From carsonhh at gmail.com  Tue May  1 17:07:47 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 01 May 2012 18:07:47 -0400
Subject: [maker-devel] gff3_preds2models usage question
In-Reply-To: <CANRPJSdHUx_BmAzb+OBLFab02dDtugM9Jf3zsXqjThrKauX29g@mail.gmail.com>
Message-ID: <CBC5D543.C151%carsonhh@gmail.com>

Sorry for the slow response.  The gff3_preds2models script has been
deprecated for some time now (isn't even in the release code anymore), and
the old one won't work with the new library.

I've attached a made from scratch drop-in replacement that you can use to do
what the old script would have done.  In the current release of MAKER,
instead of the gff3_preds2models script users can just give MAKER  a set of
predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then
leave all other options blank).  The predictions given will the be converted
into gene models.

Thanks,
Carson



From:  Walter Eckalbar <weckalba at asu.edu>
Date:  Tuesday, 3 April, 2012 7:28 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] gff3_preds2models usage question

Hello maker developers and users,

I am attempting to use the gff3_preds2models scripts, but running into a few
issues.

Initially, I hit errors that seemed to be fixed by installing CGI and its
dependancies.  However, that during that installation a few tests did fail.
I can provide error logs if that would be helpful, however, I went on to
install and attempt gff3_preds2models anyway.

What I am currently doing is running gff3_merge first, to gather the maker
outputs.  I am doing so with both the -n option on and off.  When providing
the gff3 file with the sequence I get the following error from
gff3_preds2models:

Undefined subroutine &maker::auto_annotator::annotate called at
/Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97,
<GEN16> line 992291.

This seemed to be the same error as that of what someone else saw on these
boards, but I did not see a later email resolving the issue.

I also tried giving it just the gff3 without the sequences at the bottom of
the file and then I get this error:

ERROR: There was a problem in the writing the fasta entry
Either no sequence was given, or there was an error in writing

This leads me to believe I should be using the one with the sequence, but I
am not certain of that.

I see it might be possible to go from maker outputs to chado database then
to gene->mRNA->exon gff3s, but I have not set up my machine for XML or chado
yet, and it does not appear trivial.

Thanks for the help,

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

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From weckalba at asu.edu  Tue May  1 20:33:00 2012
From: weckalba at asu.edu (Walter Eckalbar)
Date: Tue, 1 May 2012 18:33:00 -0700
Subject: [maker-devel] gff3_preds2models usage question
In-Reply-To: <CBC5D543.C151%carsonhh@gmail.com>
References: <CANRPJSdHUx_BmAzb+OBLFab02dDtugM9Jf3zsXqjThrKauX29g@mail.gmail.com>
	<CBC5D543.C151%carsonhh@gmail.com>
Message-ID: <CANRPJSc-EN9jgqW3dJRJmLJ_4SyhavqsOCH+h-031PPtiBHONA@mail.gmail.com>

Hi Carson,

Thanks for the response, even a late one, and thanks for the script.  I'll
certainly be giving that a try.

Walter

On 1 May 2012 15:07, Carson Holt <carsonhh at gmail.com> wrote:

> Sorry for the slow response.  The gff3_preds2models script has been
> deprecated for some time now (isn't even in the release code anymore), and
> the old one won't work with the new library.
>
> I've attached a made from scratch drop-in replacement that you can use to
> do what the old script would have done.  In the current release of MAKER,
> instead of the gff3_preds2models script users can just give MAKER  a set of
> predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then
> leave all other options blank).  The predictions given will the be
> converted into gene models.
>
> Thanks,
> Carson
>
>
>
> From: Walter Eckalbar <weckalba at asu.edu>
> Date: Tuesday, 3 April, 2012 7:28 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] gff3_preds2models usage question
>
> Hello maker developers and users,
>
> I am attempting to use the gff3_preds2models scripts, but running into a
> few issues.
>
> Initially, I hit errors that seemed to be fixed by installing CGI and its
> dependancies.  However, that during that installation a few tests did fail.
>  I can provide error logs if that would be helpful, however, I went on to
> install and attempt gff3_preds2models anyway.
>
> What I am currently doing is running gff3_merge first, to gather the maker
> outputs.  I am doing so with both the -n option on and off.  When providing
> the gff3 file with the sequence I get the following error from
> gff3_preds2models:
>
> Undefined subroutine &maker::auto_annotator::annotate called at
> /Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97,
> <GEN16> line 992291.
>
> This seemed to be the same error as that of what someone else saw on these
> boards, but I did not see a later email resolving the issue.
>
> I also tried giving it just the gff3 without the sequences at the bottom
> of the file and then I get this error:
>
> ERROR: There was a problem in the writing the fasta entry
> Either no sequence was given, or there was an error in writing
>
> This leads me to believe I should be using the one with the sequence, but
> I am not certain of that.
>
> I see it might be possible to go from maker outputs to chado database then
> to gene->mRNA->exon gff3s, but I have not set up my machine for XML or
> chado yet, and it does not appear trivial.
>
> Thanks for the help,
>
> Walter
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From qwang at uwyo.edu  Thu May  3 11:23:16 2012
From: qwang at uwyo.edu (Qiurong Wang)
Date: Thu, 3 May 2012 10:23:16 -0600
Subject: [maker-devel] MAKER download problem
Message-ID: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>

