From eennadi at gmail.com  Tue Oct  1 07:59:57 2019
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Tue, 1 Oct 2019 14:59:57 +0100
Subject: [maker-devel] How to make maker output into another directory
Message-ID: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>

Hi Carson
I want marker to output into a directory  /mnt/data/emmanuel/Makersupport.
Please how can I make that?

OPTS=/home/emmanuel/maker/bin

BOPTS=/home/emmanuel/maker/bin

EXE=/home/emmanuel/maker/bin

MAKER=/home/emmanuel/maker/bin

OUT=/mnt/data/emmanuel/Makersupport


${MAKER}/maker  -cpus 26 ${OPTS}/maker_opts.ctl ${BOPTS}/maker_bopts.ctl
${EXE}/maker_exe.ctl



Also,


I added RepBaseRepeatMaskerEdition-20170127.tar into the directory
/home/emmanuel/maker/exe/RepeatMasker


used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In
my /home/emmanuel/maker/exe/RepeatMasker/Libraries
I have RMRBSeqs.embl  but running maker it tells me it repbase is not
installed.
Nnadi Nnaemeka Emmanuel,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Tue Oct  1 10:34:38 2019
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 1 Oct 2019 10:34:38 -0600
Subject: [maker-devel] How to make maker output into another directory
In-Reply-To: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>
References: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>
Message-ID: <834E275E-A122-425B-94DB-1A9484505076@gmail.com>



> On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson
> I want marker to output into a directory  /mnt/data/emmanuel/Makersupport. Please how can I make that?



From the usage statement ?>

     -base    <string>   Set the base name MAKER uses to save output files.
                                  MAKER uses the input genome file name by default.



> 
> 
> Also,
> 
> I added RepBaseRepeatMaskerEdition-20170127.tar into the directory /home/emmanuel/maker/exe/RepeatMasker
> 
> used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my /home/emmanuel/maker/exe/RepeatMasker/Libraries I have RMRBSeqs.embl  but running maker it tells me it repbase is not installed.


After uncaring RepBase you have to run the ./configure script with rmblast installed and it will create the needed blast indexes and libraries

RepeatMasker.lib
RepeatMaskerLib.embl
RepeatMasker.lib.nhr
RepeatMasker.lib.nin
RepeatMasker.lib.nsq
RepeatMasker.lib.xnd
RepeatMasker.lib.xni
RepeatMasker.lib.xns
RepeatMasker.lib.xnt
RepeatPeps.lib
RepeatPeps.lib.phr
RepeatPeps.lib.pin
RepeatPeps.lib.psq
RepeatPeps.lib.xpd
RepeatPeps.lib.xpi
RepeatPeps.lib.xps
RepeatPeps.lib.xpt


?Carson

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From carsonhh at gmail.com  Wed Oct  2 06:21:19 2019
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 2 Oct 2019 06:21:19 -0600
Subject: [maker-devel] How to make maker output into another directory
In-Reply-To: <CAOXM=CXu-r8-LBkfG6_=f-QtyJZmGZevLAXxQmL=h8PTFgK44g@mail.gmail.com>
References: <CAOXM=CXu-r8-LBkfG6_=f-QtyJZmGZevLAXxQmL=h8PTFgK44g@mail.gmail.com>
Message-ID: <F89F089E-6A8B-4B08-A114-C0C8345B30AC@gmail.com>

Just make the desired path be your working directory then use -base to specify a name for the maker.output directory.

?Carson

Sent from my iPhone

> On Oct 1, 2019, at 11:15 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> ?
> Hi Carson
> Thanks for your email
> 
> I tried to use the -base option to make maker output into a new directory /mnt/data/emmanuel/Makersupport/mucuna
> 
> The log report is found below 
> 
> The 'base' option is an ID used in generating names for
> multiple files and directories. It is not a directory path.
> You must remove all '/' characters from '/mnt/data/emmanuel/Makersupport/mucuna'
> 
> Thanks
> 
> Emmanuel
> 
> Nnadi Nnaemeka Emmanuel,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
> 
> 
>> On Tue, Oct 1, 2019 at 5:34 PM Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> 
>>> On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>>> 
>>> Hi Carson
>>> I want marker to output into a directory  /mnt/data/emmanuel/Makersupport. Please how can I make that?
>> 
>> 
>> 
>> From the usage statement ?>
>> 
>>      -base    <string>   Set the base name MAKER uses to save output files.
>>                                   MAKER uses the input genome file name by default.
>> 
>> 
>> 
>>> 
>>> 
>>> Also,
>>> 
>>> I added RepBaseRepeatMaskerEdition-20170127.tar into the directory /home/emmanuel/maker/exe/RepeatMasker
>>> 
>>> used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my /home/emmanuel/maker/exe/RepeatMasker/Libraries I have RMRBSeqs.embl  but running maker it tells me it repbase is not installed.
>> 
>> 
>> After uncaring RepBase you have to run the ./configure script with rmblast installed and it will create the needed blast indexes and libraries
>> 
>> RepeatMasker.lib
>> RepeatMaskerLib.embl
>> RepeatMasker.lib.nhr
>> RepeatMasker.lib.nin
>> RepeatMasker.lib.nsq
>> RepeatMasker.lib.xnd
>> RepeatMasker.lib.xni
>> RepeatMasker.lib.xns
>> RepeatMasker.lib.xnt
>> RepeatPeps.lib
>> RepeatPeps.lib.phr
>> RepeatPeps.lib.pin
>> RepeatPeps.lib.psq
>> RepeatPeps.lib.xpd
>> RepeatPeps.lib.xpi
>> RepeatPeps.lib.xps
>> RepeatPeps.lib.xpt
>> 
>> 
>> ?Carson
>> 
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From scott at scottcain.net  Thu Oct 10 15:40:27 2019
From: scott at scottcain.net (Scott Cain)
Date: Thu, 10 Oct 2019 14:40:27 -0700
Subject: [maker-devel] GMOD codefest before PAG
Message-ID: <CA+JTaozeK31rvQAT69r+CUHRph9Ajx-rQivwbVe4QePoHoPKcQ@mail.gmail.com>

I am pleased to announce there will be a GMOD codefest occurring before the
Plant and Animal Genomes meeting in San Diego. The codefest will be at the
Town and Country hotel on January 9 and 10. If you would like to suggest a
problem or project to address, add it to this Google Doc
<https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing>.
The codefest is open to anyone who'd like to work on any GMOD project (or,
better yet, any combination of GMOD projects), including but not limited to
Tripal <http://gmod.org/wiki/Tripal>, Chado <http://gmod.org/wiki/Chado>,
JBrowse <http://gmod.org/wiki/JBrowse> (1 and 2), Galaxy
<http://gmod.org/wiki/Galaxy> and InterMine <http://gmod.org/wiki/InterMine>.
We already know that there will be Tripal, Chado and JBrowse developers
present. Registration information will be coming soon.

You can follow the changes to this page:

  http://gmod.org/wiki/Codefest_2020

to keep up to date, or follow The Tweet of GMOD (@gmodproject) on Twitter.

See you in San Diego,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From eennadi at gmail.com  Tue Oct  1 23:15:13 2019
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Wed, 2 Oct 2019 06:15:13 +0100
Subject: [maker-devel] How to make maker output into another directory
In-Reply-To: <834E275E-A122-425B-94DB-1A9484505076@gmail.com>
References: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>
	<834E275E-A122-425B-94DB-1A9484505076@gmail.com>
Message-ID: <CAOXM=CXu-r8-LBkfG6_=f-QtyJZmGZevLAXxQmL=h8PTFgK44g@mail.gmail.com>

Hi Carson
Thanks for your email


I tried to use the -base option to make maker output into a new directory
/mnt/data/emmanuel/Makersupport/mucuna


The log report is found below


The 'base' option is an ID used in generating names for

multiple files and directories. It is not a directory path.

