From carsonhh at gmail.com  Tue Nov  1 15:37:39 2022
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 1 Nov 2022 15:37:39 -0600
Subject: [maker-devel] ERROR: Unknown strand in GFFDB::_sort_exons!
In-Reply-To: <MN2PR04MB6158846A27716FB3E691221BF7649@MN2PR04MB6158.namprd04.prod.outlook.com>
References: <MN2PR04MB6158846A27716FB3E691221BF7649@MN2PR04MB6158.namprd04.prod.outlook.com>
Message-ID: <E7E6E2A4-24EA-4D83-913A-389FD14D424E@gmail.com>

The issue is your input GFF3 file. It has a format issue somewwhere. Likely invalid strand info or coordinate info for a feature

?Carson

> On Aug 10, 2022, at 7:01 PM, Jingyin Yu <jy526 at cornell.edu> wrote:
> 
> Hello All,
> 
> I ran maker3 and got the error message, but did not get way how to solve it, 
> ##############################################
> ERROR: Unknown strand in GFFDB::_sort_exons!
> --> rank=NA, hostname=swift
> ERROR: Failed while doing repeat masking
> ERROR: Chunk failed at level:0, tier_type:1
> FAILED CONTIG:chr1
> 
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:chr1
> 
> examining contents of the fasta file and run log
> ##############################################
> I am not sure if you guys can give me some suggestions. Thanks a lot.
> 
> Best,
> Jingyin
> 
> PostDoc, Boyce Thompson Institute for Plant Research?
> Cornell University?
> Ithaca, NY 14853?
> Email: jy526 at cornell.edu <mailto:jy526 at cornell.edu> ?
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Thu Nov  3 11:47:26 2022
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 3 Nov 2022 11:47:26 -0600
Subject: [maker-devel] Maker always fails to run on a particular
 chromosome.
In-Reply-To: <CABcOqf0wLvvd-7mBCAqqhJ7boesPz_Q=xASGy3-BnbjE+75LMQ@mail.gmail.com>
References: <CABcOqf0wLvvd-7mBCAqqhJ7boesPz_Q=xASGy3-BnbjE+75LMQ@mail.gmail.com>
Message-ID: <34134473-FDD6-4030-829B-DE3D7B532761@gmail.com>

You have a number of initial GFF3 related errors. I think one of your input files has an issue somewhere. Likely a truncated line in the GFF3. You will have to find and fix the feature with issues, then delete any *.db files under the *.maker.output directory before restarting. That will force it to rebuild the database that maps the current GFF3 files.

Thanks,
Carson


> On Oct 23, 2022, at 12:08 AM, WIIE AY <aywiiee at gmail.com> wrote:
> 
> Hi,
> 
> Thanks for this excellent software.
> However, when we annotated a rice genome (chr1-12) using Maker/3.01.03, the first round ran very well.
> When we added the snap and gmhmm models in the second round, only chr04 always failed in 12 chromosomes.
> Here is my chr4_run.log, stderr.out.(Maybe need maker_opts.ctl.)
> Looking forward to your reply.
>  
> ?maker_opts.ctl <https://drive.google.com/file/d/1TCjAPWGbQSMA4g49wQWySzROvsCY_rRg/view?usp=drive_web>
> ?run.log <https://drive.google.com/file/d/1li8Fn-AjOFfbLmcF_PFwpI6Eq-q9qeGs/view?usp=drive_web>
> ?stderr_73012967.err <https://drive.google.com/file/d/1hEYAcxgyLNeuWCHOcKQbpwyCesfWDHbg/view?usp=drive_web>THANKS 
> Peter
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From elissaralam at ufl.edu  Wed Nov 23 07:46:08 2022
From: elissaralam at ufl.edu (Alam,Elissar)
Date: Wed, 23 Nov 2022 14:46:08 +0000
Subject: [maker-devel] Augustus predictions within MAKER2
Message-ID: <SJ0PR22MB352874B08FE963FE4C25A3C9AD0C9@SJ0PR22MB3528.namprd22.prod.outlook.com>

Hello,

I ran Augustus and SNAP as part of the MAKER2 gene annotation pipeline. I would like to use the gene predictions generated by Augustus (prior to MAKER selecting the final gene model based on all ab initio predictions) for downstream analyses. Is there a way to obtain the Augustus gene predictions in gff3 format from MAKER2?