Hi,

I was trying to download MAKER, but I couldn't open the download page.  
Could you please help me to figure out the problem? Thanks a lot!


Qiurong Wang
PhD candidate
Department of Botany
University of Wyoming
Department 3165, 1000 E University Ave. Laramie, Wyoming 82071, USA
Phone: 307-766-2634
Email: qwang at uwyo.edu




From barry.moore at genetics.utah.edu  Thu May  3 12:51:48 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Thu, 3 May 2012 11:51:48 -0600
Subject: [maker-devel] MAKER download problem
In-Reply-To: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>
References: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>
Message-ID: <6B24C00B-6C70-4A40-BA7C-E3AC0C7F5E25@genetics.utah.edu>

Hi all,

The web server hosting the MAKER licensing application and MAKER code distribution was attacked this week.  The University of Utah is currently blocking access to that server from outside University IP space.  We are working hard to move all of the content and web-applications from that machine to a new server and I expect to have the MAKER services restored over the weekend.  This is affecting the ability to submit new licenses for MAKER and to download the MAKER code.  In addition those with existing licenses will need to update their code links for future code updates.  For those of you on campus in Utah or with campus VPN access, the server is running and available.  Updates on the status of the server and details about new links to the MAKER code will be posted to the mailing list soon.

Barry

On May 3, 2012, at 10:23 AM, Qiurong Wang wrote:

> Hi,
> 
> I was trying to download MAKER, but I couldn't open the download page. Could you please help me to figure out the problem? Thanks a lot!
> 
> 
> Qiurong Wang
> PhD candidate
> Department of Botany
> University of Wyoming
> Department 3165, 1000 E University Ave. Laramie, Wyoming 82071, USA
> Phone: 307-766-2634
> Email: qwang at uwyo.edu
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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




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From carsonhh at gmail.com  Thu May  3 13:00:01 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 03 May 2012 14:00:01 -0400
Subject: [maker-devel] MAKER download problem
In-Reply-To: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>
Message-ID: <CBC83F6D.C3B0%carsonhh@gmail.com>

The server hosting the file to download is down temporarily.  I'll put a
copy of MAKER on a separate server and e-mail the link to you.

--Carson



On 12-05-03 12:23 PM, "Qiurong Wang" <qwang at uwyo.edu> wrote:

>Hi,
>
>I was trying to download MAKER, but I couldn't open the download page.
>Could you please help me to figure out the problem? Thanks a lot!
>
>
>Qiurong Wang
>PhD candidate
>Department of Botany
>University of Wyoming
>Department 3165, 1000 E University Ave. Laramie, Wyoming 82071, USA
>Phone: 307-766-2634
>Email: qwang at uwyo.edu
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From cjfields at illinois.edu  Tue May 15 10:01:31 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 15 May 2012 15:01:31 +0000
Subject: [maker-devel] mail list and Trac
Message-ID: <64A6759A-9FD1-4AEE-BCEA-151B0D791ADD@illinois.edu>

Just wanted to point out, I noticed the mail list is not being indexed on Google Groups any more (nothing in May).  Also, any status on Trac?

chris


From barry.moore at genetics.utah.edu  Tue May 15 11:34:29 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 15 May 2012 10:34:29 -0600
Subject: [maker-devel] mail list and Trac
In-Reply-To: <64A6759A-9FD1-4AEE-BCEA-151B0D791ADD@illinois.edu>
References: <64A6759A-9FD1-4AEE-BCEA-151B0D791ADD@illinois.edu>
Message-ID: <C2170DBB-75CB-423D-82E3-C56572B57753@genetics.utah.edu>

Thanks Chris,  I'll check on the Google groups.  The MAKER Trac server was on a server that we had to shut down a couple weeks ago and I had made moving it a lower priority since I didn't think it was getting much use.  I'll get it moved over and bump up the priority on that move since I know someone is looking at it.

