the start
>>>> codon placement. It started happening with maker version 2.27! About
>>>>1/3
>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>> files gene predictors and est evidence standalone would predict the
>>>> right gene structure including the start codon. I was thinking that
>>>>this
>>>> problem was somehow linked to my gene models but looking at their
>>>> standalone prediction I discarded that theory. Just some stats about
>>>> proteins with proper start codon (first column) and missing start
>>>>codon
>>>> (second column).
>>>>
>>>> Maker              9268    4215
>>>> SNAP               16577   896
>>>> Genemark   18764   290
>>>>
>>>> Numbers look the same when Augustus is used (currently retraining).
>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>want
>>>> to check > 4000 genes for this.
>>>>
>>>> Do you have any idea what could cause such a problem? If you need some
>>>> example gff files I can send you.
>>>>
>>>> Best regards
>>>> Felix
>>>>
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>>
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>--
>>Felix Bemm
>>Department of Bioinformatics
>>University of W?rzburg, Germany
>>Tel: +49 931 - 31 83696
>>Fax: +49 931 - 31 84552
>>felix.bemm at uni-wuerzburg.de
>
>
>
>_______________________________________________
>maker-devel mailing list
>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
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


From felix.bemm at uni-wuerzburg.de  Thu Oct 24 08:03:27 2013
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Thu, 24 Oct 2013 16:03:27 +0200
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>,
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
Message-ID: <526928AF.90108@uni-wuerzburg.de>

Hi,

I used the temporary fix of the Bio::Tools::CodonTable. It's working 
pretty nice. Almost every predicted proteins now start with a M ;)

Bests
Felix

On 24.10.2013 15:55, Mark Yandell wrote:
> Hi Graham,
>
>   Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>
>
> --mark
>
>
> Mark Yandell
> Professor of Human Genetics
> H.A. & Edna Benning Presidential Endowed Chair
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ph:801-587-7707
>
> ________________________________________
> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
> Sent: Thursday, October 24, 2013 7:42 AM
> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
> Cc: Kate Bailey (TSL)
> Subject: Re: [maker-devel] Serious Start Codon Problem
>
> Hi,
> I notice that the latest version of Maker available from
> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
> 2013). As we're also having the start codon problem we'd like to get hold
> of v2.30. Do you know when this will be released?
> Many thanks,
> Graham
>
>
> Dr. Graham Etherington
> Bioinformatics Support Officer,
> The Sainsbury Laboratory,
> Norwich Research Park,
> Norwich NR4 7UH.
> UK
> Tel: +44 (0)1603 450601
>
>
>
>
>
> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>
>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>> to have it wrapped up before I leave.
>>
>> --Carson
>>
>>
>>
>>
>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>
>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>> This issue just came up this week on another e-mail as well.
>>>>
>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>> around.
>>>>
>>>> You change line 256 from -->
>>>> ---M---------------M---------------M----------------------------
>>>>
>>>> To-->
>>>> -----------------------------------M----------------------------
>>>>
>>>>
>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>> codon
>>>> used in a result it receives is acceptable or if it should look
>>>> upstream
>>>> or downstream for a different one. Apparently there are actually 3
>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>> one
>>>> common), so making the edit removes the two rare ones from the list.
>>>>
>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>> to
>>>> the BioPerl module, that will be used by default and should fix the
>>>> issue.
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>>
>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I have a serious problems with maker annotations especially the start
>>>>> codon placement. It started happening with maker version 2.27! About
>>>>> 1/3
>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>> files gene predictors and est evidence standalone would predict the
>>>>> right gene structure including the start codon. I was thinking that
>>>>> this
>>>>> problem was somehow linked to my gene models but looking at their
>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>> proteins with proper start codon (first column) and missing start
>>>>> codon
>>>>> (second column).
>>>>>
>>>>> Maker              9268    4215
>>>>> SNAP               16577   896
>>>>> Genemark   18764   290
>>>>>
>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>> want
>>>>> to check > 4000 genes for this.
>>>>>
>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>> example gff files I can send you.
>>>>>
>>>>> Best regards
>>>>> Felix
>>>>>
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>>
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>

-- 
Felix Bemm
Department of Bioinformatics
University of W?rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de



From jim.hu.biobio at gmail.com  Thu Oct 24 08:32:01 2013
From: jim.hu.biobio at gmail.com (JH Gmail)
Date: Thu, 24 Oct 2013 09:32:01 -0500
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
Message-ID: <69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>

Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 

Does maker handle ribosome profiling yet?