You must remove all '/' characters from
'/mnt/data/emmanuel/Makersupport/mucuna'


Thanks


Emmanuel


Nnadi Nnaemeka Emmanuel,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications


On Tue, Oct 1, 2019 at 5:34 PM Carson Holt <carsonhh at gmail.com> wrote:

>
>
> On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>
> Hi Carson
> I want marker to output into a directory  /mnt/data/emmanuel/Makersupport.
> Please how can I make that?
>
>
>
>
> From the usage statement ?>
>
>      -base    <string>   Set the base name MAKER uses to save output files.
>                                   MAKER uses the input genome file name by
> default.
>
>
>
>
>
> Also,
>
> I added RepBaseRepeatMaskerEdition-20170127.tar into the directory
> /home/emmanuel/maker/exe/RepeatMasker
>
> used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my /home/emmanuel/maker/exe/RepeatMasker/Libraries
> I have RMRBSeqs.embl  but running maker it tells me it repbase is not
> installed.
>
>
>
> After uncaring RepBase you have to run the ./configure script with rmblast
> installed and it will create the needed blast indexes and libraries
>
> RepeatMasker.lib
> RepeatMaskerLib.embl
> RepeatMasker.lib.nhr
> RepeatMasker.lib.nin
> RepeatMasker.lib.nsq
> RepeatMasker.lib.xnd
> RepeatMasker.lib.xni
> RepeatMasker.lib.xns
> RepeatMasker.lib.xnt
> RepeatPeps.lib
> RepeatPeps.lib.phr
> RepeatPeps.lib.pin
> RepeatPeps.lib.psq
> RepeatPeps.lib.xpd
> RepeatPeps.lib.xpi
> RepeatPeps.lib.xps
> RepeatPeps.lib.xpt
>
>
> ?Carson
>
>
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From nathandunn at lbl.gov  Thu Oct 10 17:00:56 2019
From: nathandunn at lbl.gov (Nathan Dunn)
Date: Thu, 10 Oct 2019 16:00:56 -0700
Subject: [maker-devel] [GMOD-devel] GMOD codefest before PAG
In-Reply-To: <CA+JTaozeK31rvQAT69r+CUHRph9Ajx-rQivwbVe4QePoHoPKcQ@mail.gmail.com>
References: <CA+JTaozeK31rvQAT69r+CUHRph9Ajx-rQivwbVe4QePoHoPKcQ@mail.gmail.com>
Message-ID: <CEA978E2-D37F-43F7-B929-128FCAD8178D@lbl.gov>


I plan on being there to work on user?s Apollo-based problems (or JBrowse ones if that is more pertinent). 

I?ve copied on the Apollo list. 

Looking forward to seeing you there,

Nathan


> On Oct 10, 2019, at 2:40 PM, Scott Cain <scott at scottcain.net> wrote:
> 
> I am pleased to announce there will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc <https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing>. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to Tripal <http://gmod.org/wiki/Tripal>, Chado <http://gmod.org/wiki/Chado>, JBrowse <http://gmod.org/wiki/JBrowse> (1 and 2), Galaxy <http://gmod.org/wiki/Galaxy> and InterMine <http://gmod.org/wiki/InterMine>. We already know that there will be Tripal, Chado and JBrowse developers present. Registration information will be coming soon. 
> 
> You can follow the changes to this page:
> 
>   http://gmod.org/wiki/Codefest_2020 <http://gmod.org/wiki/Codefest_2020>
> 
> to keep up to date, or follow The Tweet of GMOD (@gmodproject) on Twitter.
> 
> See you in San Diego,
> Scott
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/ <http://gmod.org/>)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> Gmod-devel mailing list
> Gmod-devel at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-devel

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From david.hughes at rothamsted.ac.uk  Wed Oct 23 08:24:24 2019
From: david.hughes at rothamsted.ac.uk (David Hughes)
Date: Wed, 23 Oct 2019 14:24:24 +0000
Subject: [maker-devel] MAKER v3.0.0.
Message-ID: <CWLP123MB19243B821D8784707B70A08DB96B0@CWLP123MB1924.GBRP123.PROD.OUTLOOK.COM>

When we set  est2genome=1  in maker_opts.transfer.ctl, we find that   maker_bopts.ctl   seems not to be used.

Instead,   maker_bopts.log  sets  ep_score_limit=10  and  en_score_limit=20   and will not us change these parameters.

Is this intended?   Very grateful for your advice

Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.
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From carsonhh at gmail.com  Wed Oct 23 12:11:05 2019
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 23 Oct 2019 12:11:05 -0600
Subject: [maker-devel] maker-devel post from
 david.hughes@rothamsted.ac.uk requires approval
In-Reply-To: <mailman.222.1571840681.43761.maker-devel_yandell-lab.org@yandell-lab.org>
References: <mailman.222.1571840681.43761.maker-devel_yandell-lab.org@yandell-lab.org>
Message-ID: <0AD06698-5099-4783-BF01-3EDEF81AD320@gmail.com>

MAKER will use the files that you provide on the command line in the order they are provided. It will not check the names, it will just read them in one at a time and add their internal options in the order they are encountered. If no files are provided on the command line, then it will open the following files in order if they exist in the working directory: maker_opts.ctl, maker_bopts.ctl, maker_exe.ctl, and maker_evm.ctl.

If the same option is supplied twice, subsequent values will override and replace the first. The est2genome=1 option will not cause other values to be ignored or altered. However if you use the hidden and undocumented est_forward=1 option, it will override a number of internal values.

?Carson


> From: David Hughes <david.hughes at rothamsted.ac.uk <mailto:david.hughes at rothamsted.ac.uk>>
> Subject: MAKER v3.0.0.
> Date: October 23, 2019 at 8:24:24 AM MDT
> To: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> 
> 
> When we set  est2genome=1  in maker_opts.transfer.ctl, we find that   maker_bopts.ctl   seems not to be used.
>  
> Instead,   maker_bopts.log  sets  ep_score_limit=10  and  en_score_limit=20   and will not us change these parameters.
>  
> Is this intended?   Very grateful for your advice
> 
> Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038. 
> 

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From david.hughes at rothamsted.ac.uk  Thu Oct 24 01:31:15 2019
From: david.hughes at rothamsted.ac.uk (David Hughes)
Date: Thu, 24 Oct 2019 07:31:15 +0000
Subject: [maker-devel] maker-devel post from
 david.hughes@rothamsted.ac.uk requires approval
In-Reply-To: <0AD06698-5099-4783-BF01-3EDEF81AD320@gmail.com>
References: <mailman.222.1571840681.43761.maker-devel_yandell-lab.org@yandell-lab.org>
	<0AD06698-5099-4783-BF01-3EDEF81AD320@gmail.com>
Message-ID: <CWLP123MB1924C52068E2804B90C82FE3B96A0@CWLP123MB1924.GBRP123.PROD.OUTLOOK.COM>

Thanks Carson, very helpful.  We will investigate further.
From: Carson Holt <carsonhh at gmail.com>
Sent: 23 October 2019 19:11
To: David Hughes <david.hughes at rothamsted.ac.uk>; Maker Mailing List <maker-devel at yandell-lab.org>
Subject: Re: maker-devel post from david.hughes at rothamsted.ac.uk requires approval

MAKER will use the files that you provide on the command line in the order they are provided. It will not check the names, it will just read them in one at a time and add their internal options in the order they are encountered. If no files are provided on the command line, then it will open the following files in order if they exist in the working directory: maker_opts.ctl, maker_bopts.ctl, maker_exe.ctl, and maker_evm.ctl.

If the same option is supplied twice, subsequent values will override and replace the first. The est2genome=1 option will not cause other values to be ignored or altered. However if you use the hidden and undocumented est_forward=1 option, it will override a number of internal values.

?Carson



From: David Hughes <david.hughes at rothamsted.ac.uk<mailto:david.hughes at rothamsted.ac.uk>>
Subject: MAKER v3.0.0.
Date: October 23, 2019 at 8:24:24 AM MDT
To: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>


When we set  est2genome=1  in maker_opts.transfer.ctl, we find that   maker_bopts.ctl   seems not to be used.

Instead,   maker_bopts.log  sets  ep_score_limit=10  and  en_score_limit=20   and will not us change these parameters.

Is this intended?   Very grateful for your advice

Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.


Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.
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From peachandolives at gmail.com  Fri Oct 25 11:52:45 2019
From: peachandolives at gmail.com (Linnie Linnie)
Date: Fri, 25 Oct 2019 13:52:45 -0400
Subject: [maker-devel] Fungal genome annotation
Message-ID: <CAL5jVcwYJmHtiCTpErwcX-WaCXU4-wp4zpnFzHiFR9GS2F8e5w@mail.gmail.com>

Dear maker team,

I am annotating a small fungal genome (~30Mb) and I have several questions
as I move forward. My plan is to do:
1. custom repeat library
2. evidence-based maker (custom repeat library, repbase fungi database,
te_proteins.fa, ESTs from a somewhat related organism, proteome from
related organisms, transcripts from the same species)
3. train snap
4. maker run
5. re train snap (if it improves the models)
6. maker run
7. train Augustus
8. maker run
9. retrain augustus, if necessary
10. maker run
11. genemark
12. final maker run

My questions are:

a. Do I have to run RepeatMasker at every maker iteration?
b. Since I am dealing with a fungal genome, is it wise to change the
maker_opts.ctl with singe_exon=1, keep_phreds=1, correct_es_fusion=1?
c. If so, should I keep those parameters in every maker iteration?

Thank you so much for your help!