Thanks a million,
Elissar
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From jason.stajich at gmail.com  Fri Nov 25 09:49:55 2022
From: jason.stajich at gmail.com (Jason Stajich)
Date: Fri, 25 Nov 2022 08:49:55 -0800
Subject: [maker-devel] Augustus predictions within MAKER2
In-Reply-To: <SJ0PR22MB352874B08FE963FE4C25A3C9AD0C9@SJ0PR22MB3528.namprd22.prod.outlook.com>
References: <SJ0PR22MB352874B08FE963FE4C25A3C9AD0C9@SJ0PR22MB3528.namprd22.prod.outlook.com>
Message-ID: <CALf8LpzD5vEi86NvUY93VDcaHD7empQHN=gi0uGuWcWB4vENog@mail.gmail.com>

After you run the gff3_merge step you can
grep augustus final.gff > augustus.gff3

On Wed, Nov 23, 2022 at 8:02 AM Alam,Elissar <elissaralam at ufl.edu> wrote:

> Hello,
>
>
>
> I ran Augustus and SNAP as part of the MAKER2 gene annotation pipeline. I
> would like to use the gene predictions generated by Augustus (prior to
> MAKER selecting the final gene model based on all ab initio predictions)
> for downstream analyses. Is there a way to obtain the Augustus gene
> predictions in gff3 format from MAKER2?
>
>
>
> Thanks a million,
>
> Elissar
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
-- 
Jason Stajich
jason.stajich at gmail.com
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From elissaralam at ufl.edu  Fri Nov 25 09:56:49 2022
From: elissaralam at ufl.edu (Alam,Elissar)
Date: Fri, 25 Nov 2022 16:56:49 +0000
Subject: [maker-devel] Augustus predictions within MAKER2
In-Reply-To: <CALf8LpzD5vEi86NvUY93VDcaHD7empQHN=gi0uGuWcWB4vENog@mail.gmail.com>
References: <SJ0PR22MB352874B08FE963FE4C25A3C9AD0C9@SJ0PR22MB3528.namprd22.prod.outlook.com>
 <CALf8LpzD5vEi86NvUY93VDcaHD7empQHN=gi0uGuWcWB4vENog@mail.gmail.com>
Message-ID: <SJ0PR22MB352871E05FEADC7B7F348C26AD0E9@SJ0PR22MB3528.namprd22.prod.outlook.com>

Would that include all the gene models predicted by Augustus or only the ones that Maker retains after considering all ab initio gene predictions (SNAP + Augustus) and the EST evidence?

Thanks a lot,
Elissar

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

From: Jason Stajich<mailto:jason.stajich at gmail.com>
Sent: Friday, November 25, 2022 11:51 AM
To: Alam,Elissar<mailto:elissaralam at ufl.edu>
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Augustus predictions within MAKER2

[External Email]
After you run the gff3_merge step you can
grep augustus final.gff > augustus.gff3

On Wed, Nov 23, 2022 at 8:02 AM Alam,Elissar <elissaralam at ufl.edu<mailto:elissaralam at ufl.edu>> wrote:
Hello,

I ran Augustus and SNAP as part of the MAKER2 gene annotation pipeline. I would like to use the gene predictions generated by Augustus (prior to MAKER selecting the final gene model based on all ab initio predictions) for downstream analyses. Is there a way to obtain the Augustus gene predictions in gff3 format from MAKER2?

Thanks a million,
Elissar
_______________________________________________
maker-devel mailing list
maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fyandell-lab.org%2Fmailman%2Flistinfo%2Fmaker-devel_yandell-lab.org&data=05%7C01%7Celissaralam%40ufl.edu%7C0ece808fa41e4d71ea2008dacf051c8d%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638049918746729551%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5O%2Fg%2F2ZbQX0vxETbe3tBAlCbocsfFuu5xtfTlWkMO4E%3D&reserved=0>
--
Jason Stajich
jason.stajich at gmail.com<mailto:jason.stajich at gmail.com>

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From jason.stajich at gmail.com  Sat Nov 26 12:29:27 2022
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 26 Nov 2022 11:29:27 -0800
Subject: [maker-devel] Augustus predictions within MAKER2
In-Reply-To: <SJ0PR22MB352871E05FEADC7B7F348C26AD0E9@SJ0PR22MB3528.namprd22.prod.outlook.com>
References: <SJ0PR22MB352874B08FE963FE4C25A3C9AD0C9@SJ0PR22MB3528.namprd22.prod.outlook.com>
 <CALf8LpzD5vEi86NvUY93VDcaHD7empQHN=gi0uGuWcWB4vENog@mail.gmail.com>
 <SJ0PR22MB352871E05FEADC7B7F348C26AD0E9@SJ0PR22MB3528.namprd22.prod.outlook.com>
Message-ID: <CALf8LpyOTxPj9xH8xXeRyXcUoHfObpSbbekk7orkCpRzwBuBnA@mail.gmail.com>

I?d check the documentation and the raw files in the run folder if you
aren?t sure but The maker consensus models will have maker in the 2nd
column and the augustus will have augustus in second  column of gff
(?source?)