jim

Sent from my iPad

> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
> 
> Hi Graham,
> 
> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
> 
> 
> --mark
> 
> 
> Mark Yandell
> Professor of Human Genetics
> H.A. & Edna Benning Presidential Endowed Chair
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ph:801-587-7707
> 
> ________________________________________
> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
> Sent: Thursday, October 24, 2013 7:42 AM
> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
> Cc: Kate Bailey (TSL)
> Subject: Re: [maker-devel] Serious Start Codon Problem
> 
> Hi,
> I notice that the latest version of Maker available from
> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
> 2013). As we're also having the start codon problem we'd like to get hold
> of v2.30. Do you know when this will be released?
> Many thanks,
> Graham
> 
> 
> Dr. Graham Etherington
> Bioinformatics Support Officer,
> The Sainsbury Laboratory,
> Norwich Research Park,
> Norwich NR4 7UH.
> UK
> Tel: +44 (0)1603 450601
> 
> 
> 
> 
> 
>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>> 
>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>> to have it wrapped up before I leave.
>> 
>> --Carson
>> 
>> 
>> 
>> 
>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>> 
>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>> 
>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>> This issue just came up this week on another e-mail as well.
>>>> 
>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>> around.
>>>> 
>>>> You change line 256 from -->
>>>> ---M---------------M---------------M----------------------------
>>>> 
>>>> To-->
>>>> -----------------------------------M----------------------------
>>>> 
>>>> 
>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>> codon
>>>> used in a result it receives is acceptable or if it should look
>>>> upstream
>>>> or downstream for a different one. Apparently there are actually 3
>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>> one
>>>> common), so making the edit removes the two rare ones from the list.
>>>> 
>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>> to
>>>> the BioPerl module, that will be used by default and should fix the
>>>> issue.
>>>> 
>>>> Thanks,
>>>> Carson
>>>> 
>>>> 
>>>> 
>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> I have a serious problems with maker annotations especially the start
>>>>> codon placement. It started happening with maker version 2.27! About
>>>>> 1/3
>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>> files gene predictors and est evidence standalone would predict the
>>>>> right gene structure including the start codon. I was thinking that
>>>>> this
>>>>> problem was somehow linked to my gene models but looking at their
>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>> proteins with proper start codon (first column) and missing start
>>>>> codon
>>>>> (second column).
>>>>> 
>>>>> Maker              9268    4215
>>>>> SNAP               16577   896
>>>>> Genemark   18764   290
>>>>> 
>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>> want
>>>>> to check > 4000 genes for this.
>>>>> 
>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>> example gff files I can send you.
>>>>> 
>>>>> Best regards
>>>>> Felix
>>>>> 
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of W?rzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>> 
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



From amelia.ireland at gmod.org  Thu Oct 24 12:52:17 2013
From: amelia.ireland at gmod.org (Amelia Ireland)
Date: Thu, 24 Oct 2013 11:52:17 -0700
Subject: [maker-devel] GMOD 2014: San Diego
Message-ID: <CAALsq00kuy83m4_k_rcWLSpwFYwMCYm5LXEkUgwzqCOUGfryBw@mail.gmail.com>

Greetings GMOD community citizens!

Online registration is now open for the 2014 GMOD meeting, to be held at
the Best Western Seven Seas, San Diego, CA, on January 16-17, 2014 (after
PAG). The meeting is open to GMOD users, developers, and anyone interested
in the project and the software we provide.

Online registration is now open; please see the meeting page,
http://gmod.org/wiki/Jan_2014_GMOD_Meeting, for more information. Early
bird registration rates apply until Dec. 14th.

We have secured a discount on a block of rooms at the Best Western Seven
Seas; please see the wiki for more information on booking.

Please feel free to contact the GMOD helpdesk on help at gmod.org if you have
any questions. Thanks!

-- 
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject
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From barry.moore at genetics.utah.edu  Thu Oct 24 15:09:20 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Thu, 24 Oct 2013 15:09:20 -0600
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
	<69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
Message-ID: <1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>

Hi Jim,

You can and any kind of evidence you want to MAKER including ribosomal profiling data as long as you format it in GFF3 format.  You could pass in your GFF3 formatted ribosomal profiling data in maker_opt.ctl with the protein_gff option and it will be treated as protein evidence.  However if you are wondering if anyone has coded a specific addition to MAKER to accept ribosomal profiling data and treat it as a different kind of evidence then no, this hasn't been done.