Linnie
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From eennadi at gmail.com  Tue Oct  1 07:59:57 2019
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Tue, 1 Oct 2019 14:59:57 +0100
Subject: [maker-devel] How to make maker output into another directory
Message-ID: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>

Hi Carson
I want marker to output into a directory  /mnt/data/emmanuel/Makersupport.
Please how can I make that?

OPTS=/home/emmanuel/maker/bin

BOPTS=/home/emmanuel/maker/bin

EXE=/home/emmanuel/maker/bin

MAKER=/home/emmanuel/maker/bin

OUT=/mnt/data/emmanuel/Makersupport


${MAKER}/maker  -cpus 26 ${OPTS}/maker_opts.ctl ${BOPTS}/maker_bopts.ctl
${EXE}/maker_exe.ctl



Also,


I added RepBaseRepeatMaskerEdition-20170127.tar into the directory
/home/emmanuel/maker/exe/RepeatMasker


used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In
my /home/emmanuel/maker/exe/RepeatMasker/Libraries
I have RMRBSeqs.embl  but running maker it tells me it repbase is not
installed.
Nnadi Nnaemeka Emmanuel,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Tue Oct  1 10:34:38 2019
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 1 Oct 2019 10:34:38 -0600
Subject: [maker-devel] How to make maker output into another directory
In-Reply-To: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>
References: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>
Message-ID: <834E275E-A122-425B-94DB-1A9484505076@gmail.com>



> On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson
> I want marker to output into a directory  /mnt/data/emmanuel/Makersupport. Please how can I make that?



From the usage statement ?>

     -base    <string>   Set the base name MAKER uses to save output files.
                                  MAKER uses the input genome file name by default.



> 
> 
> Also,
> 
> I added RepBaseRepeatMaskerEdition-20170127.tar into the directory /home/emmanuel/maker/exe/RepeatMasker
> 
> used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my /home/emmanuel/maker/exe/RepeatMasker/Libraries I have RMRBSeqs.embl  but running maker it tells me it repbase is not installed.


After uncaring RepBase you have to run the ./configure script with rmblast installed and it will create the needed blast indexes and libraries

RepeatMasker.lib
RepeatMaskerLib.embl
RepeatMasker.lib.nhr
RepeatMasker.lib.nin
RepeatMasker.lib.nsq
RepeatMasker.lib.xnd
RepeatMasker.lib.xni
RepeatMasker.lib.xns
RepeatMasker.lib.xnt
RepeatPeps.lib
RepeatPeps.lib.phr
RepeatPeps.lib.pin
RepeatPeps.lib.psq
RepeatPeps.lib.xpd
RepeatPeps.lib.xpi
RepeatPeps.lib.xps
RepeatPeps.lib.xpt


?Carson

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From carsonhh at gmail.com  Wed Oct  2 06:21:19 2019
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 2 Oct 2019 06:21:19 -0600
Subject: [maker-devel] How to make maker output into another directory
In-Reply-To: <CAOXM=CXu-r8-LBkfG6_=f-QtyJZmGZevLAXxQmL=h8PTFgK44g@mail.gmail.com>
References: <CAOXM=CXu-r8-LBkfG6_=f-QtyJZmGZevLAXxQmL=h8PTFgK44g@mail.gmail.com>
Message-ID: <F89F089E-6A8B-4B08-A114-C0C8345B30AC@gmail.com>

Just make the desired path be your working directory then use -base to specify a name for the maker.output directory.

?Carson

Sent from my iPhone

> On Oct 1, 2019, at 11:15 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> ?
> Hi Carson
> Thanks for your email
> 
> I tried to use the -base option to make maker output into a new directory /mnt/data/emmanuel/Makersupport/mucuna
> 
> The log report is found below 
> 
> The 'base' option is an ID used in generating names for
> multiple files and directories. It is not a directory path.
> You must remove all '/' characters from '/mnt/data/emmanuel/Makersupport/mucuna'
> 
> Thanks
> 
> Emmanuel
> 
> Nnadi Nnaemeka Emmanuel,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
> 
> 
>> On Tue, Oct 1, 2019 at 5:34 PM Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> 
>>> On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>>> 
>>> Hi Carson
>>> I want marker to output into a directory  /mnt/data/emmanuel/Makersupport. Please how can I make that?
>> 
>> 
>> 
>> From the usage statement ?>
>> 
>>      -base    <string>   Set the base name MAKER uses to save output files.
>>                                   MAKER uses the input genome file name by default.
>> 
>> 
>> 
>>> 
>>> 
>>> Also,
>>> 
>>> I added RepBaseRepeatMaskerEdition-20170127.tar into the directory /home/emmanuel/maker/exe/RepeatMasker
>>> 
>>> used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my /home/emmanuel/maker/exe/RepeatMasker/Libraries I have RMRBSeqs.embl  but running maker it tells me it repbase is not installed.
>> 
>> 
>> After uncaring RepBase you have to run the ./configure script with rmblast installed and it will create the needed blast indexes and libraries
>> 
>> RepeatMasker.lib
>> RepeatMaskerLib.embl
>> RepeatMasker.lib.nhr
>> RepeatMasker.lib.nin
>> RepeatMasker.lib.nsq
>> RepeatMasker.lib.xnd
>> RepeatMasker.lib.xni
>> RepeatMasker.lib.xns
>> RepeatMasker.lib.xnt
>> RepeatPeps.lib
>> RepeatPeps.lib.phr
>> RepeatPeps.lib.pin
>> RepeatPeps.lib.psq
>> RepeatPeps.lib.xpd
>> RepeatPeps.lib.xpi
>> RepeatPeps.lib.xps
>> RepeatPeps.lib.xpt
>> 
>> 
>> ?Carson
>> 
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From scott at scottcain.net  Thu Oct 10 15:40:27 2019
From: scott at scottcain.net (Scott Cain)
Date: Thu, 10 Oct 2019 14:40:27 -0700
Subject: [maker-devel] GMOD codefest before PAG
Message-ID: <CA+JTaozeK31rvQAT69r+CUHRph9Ajx-rQivwbVe4QePoHoPKcQ@mail.gmail.com>

I am pleased to announce there will be a GMOD codefest occurring before the
Plant and Animal Genomes meeting in San Diego. The codefest will be at the
Town and Country hotel on January 9 and 10. If you would like to suggest a
problem or project to address, add it to this Google Doc
<https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing>.
The codefest is open to anyone who'd like to work on any GMOD project (or,
better yet, any combination of GMOD projects), including but not limited to
Tripal <http://gmod.org/wiki/Tripal>, Chado <http://gmod.org/wiki/Chado>,
JBrowse <http://gmod.org/wiki/JBrowse> (1 and 2), Galaxy
<http://gmod.org/wiki/Galaxy> and InterMine <http://gmod.org/wiki/InterMine>.
We already know that there will be Tripal, Chado and JBrowse developers
present. Registration information will be coming soon.

You can follow the changes to this page:

  http://gmod.org/wiki/Codefest_2020

to keep up to date, or follow The Tweet of GMOD (@gmodproject) on Twitter.

See you in San Diego,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From eennadi at gmail.com  Tue Oct  1 23:15:13 2019
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Wed, 2 Oct 2019 06:15:13 +0100
Subject: [maker-devel] How to make maker output into another directory
In-Reply-To: <834E275E-A122-425B-94DB-1A9484505076@gmail.com>
References: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>
	<834E275E-A122-425B-94DB-1A9484505076@gmail.com>
Message-ID: <CAOXM=CXu-r8-LBkfG6_=f-QtyJZmGZevLAXxQmL=h8PTFgK44g@mail.gmail.com>

Hi Carson
Thanks for your email


I tried to use the -base option to make maker output into a new directory
/mnt/data/emmanuel/Makersupport/mucuna


The log report is found below


The 'base' option is an ID used in generating names for

multiple files and directories. It is not a directory path.