B

On May 15, 2012, at 9:01 AM, Fields, Christopher J wrote:

> Just wanted to point out, I noticed the mail list is not being indexed on Google Groups any more (nothing in May).  Also, any status on Trac?
> 
> chris
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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




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From anastasia.gioti at scilifelab.se  Thu May 17 06:27:04 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Thu, 17 May 2012 13:27:04 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
	<03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <4D9922AF-A917-4747-9B7C-CFE9F142D51C@scilifelab.se>

Hi Barry,
Thanks for your detailed instructions. You well understood that I have  
already included the proteins of the closely related species in my  
protein evidence dataset, but still did not get the genes. I have now  
blasted (P) the missing 949 proteins from this species against my  
nonoverlaping_abinits.fasta proteins and have found 618 good hits,  
which i guess I can promote to models using the routine no 2 of your  
last email and Carson's script gff3_select.
I have also looked at the rest of the proteins (331) for which there  
was no model in the nonoverlaping_abinits.fasta. I will try to  
describe 2 examples I looked at in apollo:

1) ab initio models predicted a ~7.5 kb gene covering 3 genes (as  
predicted in the closely related species). Blastx+protein2genome  
similarities were reported for two of these genes, but not for the 3rd  
(the one in the middle). MAKER finally decided to call two genes,  
respecting the blastx+protein2genome evidence, but the 3rd was lost.
I have previously  reported here that MAKER tends to  fuse genes in  
multi-exonic genes and others reported that too, I remember you  
proposed changing a papameter to alter this. To keep in mind for my  
final strategy that i am trying to decide on (for the moment i have  
not rerun MAKER).
For this case, abinitio models do not exist for the gene (in the sense  
that the existing models overlap many genes) and the similarity to the  
protein of the closely related species was not judged sufficient,  
although when i look at a TblastN alignment for this area it looks  
fine to me.

2) Only the 3' end of the gene was called by MAKER, despite blastx  
+protein2genome evidence from the closely related species for the  
entire region. Abinitio models existed as 2 separate genes , one for  
the 3' end region (finally retained by MAKER in a consensus decision I  
guess) and one for the 5' region, but here not all predictors called  
an orf, and finally nothing was called in this region.
In this case, it is a misannotation rather, but which misses a very  
important part of the gene.
I hope my descriptions are clear, otherwise I can provide you the gff  
file of these 2 examples to look by yourself.