B

On Oct 24, 2013, at 8:32 AM, JH Gmail wrote:

> Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 
> 
> Does maker handle ribosome profiling yet?
> 
> jim
> 
> Sent from my iPad
> 
>> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
>> 
>> Hi Graham,
>> 
>> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>> 
>> 
>> --mark
>> 
>> 
>> Mark Yandell
>> Professor of Human Genetics
>> H.A. & Edna Benning Presidential Endowed Chair
>> Eccles Institute of Human Genetics
>> University of Utah
>> 15 North 2030 East, Room 2100
>> Salt Lake City, UT 84112-5330
>> ph:801-587-7707
>> 
>> ________________________________________
>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
>> Sent: Thursday, October 24, 2013 7:42 AM
>> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
>> Cc: Kate Bailey (TSL)
>> Subject: Re: [maker-devel] Serious Start Codon Problem
>> 
>> Hi,
>> I notice that the latest version of Maker available from
>> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
>> 2013). As we're also having the start codon problem we'd like to get hold
>> of v2.30. Do you know when this will be released?
>> Many thanks,
>> Graham
>> 
>> 
>> Dr. Graham Etherington
>> Bioinformatics Support Officer,
>> The Sainsbury Laboratory,
>> Norwich Research Park,
>> Norwich NR4 7UH.
>> UK
>> Tel: +44 (0)1603 450601
>> 
>> 
>> 
>> 
>> 
>>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>>> 
>>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>>> to have it wrapped up before I leave.
>>> 
>>> --Carson
>>> 
>>> 
>>> 
>>> 
>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>> 
>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>> 
>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>> This issue just came up this week on another e-mail as well.
>>>>> 
>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>> around.
>>>>> 
>>>>> You change line 256 from -->
>>>>> ---M---------------M---------------M----------------------------
>>>>> 
>>>>> To-->
>>>>> -----------------------------------M----------------------------
>>>>> 
>>>>> 
>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>> codon
>>>>> used in a result it receives is acceptable or if it should look
>>>>> upstream
>>>>> or downstream for a different one. Apparently there are actually 3
>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>> one
>>>>> common), so making the edit removes the two rare ones from the list.
>>>>> 
>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>> to
>>>>> the BioPerl module, that will be used by default and should fix the
>>>>> issue.
>>>>> 
>>>>> Thanks,
>>>>> Carson
>>>>> 
>>>>> 
>>>>> 
>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I have a serious problems with maker annotations especially the start
>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>> 1/3
>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>> right gene structure including the start codon. I was thinking that
>>>>>> this
>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>> proteins with proper start codon (first column) and missing start
>>>>>> codon
>>>>>> (second column).
>>>>>> 
>>>>>> Maker              9268    4215
>>>>>> SNAP               16577   896
>>>>>> Genemark   18764   290
>>>>>> 
>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>> want
>>>>>> to check > 4000 genes for this.
>>>>>> 
>>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>>> example gff files I can send you.
>>>>>> 
>>>>>> Best regards
>>>>>> Felix
>>>>>> 
>>>>>> --
>>>>>> Felix Bemm
>>>>>> Department of Bioinformatics
>>>>>> University of W?rzburg, Germany
>>>>>> Tel: +49 931 - 31 83696
>>>>>> Fax: +49 931 - 31 84552
>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>> 
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> 
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> 
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of W?rzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> 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
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> _______________________________________________
>> maker-devel mailing list
>> 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
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From marc.hoeppner at imbim.uu.se  Fri Oct 25 08:20:04 2013
From: marc.hoeppner at imbim.uu.se (Marc P. Hoeppner)
Date: Fri, 25 Oct 2013 16:20:04 +0200
Subject: [maker-devel] Maker MPICH2 issue (Multiple MAKER processes have
 been started in the same directory)
Message-ID: <526A7E14.9010906@imbim.uu.se>

Dear list,

I know that MPICH2 related issues have been discussed previously, but 
the suggested solutions don't seem to work for me.
Briefly, I have set up a new cluster, with a fresh install of mpich2 (SL 
6.4, from the yum repos) and a newly compiled build of Maker 2.28.

When I start maker with mpiexec, I get spammed with
'WARNING: Multiple MAKER processes have been started in the same 
directory.'

Here is what I have tried so far - still getting the error :-< Any 
suggestions would be appreciated

--------
MPICH2
---------

which mpiexec:
/usr/lib64/mpich2/bin/mpiexec

Started the mpd ring as normal user across 5 nodes (bnode-01 to 
bnode-04, and the head node bhead)

mpdtrace:
bhead
bnode-02
bnode-03
bnode-04
bnode-01

mpdringtest:
time for 1 loops = 0.00128293037415 seconds

mpixec -n 32 -machinefile hostfile hostname:

<long list of host names, as ecpected>

I also ran the Skampi Mpi Benchmark, which ran through just fine.

-----------
MAKER
-----------

./Build status

PERL Dependencies:      VERIFIED
External Programs:      VERIFIED
External C Libraries:   VERIFIED
MPI SUPPORT:            ENABLED
MWAS Web Interface:     DISABLED
MAKER PACKAGE:          CONFIGURATION OK

During configuration/installation, Build.PL automatically detected all 
MPI data and never complained, so I have to assume that everything went 
fine there.