You must remove all '/' characters from
'/mnt/data/emmanuel/Makersupport/mucuna'


Thanks


Emmanuel


Nnadi Nnaemeka Emmanuel,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications


On Tue, Oct 1, 2019 at 5:34 PM Carson Holt <carsonhh at gmail.com> wrote:

>
>
> On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>
> Hi Carson
> I want marker to output into a directory  /mnt/data/emmanuel/Makersupport.
> Please how can I make that?
>
>
>
>
> From the usage statement ?>
>
>      -base    <string>   Set the base name MAKER uses to save output files.
>                                   MAKER uses the input genome file name by
> default.
>
>
>
>
>
> Also,
>
> I added RepBaseRepeatMaskerEdition-20170127.tar into the directory
> /home/emmanuel/maker/exe/RepeatMasker
>
> used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my /home/emmanuel/maker/exe/RepeatMasker/Libraries
> I have RMRBSeqs.embl  but running maker it tells me it repbase is not
> installed.
>
>
>
> After uncaring RepBase you have to run the ./configure script with rmblast
> installed and it will create the needed blast indexes and libraries
>
> RepeatMasker.lib
> RepeatMaskerLib.embl
> RepeatMasker.lib.nhr
> RepeatMasker.lib.nin
> RepeatMasker.lib.nsq
> RepeatMasker.lib.xnd
> RepeatMasker.lib.xni
> RepeatMasker.lib.xns
> RepeatMasker.lib.xnt
> RepeatPeps.lib
> RepeatPeps.lib.phr
> RepeatPeps.lib.pin
> RepeatPeps.lib.psq
> RepeatPeps.lib.xpd
> RepeatPeps.lib.xpi
> RepeatPeps.lib.xps
> RepeatPeps.lib.xpt
>
>
> ?Carson
>
>
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From nathandunn at lbl.gov  Thu Oct 10 17:00:56 2019
From: nathandunn at lbl.gov (Nathan Dunn)
Date: Thu, 10 Oct 2019 16:00:56 -0700
Subject: [maker-devel] [GMOD-devel] GMOD codefest before PAG
In-Reply-To: <CA+JTaozeK31rvQAT69r+CUHRph9Ajx-rQivwbVe4QePoHoPKcQ@mail.gmail.com>
References: <CA+JTaozeK31rvQAT69r+CUHRph9Ajx-rQivwbVe4QePoHoPKcQ@mail.gmail.com>
Message-ID: <CEA978E2-D37F-43F7-B929-128FCAD8178D@lbl.gov>


I plan on being there to work on user?s Apollo-based problems (or JBrowse ones if that is more pertinent). 

I?ve copied on the Apollo list. 

Looking forward to seeing you there,

Nathan


> On Oct 10, 2019, at 2:40 PM, Scott Cain <scott at scottcain.net> wrote:
> 
> I am pleased to announce there will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc <https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing>. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to Tripal <http://gmod.org/wiki/Tripal>, Chado <http://gmod.org/wiki/Chado>, JBrowse <http://gmod.org/wiki/JBrowse> (1 and 2), Galaxy <http://gmod.org/wiki/Galaxy> and InterMine <http://gmod.org/wiki/InterMine>. We already know that there will be Tripal, Chado and JBrowse developers present. Registration information will be coming soon. 
> 
> You can follow the changes to this page:
> 
>   http://gmod.org/wiki/Codefest_2020 <http://gmod.org/wiki/Codefest_2020>
> 
> to keep up to date, or follow The Tweet of GMOD (@gmodproject) on Twitter.
> 
> See you in San Diego,
> Scott
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/ <http://gmod.org/>)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> Gmod-devel mailing list
> Gmod-devel at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-devel

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From david.hughes at rothamsted.ac.uk  Wed Oct 23 08:24:24 2019
From: david.hughes at rothamsted.ac.uk (David Hughes)
Date: Wed, 23 Oct 2019 14:24:24 +0000
Subject: [maker-devel] MAKER v3.0.0.
Message-ID: <CWLP123MB19243B821D8784707B70A08DB96B0@CWLP123MB1924.GBRP123.PROD.OUTLOOK.COM>

When we set  est2genome=1  in maker_opts.transfer.ctl, we find that   maker_bopts.ctl   seems not to be used.

Instead,   maker_bopts.log  sets  ep_score_limit=10  and  en_score_limit=20   and will not us change these parameters.

Is this intended?   Very grateful for your advice

Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.
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From carsonhh at gmail.com  Wed Oct 23 12:11:05 2019
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 23 Oct 2019 12:11:05 -0600
Subject: [maker-devel] maker-devel post from
 david.hughes@rothamsted.ac.uk requires approval
In-Reply-To: <mailman.222.1571840681.43761.maker-devel_yandell-lab.org@yandell-lab.org>
References: <mailman.222.1571840681.43761.maker-devel_yandell-lab.org@yandell-lab.org>
Message-ID: <0AD06698-5099-4783-BF01-3EDEF81AD320@gmail.com>

MAKER will use the files that you provide on the command line in the order they are provided. It will not check the names, it will just read them in one at a time and add their internal options in the order they are encountered. If no files are provided on the command line, then it will open the following files in order if they exist in the working directory: maker_opts.ctl, maker_bopts.ctl, maker_exe.ctl, and maker_evm.ctl.

If the same option is supplied twice, subsequent values will override and replace the first. The est2genome=1 option will not cause other values to be ignored or altered. However if you use the hidden and undocumented est_forward=1 option, it will override a number of internal values.

?Carson


> From: David Hughes <david.hughes at rothamsted.ac.uk <mailto:david.hughes at rothamsted.ac.uk>>
> Subject: MAKER v3.0.0.
> Date: October 23, 2019 at 8:24:24 AM MDT
> To: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> 
> 
> When we set  est2genome=1  in maker_opts.transfer.ctl, we find that   maker_bopts.ctl   seems not to be used.
>  
> Instead,   maker_bopts.log  sets  ep_score_limit=10  and  en_score_limit=20   and will not us change these parameters.
>  
> Is this intended?   Very grateful for your advice
> 
> Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038. 
> 

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From david.hughes at rothamsted.ac.uk  Thu Oct 24 01:31:15 2019
From: david.hughes at rothamsted.ac.uk (David Hughes)
Date: Thu, 24 Oct 2019 07:31:15 +0000
Subject: [maker-devel] maker-devel post from
 david.hughes@rothamsted.ac.uk requires approval
In-Reply-To: <0AD06698-5099-4783-BF01-3EDEF81AD320@gmail.com>
References: <mailman.222.1571840681.43761.maker-devel_yandell-lab.org@yandell-lab.org>
	<0AD06698-5099-4783-BF01-3EDEF81AD320@gmail.com>
Message-ID: <CWLP123MB1924C52068E2804B90C82FE3B96A0@CWLP123MB1924.GBRP123.PROD.OUTLOOK.COM>

Thanks Carson, very helpful.  We will investigate further.
From: Carson Holt <carsonhh at gmail.com>
Sent: 23 October 2019 19:11
To: David Hughes <david.hughes at rothamsted.ac.uk>; Maker Mailing List <maker-devel at yandell-lab.org>
Subject: Re: maker-devel post from david.hughes at rothamsted.ac.uk requires approval

MAKER will use the files that you provide on the command line in the order they are provided. It will not check the names, it will just read them in one at a time and add their internal options in the order they are encountered. If no files are provided on the command line, then it will open the following files in order if they exist in the working directory: maker_opts.ctl, maker_bopts.ctl, maker_exe.ctl, and maker_evm.ctl.

If the same option is supplied twice, subsequent values will override and replace the first. The est2genome=1 option will not cause other values to be ignored or altered. However if you use the hidden and undocumented est_forward=1 option, it will override a number of internal values.

?Carson



From: David Hughes <david.hughes at rothamsted.ac.uk<mailto:david.hughes at rothamsted.ac.uk>>
Subject: MAKER v3.0.0.
Date: October 23, 2019 at 8:24:24 AM MDT
To: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>


When we set  est2genome=1  in maker_opts.transfer.ctl, we find that   maker_bopts.ctl   seems not to be used.

Instead,   maker_bopts.log  sets  ep_score_limit=10  and  en_score_limit=20   and will not us change these parameters.

Is this intended?   Very grateful for your advice

Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.


Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.
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From peachandolives at gmail.com  Fri Oct 25 11:52:45 2019
From: peachandolives at gmail.com (Linnie Linnie)
Date: Fri, 25 Oct 2019 13:52:45 -0400
Subject: [maker-devel] Fungal genome annotation
Message-ID: <CAL5jVcwYJmHtiCTpErwcX-WaCXU4-wp4zpnFzHiFR9GS2F8e5w@mail.gmail.com>

Dear maker team,

I am annotating a small fungal genome (~30Mb) and I have several questions
as I move forward. My plan is to do:
1. custom repeat library
2. evidence-based maker (custom repeat library, repbase fungi database,
te_proteins.fa, ESTs from a somewhat related organism, proteome from
related organisms, transcripts from the same species)
3. train snap
4. maker run
5. re train snap (if it improves the models)
6. maker run
7. train Augustus
8. maker run
9. retrain augustus, if necessary
10. maker run
11. genemark
12. final maker run

My questions are:

a. Do I have to run RepeatMasker at every maker iteration?
b. Since I am dealing with a fungal genome, is it wise to change the
maker_opts.ctl with singe_exon=1, keep_phreds=1, correct_es_fusion=1?
c. If so, should I keep those parameters in every maker iteration?

Thank you so much for your help!