I am not very clear about what to do about these 331 cases (which I do  
not know how to look at as well, except for random examples' viwing in  
Apollo). I feel that a second MAKER run would be probably the  
solution, this time providing as pred_gff  the result of a blast  
against the 331. But still, the existing annotations would then have  
to be somehow updated as the new predictions are in conflict with them  
(see example 2). I am a bit confused.
to recap, what would you suggest for the 331 still-missing proteins in  
terms of asessing their profiles n a rather automatic way and in  
inluding them in my annotations without going deep into manual gene  
curation?
Many thnks,
Anastasia
>
> Let me just restate what you've said so that I can be sure that I am  
> correct about what you've already done.  You have run Maker with  
> SNAP, Genemark and Augustus using EST from a closely related species  
> (passed to altest) and protein evidence from other fungi.  You are  
> missing about 1,000 genes compared to the species that provided the  
> EST alignments.  You say their is good evidence that these genes  
> exist from the alignments and I assume by this that you mean the EST/ 
> protein alignments that Maker produced.
>
> 1) Is the closely related fungus annotated and if so have you  
> included it's proteins in the evidence set that you provided to  
> Maker.  If you haven't provided these proteins as evidence to maker  
> then you should do this.  You can re-run maker passing your original  
> models back through like this:
>
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=1
> other_pass=1
>
> #-----Protein Homology Evidence (for best results provide a file for  
> at least one)
> protein=proteins_from_closely_related.fasta
> ## OR it sounds like you've already aligned these with exonerate?
> protein_gff=proteins_from_closely_related_already_aligned.gff
>
> 2) If you've already included those closely related species proteins  
> but still didn't get the 1,000 genes, then take your  
> nonoverlaping_abinits.fasta and blast them directly against your  
> closely related proteins.  Presumably they don't hit too well  
> because if they did they should have been promoted to predictions by  
> Maker the first time, but here you can decide yourself what  
> thresholds to allow to keep the abinit predictions that hit the  
> closely related species proteins.  If you filter you blast hits the  
> way you want and keep the names of the abinit predictions that pass  
> your filter, then use the script Carson attached it it will generate  
> a abinit precidtion GFF file with only the predictions you  
> selected.  You can then pass those predictions back to Maker and  
> force it to keep them and Maker will turn them from predictions  
> (match/match_part) into gene models.
>
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=0
> other_pass=1
>
> #-----Gene Prediction
> snaphmm=
> gmhmm=
> augustus_species=
> fgenesh_par_file=
> pred_gff=ab_init_predictions_rescued_by_blast.gff
>
> keep_preds=1
>
> Barry
>
>>> Thanks,
>>> Carson
>>>
>>> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
>>> Date: Wed, 25 Apr 2012 11:09:36 +0200
>>> To: <maker-devel at yandell-lab.org>
>>> Subject: [maker-devel] Use pass-through system to add missing genes
>>>
>>> Hi,
>>> I  have a set of predicted proteins from the genome of a fungus  
>>> annotated by MAKER  using EST data from a closely related species  
>>> and 3 ab initio predictors  (snap iterativelly trained 3 times,  
>>> genemark trained directly on the assembly and augustus with a  
>>> model from a less closely related species), along with a set of  
>>> fungal proteins. I am missing ~ 1000 proteins when I compare to  
>>> the species i used EST data from, and there is good evidence from  
>>> alignments that these genes exist. The question is how to proceed  
>>> from Blast hits to actual gene models here. The idea would be to  
>>> add these genes to the existing dataset, rather than reannotate  
>>> the genome. I believe that reannotating it without any further  
>>> evidence such as RNA-seq from the species itself would not change  
>>> much,and i d rather stick with actual predictions that i trust and  
>>> have used in subsequent analyses. The 1000 genes I can accept to  
>>> annotate with a less stringent and reliable way than MAKER, I just  
>>> want to add them so that the difference in gene count gets  
>>> corrected.
>>> I was reading the MAKER 2 paper and i was wondering if I can use  
>>> the legacy annotations scheme to do it, by providing GFF3 of the  
>>> alignments between the two species in the regions where genes were  
>>> missed, but as i said, I would not like to reannotate the whole  
>>> genome, and running MAKER2 might cause slight changes that i d  
>>> like to avoid. Is this possible? First, is it possible to provide  
>>> a Gff3 file of specific locations and not the entire genome  
>>> alignment? (I guess so..) Second, how can I tag the existing  
>>> annotations as 'not to be changed' or alternatively, tag the new  
>>> models only? How should I run maker2, with which predictors on and  
>>> which off?
>>> Thanks,
>>> Anastasia
>>>
>>> Anastasia Gioti
>>> Post-doctoral Researcher
>>>
>>> anastasia.gioti at scilifelab.se
>>> anastasia.gioti at ebc.uu.se
>>>
>>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>>>
>>>
>>>
>>> _______________________________________________ maker-devel  
>>> mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> <gff3_select>
>>
>> Anastasia Gioti
>> Post-doctoral Researcher
>>
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/ 
>> Gioti_Anastasia/
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell- 
> lab.org

Anastasia (Natassa) Gioti
Post-Doc Researcher
Evolutionary Biology Department Uppsala University -Science for Life  
lab, Karolinska Institute Stockholm
anastasia.gioti at ebc.uu.se
anastasia.gioti at scilifelab.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/










From yogeshp08 at gmail.com  Tue May 15 11:07:57 2012
From: yogeshp08 at gmail.com (Yogesh)
Date: Tue, 15 May 2012 11:07:57 -0500
Subject: [maker-devel] tblastn Cleanup?
Message-ID: <4478F0B20ED84A85B3C4FE4154F8FAD1@gmail.com>

Hello,

I have a few tblastn alignments with a lot of low quality hits. I have to clean that up. Can you please suggest how Maker pipeline does it? Also can I run it directly on my data without having to go through the whole pipeline?