You might need to adjust your grep to only take those with augustus in 2nd
Col. you can do grep -P ?\taugustus\t? to get those.


On Fri, Nov 25, 2022 at 8:56 AM Alam,Elissa <elissaralam at ufl.edu> wrote:

> Would that include all the gene models predicted by Augustus or only the
> ones that Maker retains after considering all ab initio gene predictions
> (SNAP + Augustus) and the EST evidence?
>
>
>
> Thanks a lot,
>
> Elissar
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows
>
>
>
> *From: *Jason Stajich <jason.stajich at gmail.com>
> *Sent: *Friday, November 25, 2022 11:51 AM
> *To: *Alam,Elissar <elissaralam at ufl.edu>
> *Cc: *maker-devel at yandell-lab.org
> *Subject: *Re: [maker-devel] Augustus predictions within MAKER2
>
>
>
> *[External Email]*
>
> After you run the gff3_merge step you can
>
> grep augustus final.gff > augustus.gff3
>
>
>
> On Wed, Nov 23, 2022 at 8:02 AM Alam,Elissar <elissaralam at ufl.edu> wrote:
>
> Hello,
>
>
>
> I ran Augustus and SNAP as part of the MAKER2 gene annotation pipeline. I
> would like to use the gene predictions generated by Augustus (prior to
> MAKER selecting the final gene model based on all ab initio predictions)
> for downstream analyses. Is there a way to obtain the Augustus gene
> predictions in gff3 format from MAKER2?
>
>
>
> Thanks a million,
>
> Elissar
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fyandell-lab.org%2Fmailman%2Flistinfo%2Fmaker-devel_yandell-lab.org&data=05%7C01%7Celissaralam%40ufl.edu%7C0ece808fa41e4d71ea2008dacf051c8d%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638049918746729551%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5O%2Fg%2F2ZbQX0vxETbe3tBAlCbocsfFuu5xtfTlWkMO4E%3D&reserved=0>
>
> --
>
> Jason Stajich
> jason.stajich at gmail.com
>
>
>
-- 
Jason Stajich
jason.stajich at gmail.com
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From carsonhh at gmail.com  Tue Nov  1 15:37:39 2022
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 1 Nov 2022 15:37:39 -0600
Subject: [maker-devel] ERROR: Unknown strand in GFFDB::_sort_exons!
In-Reply-To: <MN2PR04MB6158846A27716FB3E691221BF7649@MN2PR04MB6158.namprd04.prod.outlook.com>
References: <MN2PR04MB6158846A27716FB3E691221BF7649@MN2PR04MB6158.namprd04.prod.outlook.com>
Message-ID: <E7E6E2A4-24EA-4D83-913A-389FD14D424E@gmail.com>

The issue is your input GFF3 file. It has a format issue somewwhere. Likely invalid strand info or coordinate info for a feature

?Carson

> On Aug 10, 2022, at 7:01 PM, Jingyin Yu <jy526 at cornell.edu> wrote:
> 
> Hello All,
> 
> I ran maker3 and got the error message, but did not get way how to solve it, 
> ##############################################
> ERROR: Unknown strand in GFFDB::_sort_exons!
> --> rank=NA, hostname=swift
> ERROR: Failed while doing repeat masking
> ERROR: Chunk failed at level:0, tier_type:1
> FAILED CONTIG:chr1
> 
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:chr1
> 
> examining contents of the fasta file and run log
> ##############################################
> I am not sure if you guys can give me some suggestions. Thanks a lot.
> 
> Best,
> Jingyin
> 
> PostDoc, Boyce Thompson Institute for Plant Research?
> Cornell University?
> Ithaca, NY 14853?
> Email: jy526 at cornell.edu <mailto:jy526 at cornell.edu> ?
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Thu Nov  3 11:47:26 2022
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 3 Nov 2022 11:47:26 -0600
Subject: [maker-devel] Maker always fails to run on a particular
 chromosome.
In-Reply-To: <CABcOqf0wLvvd-7mBCAqqhJ7boesPz_Q=xASGy3-BnbjE+75LMQ@mail.gmail.com>
References: <CABcOqf0wLvvd-7mBCAqqhJ7boesPz_Q=xASGy3-BnbjE+75LMQ@mail.gmail.com>
Message-ID: <34134473-FDD6-4030-829B-DE3D7B532761@gmail.com>

You have a number of initial GFF3 related errors. I think one of your input files has an issue somewhere. Likely a truncated line in the GFF3. You will have to find and fix the feature with issues, then delete any *.db files under the *.maker.output directory before restarting. That will force it to rebuild the database that maps the current GFF3 files.