Linnie
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From eennadi at gmail.com  Tue Oct  1 07:59:57 2019
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Tue, 1 Oct 2019 14:59:57 +0100
Subject: [maker-devel] How to make maker output into another directory
Message-ID: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>

Hi Carson
I want marker to output into a directory  /mnt/data/emmanuel/Makersupport.
Please how can I make that?

OPTS=/home/emmanuel/maker/bin

BOPTS=/home/emmanuel/maker/bin

EXE=/home/emmanuel/maker/bin

MAKER=/home/emmanuel/maker/bin

OUT=/mnt/data/emmanuel/Makersupport


${MAKER}/maker  -cpus 26 ${OPTS}/maker_opts.ctl ${BOPTS}/maker_bopts.ctl
${EXE}/maker_exe.ctl



Also,


I added RepBaseRepeatMaskerEdition-20170127.tar into the directory
/home/emmanuel/maker/exe/RepeatMasker


used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In
my /home/emmanuel/maker/exe/RepeatMasker/Libraries
I have RMRBSeqs.embl  but running maker it tells me it repbase is not
installed.
Nnadi Nnaemeka Emmanuel,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Tue Oct  1 10:34:38 2019
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 1 Oct 2019 10:34:38 -0600
Subject: [maker-devel] How to make maker output into another directory
In-Reply-To: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>
References: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>
Message-ID: <834E275E-A122-425B-94DB-1A9484505076@gmail.com>



> On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson
> I want marker to output into a directory  /mnt/data/emmanuel/Makersupport. Please how can I make that?



From the usage statement ?>

     -base    <string>   Set the base name MAKER uses to save output files.
                                  MAKER uses the input genome file name by default.



> 
> 
> Also,
> 
> I added RepBaseRepeatMaskerEdition-20170127.tar into the directory /home/emmanuel/maker/exe/RepeatMasker
> 
> used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my /home/emmanuel/maker/exe/RepeatMasker/Libraries I have RMRBSeqs.embl  but running maker it tells me it repbase is not installed.


After uncaring RepBase you have to run the ./configure script with rmblast installed and it will create the needed blast indexes and libraries

RepeatMasker.lib
RepeatMaskerLib.embl
RepeatMasker.lib.nhr
RepeatMasker.lib.nin
RepeatMasker.lib.nsq
RepeatMasker.lib.xnd
RepeatMasker.lib.xni
RepeatMasker.lib.xns
RepeatMasker.lib.xnt
RepeatPeps.lib
RepeatPeps.lib.phr
RepeatPeps.lib.pin
RepeatPeps.lib.psq
RepeatPeps.lib.xpd
RepeatPeps.lib.xpi
RepeatPeps.lib.xps
RepeatPeps.lib.xpt


?Carson

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From carsonhh at gmail.com  Wed Oct  2 06:21:19 2019
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 2 Oct 2019 06:21:19 -0600
Subject: [maker-devel] How to make maker output into another directory
In-Reply-To: <CAOXM=CXu-r8-LBkfG6_=f-QtyJZmGZevLAXxQmL=h8PTFgK44g@mail.gmail.com>
References: <CAOXM=CXu-r8-LBkfG6_=f-QtyJZmGZevLAXxQmL=h8PTFgK44g@mail.gmail.com>
Message-ID: <F89F089E-6A8B-4B08-A114-C0C8345B30AC@gmail.com>

Just make the desired path be your working directory then use -base to specify a name for the maker.output directory.

?Carson

Sent from my iPhone

> On Oct 1, 2019, at 11:15 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> ?
> Hi Carson
> Thanks for your email
> 
> I tried to use the -base option to make maker output into a new directory /mnt/data/emmanuel/Makersupport/mucuna
> 
> The log report is found below 
> 
> The 'base' option is an ID used in generating names for
> multiple files and directories. It is not a directory path.
> You must remove all '/' characters from '/mnt/data/emmanuel/Makersupport/mucuna'
> 
> Thanks
> 
> Emmanuel
> 
> Nnadi Nnaemeka Emmanuel,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
> 
> 
>> On Tue, Oct 1, 2019 at 5:34 PM Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> 
>>> On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>>> 
>>> Hi Carson
>>> I want marker to output into a directory  /mnt/data/emmanuel/Makersupport. Please how can I make that?
>> 
>> 
>> 
>> From the usage statement ?>
>> 
>>      -base    <string>   Set the base name MAKER uses to save output files.
>>                                   MAKER uses the input genome file name by default.
>> 
>> 
>> 
>>> 
>>> 
>>> Also,
>>> 
>>> I added RepBaseRepeatMaskerEdition-20170127.tar into the directory /home/emmanuel/maker/exe/RepeatMasker
>>> 
>>> used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my /home/emmanuel/maker/exe/RepeatMasker/Libraries I have RMRBSeqs.embl  but running maker it tells me it repbase is not installed.
>> 
>> 
>> After uncaring RepBase you have to run the ./configure script with rmblast installed and it will create the needed blast indexes and libraries
>> 
>> RepeatMasker.lib
>> RepeatMaskerLib.embl
>> RepeatMasker.lib.nhr
>> RepeatMasker.lib.nin
>> RepeatMasker.lib.nsq
>> RepeatMasker.lib.xnd
>> RepeatMasker.lib.xni
>> RepeatMasker.lib.xns
>> RepeatMasker.lib.xnt
>> RepeatPeps.lib
>> RepeatPeps.lib.phr
>> RepeatPeps.lib.pin
>> RepeatPeps.lib.psq
>> RepeatPeps.lib.xpd
>> RepeatPeps.lib.xpi
>> RepeatPeps.lib.xps
>> RepeatPeps.lib.xpt
>> 
>> 
>> ?Carson
>> 
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From scott at scottcain.net  Thu Oct 10 15:40:27 2019
From: scott at scottcain.net (Scott Cain)
Date: Thu, 10 Oct 2019 14:40:27 -0700
Subject: [maker-devel] GMOD codefest before PAG
Message-ID: <CA+JTaozeK31rvQAT69r+CUHRph9Ajx-rQivwbVe4QePoHoPKcQ@mail.gmail.com>

I am pleased to announce there will be a GMOD codefest occurring before the
Plant and Animal Genomes meeting in San Diego. The codefest will be at the
Town and Country hotel on January 9 and 10. If you would like to suggest a
problem or project to address, add it to this Google Doc
<https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing>.
The codefest is open to anyone who'd like to work on any GMOD project (or,
better yet, any combination of GMOD projects), including but not limited to
Tripal <http://gmod.org/wiki/Tripal>, Chado <http://gmod.org/wiki/Chado>,
JBrowse <http://gmod.org/wiki/JBrowse> (1 and 2), Galaxy
<http://gmod.org/wiki/Galaxy> and InterMine <http://gmod.org/wiki/InterMine>.
We already know that there will be Tripal, Chado and JBrowse developers
present. Registration information will be coming soon.

You can follow the changes to this page:

  http://gmod.org/wiki/Codefest_2020

to keep up to date, or follow The Tweet of GMOD (@gmodproject) on Twitter.

See you in San Diego,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From eennadi at gmail.com  Tue Oct  1 23:15:13 2019
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Wed, 2 Oct 2019 06:15:13 +0100
Subject: [maker-devel] How to make maker output into another directory
In-Reply-To: <834E275E-A122-425B-94DB-1A9484505076@gmail.com>
References: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>
	<834E275E-A122-425B-94DB-1A9484505076@gmail.com>
Message-ID: <CAOXM=CXu-r8-LBkfG6_=f-QtyJZmGZevLAXxQmL=h8PTFgK44g@mail.gmail.com>

Hi Carson
Thanks for your email


I tried to use the -base option to make maker output into a new directory
/mnt/data/emmanuel/Makersupport/mucuna


The log report is found below


The 'base' option is an ID used in generating names for

multiple files and directories. It is not a directory path.