Thanks,

-Yogesh
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From carsonhh at gmail.com  Fri May 18 09:22:50 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 18 May 2012 10:22:50 -0400
Subject: [maker-devel] tblastn Cleanup?
In-Reply-To: <4478F0B20ED84A85B3C4FE4154F8FAD1@gmail.com>
Message-ID: <CBDBD0A5.C8CD%carsonhh@gmail.com>

There are several things.  I set several filtering options directly on the
BLAST command line.  These are things like maximum intron length, an e-value
filter, and simple repeat filtering (called dust filter in NCBI blast and
seg filter in WUBLAST).

I also run repeat masker over the genome first.  This allows simple and
complex repeats to be removed before running BLAST (otherwise you get many
false alignments).

Last I filter the results based on percent coverage of the hit to the
original database sequence and percent identity.  I think you can set
percent identity as a flag in BLAST, but the percent coverage filter is
being calculated by MAKER, so to do this outside of MAKER would require that
you write your own filtering script to compare the length of the alignment
to the length of the sequence in the database.

I also have an HSP depth overlap filter.  This removes weird low complexity
hits that escape repeatmasking.  They show up as multiple HSPs overlapping
multiple times in the same region (usually very high numbers like 90 HSPs
all 100 bp long in the same region).  I calculate the number of base pairs
in the alignment on the hit then divide by the number of base pairs in the
query alignment.  If it's greater than 3, I throw the hit out.

Thanks,
Carson



From:  Yogesh <yogeshp08 at gmail.com>
Date:  Tuesday, 15 May, 2012 12:07 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] tblastn Cleanup?

 
Hello,

I have a few tblastn alignments with a lot of low quality hits. I have to
clean that up. Can you please suggest how Maker pipeline does it? Also can I
run it directly on my data without having to go through the whole pipeline?

Thanks,

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

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From smg283 at gmail.com  Tue May 22 01:42:51 2012
From: smg283 at gmail.com (Scott Geib)
Date: Mon, 21 May 2012 20:42:51 -1000
Subject: [maker-devel] can't call method strand on an undefined value ERROR:
 Failed while flattening protein clusters
Message-ID: <CAH221bv8rM7w+yOg6AgW9Y9tLHLvivWgGjZFs4e4QLAyuW4pGA@mail.gmail.com>

Hi,
Using maker 2.24, I am getting the following error (see below) in
protein2genome widget.  I also get the same error with est2genome.  This
happens with my own data (testing on a single scaffold), but not with the
test data supplied with maker (dpp files in data folder).
Scott


Widget::exonerate::protein2genome:
/data0/opt/AlignmentSoftware/exonerate/exonerate-2.2.0-x86_64/bin/exonerate
-q
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/UniRef90_UPI000194D3FC.for.1588546-1589203.9.fasta
-t
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.1588546-1589203.9.fasta
-Q protein -T dna -m protein2genome --softmasktarget  --percent 20
--showcigar  >
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.1588546-1589203.UniRef90_UPI000194D3FC.p_exonerate.9
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 23
 ...processing 1 of 23
 ...processing 2 of 23
 ...processing 3 of 23
 ...processing 4 of 23
 ...processing 5 of 23
 ...processing 6 of 23
 ...processing 7 of 23
 ...processing 8 of 23
 ...processing 9 of 23
 ...processing 10 of 23
 ...processing 11 of 23
 ...processing 12 of 23
 ...processing 13 of 23
 ...processing 14 of 23
 ...processing 15 of 23
 ...processing 16 of 23
 ...processing 17 of 23
 ...processing 18 of 23
 ...processing 19 of 23
 ...processing 20 of 23
 ...processing 21 of 23
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 20
 ...processing 1 of 20
 ...processing 2 of 20
 ...processing 3 of 20
 ...processing 4 of 20
 ...processing 5 of 20
 ...processing 6 of 20
 ...processing 7 of 20
 ...processing 8 of 20
 ...processing 9 of 20
 ...processing 10 of 20
 ...processing 11 of 20
 ...processing 12 of 20
 ...processing 13 of 20
 ...processing 14 of 20
 ...processing 15 of 20
 ...processing 16 of 20
 ...processing 17 of 20
 ...processing 18 of 20
total clusters:2 now processing 0
Can't call method "strand" on an undefined valueERROR: Failed while
flattening protein clusters
ERROR: Chunk failed at level:11, tier_type:2
FAILED CONTIG:scaffold00001
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From anastasia.gioti at scilifelab.se  Tue May 22 08:14:17 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Tue, 22 May 2012 15:14:17 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
	<03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <19E36E3B-6A82-49D5-B0AC-5E521F3E8999@scilifelab.se>