-- 
----------
Marc P. Hoeppner, PhD
Department of Microbiology and Medical Biochemistry
Uppsala University, Sweden
marc.hoeppner at imbim.uu.se




From jim.hu.biobio at gmail.com  Fri Oct 25 08:51:19 2013
From: jim.hu.biobio at gmail.com (JH Gmail)
Date: Fri, 25 Oct 2013 09:51:19 -0500
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
	<69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
	<1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>
Message-ID: <596400F6-3215-4F71-A896-AF52CEC8D77D@gmail.com>

Thanks Barry,

I'm thinking about this more theoretically, as we don't have immediate plans, but...

This would work for gff derived from ribosome profiling analysis, but it would be nice to be able to start with bam files of mapped reads, or coverage scores as bigwig or gff.  RNA-seq has similar issues, but IIRC Maker expects RNA-seq data to be assembled first.  It may not be possible to do de novo cds assembly from ribosome profiling because I think the nuclease step may kill the overlaps. I'd have to look at some of the available data. 

Jim

Sent from my iPad

> On Oct 24, 2013, at 4:09 PM, Barry Moore <barry.moore at genetics.utah.edu> wrote:
> 
> Hi Jim,
> 
> You can and any kind of evidence you want to MAKER including ribosomal profiling data as long as you format it in GFF3 format.  You could pass in your GFF3 formatted ribosomal profiling data in maker_opt.ctl with the protein_gff option and it will be treated as protein evidence.  However if you are wondering if anyone has coded a specific addition to MAKER to accept ribosomal profiling data and treat it as a different kind of evidence then no, this hasn't been done.
> 
> B
> 
>> On Oct 24, 2013, at 8:32 AM, JH Gmail wrote:
>> 
>> Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 
>> 
>> Does maker handle ribosome profiling yet?
>> 
>> jim
>> 
>> Sent from my iPad
>> 
>>> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
>>> 
>>> Hi Graham,
>>> 
>>> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>>> 
>>> 
>>> --mark
>>> 
>>> 
>>> Mark Yandell
>>> Professor of Human Genetics
>>> H.A. & Edna Benning Presidential Endowed Chair
>>> Eccles Institute of Human Genetics
>>> University of Utah
>>> 15 North 2030 East, Room 2100
>>> Salt Lake City, UT 84112-5330
>>> ph:801-587-7707
>>> 
>>> ________________________________________
>>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
>>> Sent: Thursday, October 24, 2013 7:42 AM
>>> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
>>> Cc: Kate Bailey (TSL)
>>> Subject: Re: [maker-devel] Serious Start Codon Problem
>>> 
>>> Hi,
>>> I notice that the latest version of Maker available from
>>> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
>>> 2013). As we're also having the start codon problem we'd like to get hold
>>> of v2.30. Do you know when this will be released?
>>> Many thanks,
>>> Graham
>>> 
>>> 
>>> Dr. Graham Etherington
>>> Bioinformatics Support Officer,
>>> The Sainsbury Laboratory,
>>> Norwich Research Park,
>>> Norwich NR4 7UH.
>>> UK
>>> Tel: +44 (0)1603 450601
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>>>> 
>>>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>>>> to have it wrapped up before I leave.
>>>> 
>>>> --Carson
>>>> 
>>>> 
>>>> 
>>>> 
>>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>> 
>>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>>> 
>>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>>> This issue just came up this week on another e-mail as well.
>>>>>> 
>>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>>> around.
>>>>>> 
>>>>>> You change line 256 from -->
>>>>>> ---M---------------M---------------M----------------------------
>>>>>> 
>>>>>> To-->
>>>>>> -----------------------------------M----------------------------
>>>>>> 
>>>>>> 
>>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>>> codon
>>>>>> used in a result it receives is acceptable or if it should look
>>>>>> upstream
>>>>>> or downstream for a different one. Apparently there are actually 3
>>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>>> one
>>>>>> common), so making the edit removes the two rare ones from the list.
>>>>>> 
>>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>>> to
>>>>>> the BioPerl module, that will be used by default and should fix the
>>>>>> issue.
>>>>>> 
>>>>>> Thanks,
>>>>>> Carson
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I have a serious problems with maker annotations especially the start
>>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>>> 1/3
>>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>>> right gene structure including the start codon. I was thinking that
>>>>>>> this
>>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>>> proteins with proper start codon (first column) and missing start
>>>>>>> codon
>>>>>>> (second column).
>>>>>>> 
>>>>>>> Maker              9268    4215
>>>>>>> SNAP               16577   896
>>>>>>> Genemark   18764   290
>>>>>>> 
>>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>>> want
>>>>>>> to check > 4000 genes for this.
>>>>>>> 
>>>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>>>> example gff files I can send you.
>>>>>>> 
>>>>>>> Best regards
>>>>>>> Felix
>>>>>>> 
>>>>>>> --
>>>>>>> Felix Bemm
>>>>>>> Department of Bioinformatics
>>>>>>> University of W?rzburg, Germany
>>>>>>> Tel: +49 931 - 31 83696
>>>>>>> Fax: +49 931 - 31 84552
>>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> 
>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>> 
>>>>> --
>>>>> Felix Bemm
>>>>> Department of Bioinformatics
>>>>> University of W?rzburg, Germany
>>>>> Tel: +49 931 - 31 83696
>>>>> Fax: +49 931 - 31 84552
>>>>> felix.bemm at uni-wuerzburg.de
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> 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
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> _______________________________________________
>>> maker-devel mailing list
>>> 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
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
> 
> 
> 
> 
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From barry.moore at genetics.utah.edu  Fri Oct 25 09:44:55 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Fri, 25 Oct 2013 09:44:55 -0600
Subject: [maker-devel] Serious Start Codon Problem
In-Reply-To: <596400F6-3215-4F71-A896-AF52CEC8D77D@gmail.com>
References: <CE7FA55D.10C4B%carsonhh@gmail.com>
	<CE8EE16A.212BC%graham.etherington@sainsbury-laboratory.ac.uk>
	<7A60AB257EFF2B48B1F4C814817EA05365E778BF@mxb2.hg.genetics.utah.edu>
	<69247335-1227-41CB-94EA-BFEEE5207D51@gmail.com>
	<1F2D4C5A-1B72-409A-8F7D-4793F9BCEE88@genetics.utah.edu>
	<596400F6-3215-4F71-A896-AF52CEC8D77D@gmail.com>
Message-ID: <DA777487-D8DD-47E2-A852-DB123C3A1BB8@genetics.utah.edu>