You must remove all '/' characters from
'/mnt/data/emmanuel/Makersupport/mucuna'


Thanks


Emmanuel


Nnadi Nnaemeka Emmanuel,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications


On Tue, Oct 1, 2019 at 5:34 PM Carson Holt <carsonhh at gmail.com> wrote:

>
>
> On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>
> Hi Carson
> I want marker to output into a directory  /mnt/data/emmanuel/Makersupport.
> Please how can I make that?
>
>
>
>
> From the usage statement ?>
>
>      -base    <string>   Set the base name MAKER uses to save output files.
>                                   MAKER uses the input genome file name by
> default.
>
>
>
>
>
> Also,
>
> I added RepBaseRepeatMaskerEdition-20170127.tar into the directory
> /home/emmanuel/maker/exe/RepeatMasker
>
> used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my /home/emmanuel/maker/exe/RepeatMasker/Libraries
> I have RMRBSeqs.embl  but running maker it tells me it repbase is not
> installed.
>
>
>
> After uncaring RepBase you have to run the ./configure script with rmblast
> installed and it will create the needed blast indexes and libraries
>
> RepeatMasker.lib
> RepeatMaskerLib.embl
> RepeatMasker.lib.nhr
> RepeatMasker.lib.nin
> RepeatMasker.lib.nsq
> RepeatMasker.lib.xnd
> RepeatMasker.lib.xni
> RepeatMasker.lib.xns
> RepeatMasker.lib.xnt
> RepeatPeps.lib
> RepeatPeps.lib.phr
> RepeatPeps.lib.pin
> RepeatPeps.lib.psq
> RepeatPeps.lib.xpd
> RepeatPeps.lib.xpi
> RepeatPeps.lib.xps
> RepeatPeps.lib.xpt
>
>
> ?Carson
>
>
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From nathandunn at lbl.gov  Thu Oct 10 17:00:56 2019
From: nathandunn at lbl.gov (Nathan Dunn)
Date: Thu, 10 Oct 2019 16:00:56 -0700
Subject: [maker-devel] [GMOD-devel] GMOD codefest before PAG
In-Reply-To: <CA+JTaozeK31rvQAT69r+CUHRph9Ajx-rQivwbVe4QePoHoPKcQ@mail.gmail.com>
References: <CA+JTaozeK31rvQAT69r+CUHRph9Ajx-rQivwbVe4QePoHoPKcQ@mail.gmail.com>
Message-ID: <CEA978E2-D37F-43F7-B929-128FCAD8178D@lbl.gov>


I plan on being there to work on user?s Apollo-based problems (or JBrowse ones if that is more pertinent). 

I?ve copied on the Apollo list. 

Looking forward to seeing you there,

Nathan


> On Oct 10, 2019, at 2:40 PM, Scott Cain <scott at scottcain.net> wrote:
> 
> I am pleased to announce there will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc <https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing>. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to Tripal <http://gmod.org/wiki/Tripal>, Chado <http://gmod.org/wiki/Chado>, JBrowse <http://gmod.org/wiki/JBrowse> (1 and 2), Galaxy <http://gmod.org/wiki/Galaxy> and InterMine <http://gmod.org/wiki/InterMine>. We already know that there will be Tripal, Chado and JBrowse developers present. Registration information will be coming soon. 
> 
> You can follow the changes to this page:
> 
>   http://gmod.org/wiki/Codefest_2020 <http://gmod.org/wiki/Codefest_2020>
> 
> to keep up to date, or follow The Tweet of GMOD (@gmodproject) on Twitter.
> 
> See you in San Diego,
> Scott
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/ <http://gmod.org/>)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> Gmod-devel mailing list
> Gmod-devel at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-devel

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From david.hughes at rothamsted.ac.uk  Wed Oct 23 08:24:24 2019
From: david.hughes at rothamsted.ac.uk (David Hughes)
Date: Wed, 23 Oct 2019 14:24:24 +0000
Subject: [maker-devel] MAKER v3.0.0.
Message-ID: <CWLP123MB19243B821D8784707B70A08DB96B0@CWLP123MB1924.GBRP123.PROD.OUTLOOK.COM>

When we set  est2genome=1  in maker_opts.transfer.ctl, we find that   maker_bopts.ctl   seems not to be used.

Instead,   maker_bopts.log  sets  ep_score_limit=10  and  en_score_limit=20   and will not us change these parameters.

Is this intended?   Very grateful for your advice

Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.
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From carsonhh at gmail.com  Wed Oct 23 12:11:05 2019
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 23 Oct 2019 12:11:05 -0600
Subject: [maker-devel] maker-devel post from
 david.hughes@rothamsted.ac.uk requires approval
In-Reply-To: <mailman.222.1571840681.43761.maker-devel_yandell-lab.org@yandell-lab.org>
References: <mailman.222.1571840681.43761.maker-devel_yandell-lab.org@yandell-lab.org>
Message-ID: <0AD06698-5099-4783-BF01-3EDEF81AD320@gmail.com>

MAKER will use the files that you provide on the command line in the order they are provided. It will not check the names, it will just read them in one at a time and add their internal options in the order they are encountered. If no files are provided on the command line, then it will open the following files in order if they exist in the working directory: maker_opts.ctl, maker_bopts.ctl, maker_exe.ctl, and maker_evm.ctl.

If the same option is supplied twice, subsequent values will override and replace the first. The est2genome=1 option will not cause other values to be ignored or altered. However if you use the hidden and undocumented est_forward=1 option, it will override a number of internal values.

?Carson


> From: David Hughes <david.hughes at rothamsted.ac.uk <mailto:david.hughes at rothamsted.ac.uk>>
> Subject: MAKER v3.0.0.
> Date: October 23, 2019 at 8:24:24 AM MDT
> To: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> 
> 
> When we set  est2genome=1  in maker_opts.transfer.ctl, we find that   maker_bopts.ctl   seems not to be used.
>  
> Instead,   maker_bopts.log  sets  ep_score_limit=10  and  en_score_limit=20   and will not us change these parameters.
>  
> Is this intended?   Very grateful for your advice
> 
> Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038. 
> 

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From david.hughes at rothamsted.ac.uk  Thu Oct 24 01:31:15 2019
From: david.hughes at rothamsted.ac.uk (David Hughes)
Date: Thu, 24 Oct 2019 07:31:15 +0000
Subject: [maker-devel] maker-devel post from
 david.hughes@rothamsted.ac.uk requires approval
In-Reply-To: <0AD06698-5099-4783-BF01-3EDEF81AD320@gmail.com>
References: <mailman.222.1571840681.43761.maker-devel_yandell-lab.org@yandell-lab.org>
	<0AD06698-5099-4783-BF01-3EDEF81AD320@gmail.com>
Message-ID: <CWLP123MB1924C52068E2804B90C82FE3B96A0@CWLP123MB1924.GBRP123.PROD.OUTLOOK.COM>

Thanks Carson, very helpful.  We will investigate further.
From: Carson Holt <carsonhh at gmail.com>
Sent: 23 October 2019 19:11
To: David Hughes <david.hughes at rothamsted.ac.uk>; Maker Mailing List <maker-devel at yandell-lab.org>
Subject: Re: maker-devel post from david.hughes at rothamsted.ac.uk requires approval

MAKER will use the files that you provide on the command line in the order they are provided. It will not check the names, it will just read them in one at a time and add their internal options in the order they are encountered. If no files are provided on the command line, then it will open the following files in order if they exist in the working directory: maker_opts.ctl, maker_bopts.ctl, maker_exe.ctl, and maker_evm.ctl.

If the same option is supplied twice, subsequent values will override and replace the first. The est2genome=1 option will not cause other values to be ignored or altered. However if you use the hidden and undocumented est_forward=1 option, it will override a number of internal values.

?Carson



From: David Hughes <david.hughes at rothamsted.ac.uk<mailto:david.hughes at rothamsted.ac.uk>>
Subject: MAKER v3.0.0.
Date: October 23, 2019 at 8:24:24 AM MDT
To: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>


When we set  est2genome=1  in maker_opts.transfer.ctl, we find that   maker_bopts.ctl   seems not to be used.

Instead,   maker_bopts.log  sets  ep_score_limit=10  and  en_score_limit=20   and will not us change these parameters.

Is this intended?   Very grateful for your advice

Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.


Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.
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From peachandolives at gmail.com  Fri Oct 25 11:52:45 2019
From: peachandolives at gmail.com (Linnie Linnie)
Date: Fri, 25 Oct 2019 13:52:45 -0400
Subject: [maker-devel] Fungal genome annotation
Message-ID: <CAL5jVcwYJmHtiCTpErwcX-WaCXU4-wp4zpnFzHiFR9GS2F8e5w@mail.gmail.com>

Dear maker team,

I am annotating a small fungal genome (~30Mb) and I have several questions
as I move forward. My plan is to do:
1. custom repeat library
2. evidence-based maker (custom repeat library, repbase fungi database,
te_proteins.fa, ESTs from a somewhat related organism, proteome from
related organisms, transcripts from the same species)
3. train snap
4. maker run
5. re train snap (if it improves the models)
6. maker run
7. train Augustus
8. maker run
9. retrain augustus, if necessary
10. maker run
11. genemark
12. final maker run

My questions are:

a. Do I have to run RepeatMasker at every maker iteration?
b. Since I am dealing with a fungal genome, is it wise to change the
maker_opts.ctl with singe_exon=1, keep_phreds=1, correct_es_fusion=1?
c. If so, should I keep those parameters in every maker iteration?

Thank you so much for your help!