Thanks,
Carson


> On Oct 23, 2022, at 12:08 AM, WIIE AY <aywiiee at gmail.com> wrote:
> 
> Hi,
> 
> Thanks for this excellent software.
> However, when we annotated a rice genome (chr1-12) using Maker/3.01.03, the first round ran very well.
> When we added the snap and gmhmm models in the second round, only chr04 always failed in 12 chromosomes.
> Here is my chr4_run.log, stderr.out.(Maybe need maker_opts.ctl.)
> Looking forward to your reply.
>  
> ?maker_opts.ctl <https://drive.google.com/file/d/1TCjAPWGbQSMA4g49wQWySzROvsCY_rRg/view?usp=drive_web>
> ?run.log <https://drive.google.com/file/d/1li8Fn-AjOFfbLmcF_PFwpI6Eq-q9qeGs/view?usp=drive_web>
> ?stderr_73012967.err <https://drive.google.com/file/d/1hEYAcxgyLNeuWCHOcKQbpwyCesfWDHbg/view?usp=drive_web>THANKS 
> Peter
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From elissaralam at ufl.edu  Wed Nov 23 07:46:08 2022
From: elissaralam at ufl.edu (Alam,Elissar)
Date: Wed, 23 Nov 2022 14:46:08 +0000
Subject: [maker-devel] Augustus predictions within MAKER2
Message-ID: <SJ0PR22MB352874B08FE963FE4C25A3C9AD0C9@SJ0PR22MB3528.namprd22.prod.outlook.com>

Hello,

I ran Augustus and SNAP as part of the MAKER2 gene annotation pipeline. I would like to use the gene predictions generated by Augustus (prior to MAKER selecting the final gene model based on all ab initio predictions) for downstream analyses. Is there a way to obtain the Augustus gene predictions in gff3 format from MAKER2?

Thanks a million,
Elissar
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From jason.stajich at gmail.com  Fri Nov 25 09:49:55 2022
From: jason.stajich at gmail.com (Jason Stajich)
Date: Fri, 25 Nov 2022 08:49:55 -0800
Subject: [maker-devel] Augustus predictions within MAKER2
In-Reply-To: <SJ0PR22MB352874B08FE963FE4C25A3C9AD0C9@SJ0PR22MB3528.namprd22.prod.outlook.com>
References: <SJ0PR22MB352874B08FE963FE4C25A3C9AD0C9@SJ0PR22MB3528.namprd22.prod.outlook.com>
Message-ID: <CALf8LpzD5vEi86NvUY93VDcaHD7empQHN=gi0uGuWcWB4vENog@mail.gmail.com>

After you run the gff3_merge step you can
grep augustus final.gff > augustus.gff3

On Wed, Nov 23, 2022 at 8:02 AM Alam,Elissar <elissaralam at ufl.edu> wrote:

> Hello,
>
>
>
> I ran Augustus and SNAP as part of the MAKER2 gene annotation pipeline. I
> would like to use the gene predictions generated by Augustus (prior to
> MAKER selecting the final gene model based on all ab initio predictions)
> for downstream analyses. Is there a way to obtain the Augustus gene
> predictions in gff3 format from MAKER2?
>
>
>
> Thanks a million,
>
> Elissar
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
-- 
Jason Stajich
jason.stajich at gmail.com
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From elissaralam at ufl.edu  Fri Nov 25 09:56:49 2022
From: elissaralam at ufl.edu (Alam,Elissar)
Date: Fri, 25 Nov 2022 16:56:49 +0000
Subject: [maker-devel] Augustus predictions within MAKER2
In-Reply-To: <CALf8LpzD5vEi86NvUY93VDcaHD7empQHN=gi0uGuWcWB4vENog@mail.gmail.com>
References: <SJ0PR22MB352874B08FE963FE4C25A3C9AD0C9@SJ0PR22MB3528.namprd22.prod.outlook.com>
 <CALf8LpzD5vEi86NvUY93VDcaHD7empQHN=gi0uGuWcWB4vENog@mail.gmail.com>
Message-ID: <SJ0PR22MB352871E05FEADC7B7F348C26AD0E9@SJ0PR22MB3528.namprd22.prod.outlook.com>

Would that include all the gene models predicted by Augustus or only the ones that Maker retains after considering all ab initio gene predictions (SNAP + Augustus) and the EST evidence?