Thanks Jim.

B

On Oct 25, 2013, at 8:51 AM, JH Gmail wrote:

> Thanks Barry,
> 
> I'm thinking about this more theoretically, as we don't have immediate plans, but...
> 
> This would work for gff derived from ribosome profiling analysis, but it would be nice to be able to start with bam files of mapped reads, or coverage scores as bigwig or gff.  RNA-seq has similar issues, but IIRC Maker expects RNA-seq data to be assembled first.  It may not be possible to do de novo cds assembly from ribosome profiling because I think the nuclease step may kill the overlaps. I'd have to look at some of the available data. 
> 
> Jim
> 
> Sent from my iPad
> 
> On Oct 24, 2013, at 4:09 PM, Barry Moore <barry.moore at genetics.utah.edu> wrote:
> 
>> Hi Jim,
>> 
>> You can and any kind of evidence you want to MAKER including ribosomal profiling data as long as you format it in GFF3 format.  You could pass in your GFF3 formatted ribosomal profiling data in maker_opt.ctl with the protein_gff option and it will be treated as protein evidence.  However if you are wondering if anyone has coded a specific addition to MAKER to accept ribosomal profiling data and treat it as a different kind of evidence then no, this hasn't been done.
>> 
>> B
>> 
>> On Oct 24, 2013, at 8:32 AM, JH Gmail wrote:
>> 
>>> Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 
>>> 
>>> Does maker handle ribosome profiling yet?
>>> 
>>> jim
>>> 
>>> Sent from my iPad
>>> 
>>>> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
>>>> 
>>>> Hi Graham,
>>>> 
>>>> Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.
>>>> 
>>>> 
>>>> --mark
>>>> 
>>>> 
>>>> Mark Yandell
>>>> Professor of Human Genetics
>>>> H.A. & Edna Benning Presidential Endowed Chair
>>>> Eccles Institute of Human Genetics
>>>> University of Utah
>>>> 15 North 2030 East, Room 2100
>>>> Salt Lake City, UT 84112-5330
>>>> ph:801-587-7707
>>>> 
>>>> ________________________________________
>>>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
>>>> Sent: Thursday, October 24, 2013 7:42 AM
>>>> To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
>>>> Cc: Kate Bailey (TSL)
>>>> Subject: Re: [maker-devel] Serious Start Codon Problem
>>>> 
>>>> Hi,
>>>> I notice that the latest version of Maker available from
>>>> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
>>>> 2013). As we're also having the start codon problem we'd like to get hold
>>>> of v2.30. Do you know when this will be released?
>>>> Many thanks,
>>>> Graham
>>>> 
>>>> 
>>>> Dr. Graham Etherington
>>>> Bioinformatics Support Officer,
>>>> The Sainsbury Laboratory,
>>>> Norwich Research Park,
>>>> Norwich NR4 7UH.
>>>> UK
>>>> Tel: +44 (0)1603 450601
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>>>>> 
>>>>> Before Wednesday, because after that I'm on a 6 day road trip, so I have
>>>>> to have it wrapped up before I leave.
>>>>> 
>>>>> --Carson
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>> 
>>>>>> Thx Carson! Do you now when 2.30 will be available? Bests
>>>>>> 
>>>>>>> On 12.10.2013 17:48, Carson Holt wrote:
>>>>>>> This issue just came up this week on another e-mail as well.
>>>>>>> 
>>>>>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>>>>>> BioPerl (use maker --debug to have maker print out the locations of all
>>>>>>> modules it uses).  Such a hack should only be done as a temporary work
>>>>>>> around.
>>>>>>> 
>>>>>>> You change line 256 from -->
>>>>>>> ---M---------------M---------------M----------------------------
>>>>>>> 
>>>>>>> To-->
>>>>>>> -----------------------------------M----------------------------
>>>>>>> 
>>>>>>> 
>>>>>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>>>>> codon
>>>>>>> used in a result it receives is acceptable or if it should look
>>>>>>> upstream
>>>>>>> or downstream for a different one. Apparently there are actually 3
>>>>>>> acceptable start codons in the standard codon table (2 rare ones and