Linnie
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From eennadi at gmail.com  Tue Oct  1 07:59:57 2019
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Tue, 1 Oct 2019 14:59:57 +0100
Subject: [maker-devel] How to make maker output into another directory
Message-ID: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>

Hi Carson
I want marker to output into a directory  /mnt/data/emmanuel/Makersupport.
Please how can I make that?

OPTS=/home/emmanuel/maker/bin

BOPTS=/home/emmanuel/maker/bin

EXE=/home/emmanuel/maker/bin

MAKER=/home/emmanuel/maker/bin

OUT=/mnt/data/emmanuel/Makersupport


${MAKER}/maker  -cpus 26 ${OPTS}/maker_opts.ctl ${BOPTS}/maker_bopts.ctl
${EXE}/maker_exe.ctl



Also,


I added RepBaseRepeatMaskerEdition-20170127.tar into the directory
/home/emmanuel/maker/exe/RepeatMasker


used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In
my /home/emmanuel/maker/exe/RepeatMasker/Libraries
I have RMRBSeqs.embl  but running maker it tells me it repbase is not
installed.
Nnadi Nnaemeka Emmanuel,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Tue Oct  1 10:34:38 2019
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 1 Oct 2019 10:34:38 -0600
Subject: [maker-devel] How to make maker output into another directory
In-Reply-To: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>
References: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>
Message-ID: <834E275E-A122-425B-94DB-1A9484505076@gmail.com>



> On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson
> I want marker to output into a directory  /mnt/data/emmanuel/Makersupport. Please how can I make that?



From the usage statement ?>

     -base    <string>   Set the base name MAKER uses to save output files.
                                  MAKER uses the input genome file name by default.



> 
> 
> Also,
> 
> I added RepBaseRepeatMaskerEdition-20170127.tar into the directory /home/emmanuel/maker/exe/RepeatMasker
> 
> used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my /home/emmanuel/maker/exe/RepeatMasker/Libraries I have RMRBSeqs.embl  but running maker it tells me it repbase is not installed.


After uncaring RepBase you have to run the ./configure script with rmblast installed and it will create the needed blast indexes and libraries

RepeatMasker.lib
RepeatMaskerLib.embl
RepeatMasker.lib.nhr
RepeatMasker.lib.nin
RepeatMasker.lib.nsq
RepeatMasker.lib.xnd
RepeatMasker.lib.xni
RepeatMasker.lib.xns
RepeatMasker.lib.xnt
RepeatPeps.lib
RepeatPeps.lib.phr
RepeatPeps.lib.pin
RepeatPeps.lib.psq
RepeatPeps.lib.xpd
RepeatPeps.lib.xpi
RepeatPeps.lib.xps
RepeatPeps.lib.xpt


?Carson

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From carsonhh at gmail.com  Wed Oct  2 06:21:19 2019
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 2 Oct 2019 06:21:19 -0600
Subject: [maker-devel] How to make maker output into another directory
In-Reply-To: <CAOXM=CXu-r8-LBkfG6_=f-QtyJZmGZevLAXxQmL=h8PTFgK44g@mail.gmail.com>
References: <CAOXM=CXu-r8-LBkfG6_=f-QtyJZmGZevLAXxQmL=h8PTFgK44g@mail.gmail.com>
Message-ID: <F89F089E-6A8B-4B08-A114-C0C8345B30AC@gmail.com>

Just make the desired path be your working directory then use -base to specify a name for the maker.output directory.

?Carson

Sent from my iPhone

> On Oct 1, 2019, at 11:15 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> ?
> Hi Carson
> Thanks for your email
> 
> I tried to use the -base option to make maker output into a new directory /mnt/data/emmanuel/Makersupport/mucuna
> 
> The log report is found below 
> 
> The 'base' option is an ID used in generating names for
> multiple files and directories. It is not a directory path.
> You must remove all '/' characters from '/mnt/data/emmanuel/Makersupport/mucuna'
> 
> Thanks
> 
> Emmanuel
> 
> Nnadi Nnaemeka Emmanuel,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
> 
> 
>> On Tue, Oct 1, 2019 at 5:34 PM Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> 
>>> On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>>> 
>>> Hi Carson
>>> I want marker to output into a directory  /mnt/data/emmanuel/Makersupport. Please how can I make that?
>> 
>> 
>> 
>> From the usage statement ?>
>> 
>>      -base    <string>   Set the base name MAKER uses to save output files.
>>                                   MAKER uses the input genome file name by default.
>> 
>> 
>> 
>>> 
>>> 
>>> Also,
>>> 
>>> I added RepBaseRepeatMaskerEdition-20170127.tar into the directory /home/emmanuel/maker/exe/RepeatMasker
>>> 
>>> used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my /home/emmanuel/maker/exe/RepeatMasker/Libraries I have RMRBSeqs.embl  but running maker it tells me it repbase is not installed.
>> 
>> 
>> After uncaring RepBase you have to run the ./configure script with rmblast installed and it will create the needed blast indexes and libraries
>> 
>> RepeatMasker.lib
>> RepeatMaskerLib.embl
>> RepeatMasker.lib.nhr
>> RepeatMasker.lib.nin
>> RepeatMasker.lib.nsq
>> RepeatMasker.lib.xnd
>> RepeatMasker.lib.xni
>> RepeatMasker.lib.xns
>> RepeatMasker.lib.xnt
>> RepeatPeps.lib
>> RepeatPeps.lib.phr
>> RepeatPeps.lib.pin
>> RepeatPeps.lib.psq
>> RepeatPeps.lib.xpd
>> RepeatPeps.lib.xpi
>> RepeatPeps.lib.xps
>> RepeatPeps.lib.xpt
>> 
>> 
>> ?Carson
>> 
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From scott at scottcain.net  Thu Oct 10 15:40:27 2019
From: scott at scottcain.net (Scott Cain)
Date: Thu, 10 Oct 2019 14:40:27 -0700
Subject: [maker-devel] GMOD codefest before PAG
Message-ID: <CA+JTaozeK31rvQAT69r+CUHRph9Ajx-rQivwbVe4QePoHoPKcQ@mail.gmail.com>

I am pleased to announce there will be a GMOD codefest occurring before the
Plant and Animal Genomes meeting in San Diego. The codefest will be at the
Town and Country hotel on January 9 and 10. If you would like to suggest a
problem or project to address, add it to this Google Doc
<https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing>.
The codefest is open to anyone who'd like to work on any GMOD project (or,
better yet, any combination of GMOD projects), including but not limited to
Tripal <http://gmod.org/wiki/Tripal>, Chado <http://gmod.org/wiki/Chado>,
JBrowse <http://gmod.org/wiki/JBrowse> (1 and 2), Galaxy
<http://gmod.org/wiki/Galaxy> and InterMine <http://gmod.org/wiki/InterMine>.
We already know that there will be Tripal, Chado and JBrowse developers
present. Registration information will be coming soon.

You can follow the changes to this page:

  http://gmod.org/wiki/Codefest_2020

to keep up to date, or follow The Tweet of GMOD (@gmodproject) on Twitter.

See you in San Diego,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From eennadi at gmail.com  Tue Oct  1 23:15:13 2019
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Wed, 2 Oct 2019 06:15:13 +0100
Subject: [maker-devel] How to make maker output into another directory
In-Reply-To: <834E275E-A122-425B-94DB-1A9484505076@gmail.com>
References: <CAOXM=CWistO5Uan7Q05bv1SBTLza+GoZk_nvoS+79B2VomP9sg@mail.gmail.com>
	<834E275E-A122-425B-94DB-1A9484505076@gmail.com>
Message-ID: <CAOXM=CXu-r8-LBkfG6_=f-QtyJZmGZevLAXxQmL=h8PTFgK44g@mail.gmail.com>

Hi Carson
Thanks for your email


I tried to use the -base option to make maker output into a new directory
/mnt/data/emmanuel/Makersupport/mucuna


The log report is found below


The 'base' option is an ID used in generating names for

multiple files and directories. It is not a directory path.