Thanks a lot,
Elissar

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

From: Jason Stajich<mailto:jason.stajich at gmail.com>
Sent: Friday, November 25, 2022 11:51 AM
To: Alam,Elissar<mailto:elissaralam at ufl.edu>
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Augustus predictions within MAKER2

[External Email]
After you run the gff3_merge step you can
grep augustus final.gff > augustus.gff3

On Wed, Nov 23, 2022 at 8:02 AM Alam,Elissar <elissaralam at ufl.edu<mailto:elissaralam at ufl.edu>> wrote:
Hello,

I ran Augustus and SNAP as part of the MAKER2 gene annotation pipeline. I would like to use the gene predictions generated by Augustus (prior to MAKER selecting the final gene model based on all ab initio predictions) for downstream analyses. Is there a way to obtain the Augustus gene predictions in gff3 format from MAKER2?

Thanks a million,
Elissar
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--
Jason Stajich
jason.stajich at gmail.com<mailto:jason.stajich at gmail.com>

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From jason.stajich at gmail.com  Sat Nov 26 12:29:27 2022
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 26 Nov 2022 11:29:27 -0800
Subject: [maker-devel] Augustus predictions within MAKER2
In-Reply-To: <SJ0PR22MB352871E05FEADC7B7F348C26AD0E9@SJ0PR22MB3528.namprd22.prod.outlook.com>
References: <SJ0PR22MB352874B08FE963FE4C25A3C9AD0C9@SJ0PR22MB3528.namprd22.prod.outlook.com>
 <CALf8LpzD5vEi86NvUY93VDcaHD7empQHN=gi0uGuWcWB4vENog@mail.gmail.com>
 <SJ0PR22MB352871E05FEADC7B7F348C26AD0E9@SJ0PR22MB3528.namprd22.prod.outlook.com>
Message-ID: <CALf8LpyOTxPj9xH8xXeRyXcUoHfObpSbbekk7orkCpRzwBuBnA@mail.gmail.com>

I?d check the documentation and the raw files in the run folder if you
aren?t sure but The maker consensus models will have maker in the 2nd
column and the augustus will have augustus in second  column of gff
(?source?)

You might need to adjust your grep to only take those with augustus in 2nd
Col. you can do grep -P ?\taugustus\t? to get those.


On Fri, Nov 25, 2022 at 8:56 AM Alam,Elissa <elissaralam at ufl.edu> wrote:

> Would that include all the gene models predicted by Augustus or only the
> ones that Maker retains after considering all ab initio gene predictions
> (SNAP + Augustus) and the EST evidence?
>
>
>
> Thanks a lot,
>
> Elissar
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows
>
>
>
> *From: *Jason Stajich <jason.stajich at gmail.com>
> *Sent: *Friday, November 25, 2022 11:51 AM
> *To: *Alam,Elissar <elissaralam at ufl.edu>
> *Cc: *maker-devel at yandell-lab.org
> *Subject: *Re: [maker-devel] Augustus predictions within MAKER2
>
>
>
> *[External Email]*
>
> After you run the gff3_merge step you can
>
> grep augustus final.gff > augustus.gff3
>
>
>
> On Wed, Nov 23, 2022 at 8:02 AM Alam,Elissar <elissaralam at ufl.edu> wrote:
>
> Hello,
>
>
>
> I ran Augustus and SNAP as part of the MAKER2 gene annotation pipeline. I
> would like to use the gene predictions generated by Augustus (prior to
> MAKER selecting the final gene model based on all ab initio predictions)
> for downstream analyses. Is there a way to obtain the Augustus gene
> predictions in gff3 format from MAKER2?
>
>
>
> Thanks a million,
>
> Elissar
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fyandell-lab.org%2Fmailman%2Flistinfo%2Fmaker-devel_yandell-lab.org&data=05%7C01%7Celissaralam%40ufl.edu%7C0ece808fa41e4d71ea2008dacf051c8d%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638049918746729551%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5O%2Fg%2F2ZbQX0vxETbe3tBAlCbocsfFuu5xtfTlWkMO4E%3D&reserved=0>
>
> --
>
> Jason Stajich
> jason.stajich at gmail.com
>
>
>
-- 
Jason Stajich
jason.stajich at gmail.com
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