>>>>>>> one
>>>>>>> common), so making the edit removes the two rare ones from the list.
>>>>>>> 
>>>>>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>>>>> to
>>>>>>> the BioPerl module, that will be used by default and should fix the
>>>>>>> issue.
>>>>>>> 
>>>>>>> Thanks,
>>>>>>> Carson
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>>>>>> 
>>>>>>>> Hi,
>>>>>>>> 
>>>>>>>> I have a serious problems with maker annotations especially the start
>>>>>>>> codon placement. It started happening with maker version 2.27! About
>>>>>>>> 1/3
>>>>>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>>>>>> files gene predictors and est evidence standalone would predict the
>>>>>>>> right gene structure including the start codon. I was thinking that
>>>>>>>> this
>>>>>>>> problem was somehow linked to my gene models but looking at their
>>>>>>>> standalone prediction I discarded that theory. Just some stats about
>>>>>>>> proteins with proper start codon (first column) and missing start
>>>>>>>> codon
>>>>>>>> (second column).
>>>>>>>> 
>>>>>>>> Maker              9268    4215
>>>>>>>> SNAP               16577   896
>>>>>>>> Genemark   18764   290
>>>>>>>> 
>>>>>>>> Numbers look the same when Augustus is used (currently retraining).
>>>>>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>>>>> want
>>>>>>>> to check > 4000 genes for this.
>>>>>>>> 
>>>>>>>> Do you have any idea what could cause such a problem? If you need some
>>>>>>>> example gff files I can send you.
>>>>>>>> 
>>>>>>>> Best regards
>>>>>>>> Felix
>>>>>>>> 
>>>>>>>> --
>>>>>>>> Felix Bemm
>>>>>>>> Department of Bioinformatics
>>>>>>>> University of W?rzburg, Germany
>>>>>>>> Tel: +49 931 - 31 83696
>>>>>>>> Fax: +49 931 - 31 84552
>>>>>>>> felix.bemm at uni-wuerzburg.de
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> maker-devel mailing list
>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>> 
>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>> 
>>>>>> --
>>>>>> Felix Bemm
>>>>>> Department of Bioinformatics
>>>>>> University of W?rzburg, Germany
>>>>>> Tel: +49 931 - 31 83696
>>>>>> Fax: +49 931 - 31 84552
>>>>>> felix.bemm at uni-wuerzburg.de
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> 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
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> 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
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> Barry Moore
>> Research Scientist
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT 84112
>> --------------------------------------------
>> (801) 585-3543
>> 
>> 
>> 
>> 

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From marc.hoeppner at imbim.uu.se  Sat Oct 26 05:54:07 2013
From: marc.hoeppner at imbim.uu.se (Marc P. Hoeppner)
Date: Sat, 26 Oct 2013 13:54:07 +0200
Subject: [maker-devel] Maker MPICH2 issue (Multiple MAKER processes have
 been started in the same directory)
In-Reply-To: <526A7E14.9010906@imbim.uu.se>
References: <526A7E14.9010906@imbim.uu.se>
Message-ID: <526BAD5F.2000800@imbim.uu.se>

Dear List,

after much more debugging, I found the solution myself. Here are the 
details:

The Maker installation instructions refer to 'mpich2' in multiple 
places, including weblinks (whchi are outdated btw). Some digging 
revealed that mpich2 has since been renamed and merged back into mpich. 
So the website is www.mpich.org and the current stable version is 
mpich-3.0.4.  Closely following the installation instruction yielded a 
working copy of mpiexec that Maker was willing to accept. Good news - 
but I suggest to update the documentation. Most importantly for either 
SL/CentOS users, mpich2 as packaged with e.g. Scientific Linux *does 
not* work with Maker. You will need to download the latest stable build 
and compile it yourself (the mpich2 version bundled with Maker doesn't 
work either btw).