You must remove all '/' characters from
'/mnt/data/emmanuel/Makersupport/mucuna'


Thanks


Emmanuel


Nnadi Nnaemeka Emmanuel,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications


On Tue, Oct 1, 2019 at 5:34 PM Carson Holt <carsonhh at gmail.com> wrote:

>
>
> On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>
> Hi Carson
> I want marker to output into a directory  /mnt/data/emmanuel/Makersupport.
> Please how can I make that?
>
>
>
>
> From the usage statement ?>
>
>      -base    <string>   Set the base name MAKER uses to save output files.
>                                   MAKER uses the input genome file name by
> default.
>
>
>
>
>
> Also,
>
> I added RepBaseRepeatMaskerEdition-20170127.tar into the directory
> /home/emmanuel/maker/exe/RepeatMasker
>
> used tar xvf RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my /home/emmanuel/maker/exe/RepeatMasker/Libraries
> I have RMRBSeqs.embl  but running maker it tells me it repbase is not
> installed.
>
>
>
> After uncaring RepBase you have to run the ./configure script with rmblast
> installed and it will create the needed blast indexes and libraries
>
> RepeatMasker.lib
> RepeatMaskerLib.embl
> RepeatMasker.lib.nhr
> RepeatMasker.lib.nin
> RepeatMasker.lib.nsq
> RepeatMasker.lib.xnd
> RepeatMasker.lib.xni
> RepeatMasker.lib.xns
> RepeatMasker.lib.xnt
> RepeatPeps.lib
> RepeatPeps.lib.phr
> RepeatPeps.lib.pin
> RepeatPeps.lib.psq
> RepeatPeps.lib.xpd
> RepeatPeps.lib.xpi
> RepeatPeps.lib.xps
> RepeatPeps.lib.xpt
>
>
> ?Carson
>
>
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From nathandunn at lbl.gov  Thu Oct 10 17:00:56 2019
From: nathandunn at lbl.gov (Nathan Dunn)
Date: Thu, 10 Oct 2019 16:00:56 -0700
Subject: [maker-devel] [GMOD-devel] GMOD codefest before PAG
In-Reply-To: <CA+JTaozeK31rvQAT69r+CUHRph9Ajx-rQivwbVe4QePoHoPKcQ@mail.gmail.com>
References: <CA+JTaozeK31rvQAT69r+CUHRph9Ajx-rQivwbVe4QePoHoPKcQ@mail.gmail.com>
Message-ID: <CEA978E2-D37F-43F7-B929-128FCAD8178D@lbl.gov>


I plan on being there to work on user?s Apollo-based problems (or JBrowse ones if that is more pertinent). 

I?ve copied on the Apollo list. 

Looking forward to seeing you there,

Nathan


> On Oct 10, 2019, at 2:40 PM, Scott Cain <scott at scottcain.net> wrote:
> 
> I am pleased to announce there will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc <https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing>. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to Tripal <http://gmod.org/wiki/Tripal>, Chado <http://gmod.org/wiki/Chado>, JBrowse <http://gmod.org/wiki/JBrowse> (1 and 2), Galaxy <http://gmod.org/wiki/Galaxy> and InterMine <http://gmod.org/wiki/InterMine>. We already know that there will be Tripal, Chado and JBrowse developers present. Registration information will be coming soon. 
> 
> You can follow the changes to this page:
> 
>   http://gmod.org/wiki/Codefest_2020 <http://gmod.org/wiki/Codefest_2020>
> 
> to keep up to date, or follow The Tweet of GMOD (@gmodproject) on Twitter.
> 
> See you in San Diego,
> Scott
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/ <http://gmod.org/>)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> Gmod-devel mailing list
> Gmod-devel at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-devel

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From david.hughes at rothamsted.ac.uk  Wed Oct 23 08:24:24 2019
From: david.hughes at rothamsted.ac.uk (David Hughes)
Date: Wed, 23 Oct 2019 14:24:24 +0000
Subject: [maker-devel] MAKER v3.0.0.
Message-ID: <CWLP123MB19243B821D8784707B70A08DB96B0@CWLP123MB1924.GBRP123.PROD.OUTLOOK.COM>

When we set  est2genome=1  in maker_opts.transfer.ctl, we find that   maker_bopts.ctl   seems not to be used.

Instead,   maker_bopts.log  sets  ep_score_limit=10  and  en_score_limit=20   and will not us change these parameters.

Is this intended?   Very grateful for your advice

Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.
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From carsonhh at gmail.com  Wed Oct 23 12:11:05 2019
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 23 Oct 2019 12:11:05 -0600
Subject: [maker-devel] maker-devel post from
 david.hughes@rothamsted.ac.uk requires approval
In-Reply-To: <mailman.222.1571840681.43761.maker-devel_yandell-lab.org@yandell-lab.org>
References: <mailman.222.1571840681.43761.maker-devel_yandell-lab.org@yandell-lab.org>
Message-ID: <0AD06698-5099-4783-BF01-3EDEF81AD320@gmail.com>

MAKER will use the files that you provide on the command line in the order they are provided. It will not check the names, it will just read them in one at a time and add their internal options in the order they are encountered. If no files are provided on the command line, then it will open the following files in order if they exist in the working directory: maker_opts.ctl, maker_bopts.ctl, maker_exe.ctl, and maker_evm.ctl.

If the same option is supplied twice, subsequent values will override and replace the first. The est2genome=1 option will not cause other values to be ignored or altered. However if you use the hidden and undocumented est_forward=1 option, it will override a number of internal values.

?Carson


> From: David Hughes <david.hughes at rothamsted.ac.uk <mailto:david.hughes at rothamsted.ac.uk>>
> Subject: MAKER v3.0.0.
> Date: October 23, 2019 at 8:24:24 AM MDT
> To: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> 
> 
> When we set  est2genome=1  in maker_opts.transfer.ctl, we find that   maker_bopts.ctl   seems not to be used.
>  
> Instead,   maker_bopts.log  sets  ep_score_limit=10  and  en_score_limit=20   and will not us change these parameters.
>  
> Is this intended?   Very grateful for your advice
> 
> Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038. 
> 

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From david.hughes at rothamsted.ac.uk  Thu Oct 24 01:31:15 2019
From: david.hughes at rothamsted.ac.uk (David Hughes)
Date: Thu, 24 Oct 2019 07:31:15 +0000
Subject: [maker-devel] maker-devel post from
 david.hughes@rothamsted.ac.uk requires approval
In-Reply-To: <0AD06698-5099-4783-BF01-3EDEF81AD320@gmail.com>
References: <mailman.222.1571840681.43761.maker-devel_yandell-lab.org@yandell-lab.org>
	<0AD06698-5099-4783-BF01-3EDEF81AD320@gmail.com>
Message-ID: <CWLP123MB1924C52068E2804B90C82FE3B96A0@CWLP123MB1924.GBRP123.PROD.OUTLOOK.COM>

Thanks Carson, very helpful.  We will investigate further.
From: Carson Holt <carsonhh at gmail.com>
Sent: 23 October 2019 19:11
To: David Hughes <david.hughes at rothamsted.ac.uk>; Maker Mailing List <maker-devel at yandell-lab.org>
Subject: Re: maker-devel post from david.hughes at rothamsted.ac.uk requires approval

MAKER will use the files that you provide on the command line in the order they are provided. It will not check the names, it will just read them in one at a time and add their internal options in the order they are encountered. If no files are provided on the command line, then it will open the following files in order if they exist in the working directory: maker_opts.ctl, maker_bopts.ctl, maker_exe.ctl, and maker_evm.ctl.

If the same option is supplied twice, subsequent values will override and replace the first. The est2genome=1 option will not cause other values to be ignored or altered. However if you use the hidden and undocumented est_forward=1 option, it will override a number of internal values.

?Carson



From: David Hughes <david.hughes at rothamsted.ac.uk<mailto:david.hughes at rothamsted.ac.uk>>
Subject: MAKER v3.0.0.
Date: October 23, 2019 at 8:24:24 AM MDT
To: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>


When we set  est2genome=1  in maker_opts.transfer.ctl, we find that   maker_bopts.ctl   seems not to be used.

Instead,   maker_bopts.log  sets  ep_score_limit=10  and  en_score_limit=20   and will not us change these parameters.

Is this intended?   Very grateful for your advice

Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.


Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.
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From peachandolives at gmail.com  Fri Oct 25 11:52:45 2019
From: peachandolives at gmail.com (Linnie Linnie)
Date: Fri, 25 Oct 2019 13:52:45 -0400
Subject: [maker-devel] Fungal genome annotation
Message-ID: <CAL5jVcwYJmHtiCTpErwcX-WaCXU4-wp4zpnFzHiFR9GS2F8e5w@mail.gmail.com>

Dear maker team,

I am annotating a small fungal genome (~30Mb) and I have several questions
as I move forward. My plan is to do:
1. custom repeat library
2. evidence-based maker (custom repeat library, repbase fungi database,
te_proteins.fa, ESTs from a somewhat related organism, proteome from
related organisms, transcripts from the same species)
3. train snap
4. maker run
5. re train snap (if it improves the models)
6. maker run
7. train Augustus
8. maker run
9. retrain augustus, if necessary
10. maker run
11. genemark
12. final maker run

My questions are:

a. Do I have to run RepeatMasker at every maker iteration?
b. Since I am dealing with a fungal genome, is it wise to change the
maker_opts.ctl with singe_exon=1, keep_phreds=1, correct_es_fusion=1?
c. If so, should I keep those parameters in every maker iteration?

Thank you so much for your help!

Linnie
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