Cheers,

Marc

> Dear list,
>
> I know that MPICH2 related issues have been discussed previously, but 
> the suggested solutions don't seem to work for me.
> Briefly, I have set up a new cluster, with a fresh install of mpich2 
> (SL 6.4, from the yum repos) and a newly compiled build of Maker 2.28.
>
> When I start maker with mpiexec, I get spammed with
> 'WARNING: Multiple MAKER processes have been started in the same 
> directory.'
>
> Here is what I have tried so far - still getting the error :-< Any 
> suggestions would be appreciated
>
> --------
> MPICH2
> ---------
>
> which mpiexec:
> /usr/lib64/mpich2/bin/mpiexec
>
> Started the mpd ring as normal user across 5 nodes (bnode-01 to 
> bnode-04, and the head node bhead)
>
> mpdtrace:
> bhead
> bnode-02
> bnode-03
> bnode-04
> bnode-01
>
> mpdringtest:
> time for 1 loops = 0.00128293037415 seconds
>
> mpixec -n 32 -machinefile hostfile hostname:
>
> <long list of host names, as ecpected>
>
> I also ran the Skampi Mpi Benchmark, which ran through just fine.
>
> -----------
> MAKER
> -----------
>
> ./Build status
>
> PERL Dependencies:      VERIFIED
> External Programs:      VERIFIED
> External C Libraries:   VERIFIED
> MPI SUPPORT:            ENABLED
> MWAS Web Interface:     DISABLED
> MAKER PACKAGE:          CONFIGURATION OK
>
> During configuration/installation, Build.PL automatically detected all 
> MPI data and never complained, so I have to assume that everything 
> went fine there.
>


-- 
----------
Marc P. Hoeppner, PhD
Department of Microbiology and Medical Biochemistry
Uppsala University, Sweden
marc.hoeppner at imbim.uu.se




From barry.utah at gmail.com  Sat Oct 26 08:41:24 2013
From: barry.utah at gmail.com (Barry Moore)
Date: Sat, 26 Oct 2013 08:41:24 -0600
Subject: [maker-devel] Maker MPICH2 issue (Multiple MAKER processes have
	been started in the same directory)
In-Reply-To: <526BAD5F.2000800@imbim.uu.se>
References: <526A7E14.9010906@imbim.uu.se> <526BAD5F.2000800@imbim.uu.se>
Message-ID: <DDEE11FF-9EE2-4359-9A50-3DA95770DDEC@genetics.utah.edu>

Hi Marc,

Thanks so much for sharing the results of all your hard work!  We will follow up on your feedback and incorporate the necessary updates to MAKER docs and installation procedures.

B

On Oct 26, 2013, at 5:54 AM, Marc P. Hoeppner wrote:

> Dear List,
> 
> after much more debugging, I found the solution myself. Here are the details:
> 
> The Maker installation instructions refer to 'mpich2' in multiple places, including weblinks (whchi are outdated btw). Some digging revealed that mpich2 has since been renamed and merged back into mpich. So the website is www.mpich.org and the current stable version is mpich-3.0.4.  Closely following the installation instruction yielded a working copy of mpiexec that Maker was willing to accept. Good news - but I suggest to update the documentation. Most importantly for either SL/CentOS users, mpich2 as packaged with e.g. Scientific Linux *does not* work with Maker. You will need to download the latest stable build and compile it yourself (the mpich2 version bundled with Maker doesn't work either btw).
> 
> Cheers,
> 
> Marc
> 
>> Dear list,
>> 
>> I know that MPICH2 related issues have been discussed previously, but the suggested solutions don't seem to work for me.
>> Briefly, I have set up a new cluster, with a fresh install of mpich2 (SL 6.4, from the yum repos) and a newly compiled build of Maker 2.28.
>> 
>> When I start maker with mpiexec, I get spammed with
>> 'WARNING: Multiple MAKER processes have been started in the same directory.'
>> 
>> Here is what I have tried so far - still getting the error :-< Any suggestions would be appreciated
>> 
>> --------
>> MPICH2
>> ---------
>> 
>> which mpiexec:
>> /usr/lib64/mpich2/bin/mpiexec
>> 
>> Started the mpd ring as normal user across 5 nodes (bnode-01 to bnode-04, and the head node bhead)
>> 
>> mpdtrace:
>> bhead
>> bnode-02
>> bnode-03
>> bnode-04
>> bnode-01
>> 
>> mpdringtest:
>> time for 1 loops = 0.00128293037415 seconds
>> 
>> mpixec -n 32 -machinefile hostfile hostname:
>> 
>> <long list of host names, as ecpected>
>> 
>> I also ran the Skampi Mpi Benchmark, which ran through just fine.
>> 
>> -----------
>> MAKER
>> -----------
>> 
>> ./Build status
>> 
>> PERL Dependencies:      VERIFIED
>> External Programs:      VERIFIED
>> External C Libraries:   VERIFIED
>> MPI SUPPORT:            ENABLED
>> MWAS Web Interface:     DISABLED
>> MAKER PACKAGE:          CONFIGURATION OK
>> 
>> During configuration/installation, Build.PL automatically detected all MPI data and never complained, so I have to assume that everything went fine there.
>> 
> 
> 
> -- 
> ----------
> Marc P. Hoeppner, PhD
> Department of Microbiology and Medical Biochemistry
> Uppsala University, Sweden
> marc.hoeppner at imbim.uu.se
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From wholtz at lygos.com  Wed Oct 30 12:21:52 2013
From: wholtz at lygos.com (William Holtz)
Date: Wed, 30 Oct 2013 11:21:52 -0700 (PDT)
Subject: [maker-devel] maker apollo error
Message-ID: <1383157312.95043.YahooMailNeo@web5706.biz.mail.ne1.yahoo.com>

Hi,

I'm attempting to reply to a thread on this list from before I was a member. My apologies if this gets messed up.

I've tried installing maker v2.28 and v2.29p-beta and both of them fail due to the URL of the apollo tar file being outdated as previously reported on this list.?The updated URL that Carson Holt posted,?http://sourceforge.net/code-snapshots/svn/g/gm/gmod/svn/gmod-svn-25291-apollo-trunk.zip,?is also no longer valid. I was able to find a copy of the apollo source at?http://downloads.sourceforge.net/project/gmod/Apollo/1.11.1/apollo-1.11.1.tgz. However my attempts to integrate this into the maker build process have been unsuccessful, but likely could be done by someone more skilled than I.?Any pointers on how to get past this hurdle would be appreciated.

Thanks in advance for your help.

-Will



From barry.utah at gmail.com  Wed Oct 30 16:31:58 2013
From: barry.utah at gmail.com (Barry Moore)
Date: Wed, 30 Oct 2013 16:31:58 -0600
Subject: [maker-devel] maker apollo error
In-Reply-To: <1383157312.95043.YahooMailNeo@web5706.biz.mail.ne1.yahoo.com>
References: <1383157312.95043.YahooMailNeo@web5706.biz.mail.ne1.yahoo.com>
Message-ID: <C6E0A4A7-10D2-43B4-AA77-CCF6BE62E927@genetics.utah.edu>

Hi Will,

You can edit these URLs in the following file:

maker/src/locations

In a section that looks like this:

    'apollo'       => {'Linux_x86_64'  => 'http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar',
                       'Linux_i386'    => 'http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/trunk/?view=tar',
                       'Darwin_i386'   => 'http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz',
                       'Darwin_x86_64' => 'http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz',
                       'src_'          => 'http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz',
                   },

Carson may have more feedback for you as well, but he is right in the middle of a move, so there may be a few days before he can reply, so modifying this file should work for you in the mean time.

On any of the executables that are missing you can always install them manually and add them to your path and maker will find them.  Also, maker shouldn't be required for a base maker install, so you could ignore that dependency as well.

Thanks,

B




On Oct 30, 2013, at 12:21 PM, William Holtz wrote:

> Hi,
> 
> I'm attempting to reply to a thread on this list from before I was a member. My apologies if this gets messed up.
> 
> I've tried installing maker v2.28 and v2.29p-beta and both of them fail due to the URL of the apollo tar file being outdated as previously reported on this list. The updated URL that Carson Holt posted, http://sourceforge.net/code-snapshots/svn/g/gm/gmod/svn/gmod-svn-25291-apollo-trunk.zip, is also no longer valid. I was able to find a copy of the apollo source at http://downloads.sourceforge.net/project/gmod/Apollo/1.11.1/apollo-1.11.1.tgz. However my attempts to integrate this into the maker build process have been unsuccessful, but likely could be done by someone more skilled than I. Any pointers on how to get past this hurdle would be appreciated.
> 
> Thanks in advance for your help.
> 
> -Will
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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