Hi again,
I hav sent an email a few days ago about this thread, and i am not  
sure if you have received it or you still did not have time to look at  
it. In any case, this email was dealing with the fact that some  
proteins were not retrieved in the abinitio models and how to deal  
with it. What I would like to ask here is a few confirmations on how  
to rerun maker for the proteins that were retrieved in the abinitio  
models. i have looked at the Blast results, and have done a series of  
check-ups, so now I am ready to run MAKER again with a list of models  
that I want to retain.
Regarding the following parameters:

1. Do I  set the genome= to nothing here? i.e quote it out? This is in  
the beginning of the control file
#-----Genome (Required for De-Novo Annotation)
genome=#genome sequence file in fasta format
organism_type= #eukaryotic or prokaryotic. Default is eukaryotic

>
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=0
> other_pass=1
>
> #-----Gene Prediction
2. Do i provide again the snap etc models? I am not sure, because i  
thought MAKER would not run ab initio predictors this time (this is  
why I would also quote out the genome file above, as this is not a de  
novo annotation). but if it will, i will then provide the previous  
models i used, except for snap, for which I will generate a new model   
from the gff3 file of the last run (according to snap documentation).  
Am i correct?
> snaphmm=
> gmhmm=
> augustus_species=
> fgenesh_par_file=
> pred_gff=ab_init_predictions_rescued_by_blast.gff
>
> keep_preds=1

Samely, what do i do with repeatmasking etc?
Thanks in adavance,
Anastasia

>
> Barry
>
>>> Thanks,
>>> Carson
>>>
>>> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
>>> Date: Wed, 25 Apr 2012 11:09:36 +0200
>>> To: <maker-devel at yandell-lab.org>
>>> Subject: [maker-devel] Use pass-through system to add missing genes
>>>
>>> Hi,
>>> I  have a set of predicted proteins from the genome of a fungus  
>>> annotated by MAKER  using EST data from a closely related species  
>>> and 3 ab initio predictors  (snap iterativelly trained 3 times,  
>>> genemark trained directly on the assembly and augustus with a  
>>> model from a less closely related species), along with a set of  
>>> fungal proteins. I am missing ~ 1000 proteins when I compare to  
>>> the species i used EST data from, and there is good evidence from  
>>> alignments that these genes exist. The question is how to proceed  
>>> from Blast hits to actual gene models here. The idea would be to  
>>> add these genes to the existing dataset, rather than reannotate  
>>> the genome. I believe that reannotating it without any further  
>>> evidence such as RNA-seq from the species itself would not change  
>>> much,and i d rather stick with actual predictions that i trust and  
>>> have used in subsequent analyses. The 1000 genes I can accept to  
>>> annotate with a less stringent and reliable way than MAKER, I just  
>>> want to add them so that the difference in gene count gets  
>>> corrected.
>>> I was reading the MAKER 2 paper and i was wondering if I can use  
>>> the legacy annotations scheme to do it, by providing GFF3 of the  
>>> alignments between the two species in the regions where genes were  
>>> missed, but as i said, I would not like to reannotate the whole  
>>> genome, and running MAKER2 might cause slight changes that i d  
>>> like to avoid. Is this possible? First, is it possible to provide  
>>> a Gff3 file of specific locations and not the entire genome  
>>> alignment? (I guess so..) Second, how can I tag the existing  
>>> annotations as 'not to be changed' or alternatively, tag the new  
>>> models only? How should I run maker2, with which predictors on and  
>>> which off?
>>> Thanks,
>>> Anastasia
>>>
>>> Anastasia Gioti
>>> Post-doctoral Researcher
>>>
>>> anastasia.gioti at scilifelab.se
>>> anastasia.gioti at ebc.uu.se
>>>
>>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>>>
>>>
>>>
>>> _______________________________________________ maker-devel  
>>> mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> <gff3_select>
>>
>> Anastasia Gioti
>> Post-doctoral Researcher
>>
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/ 
>> Gioti_Anastasia/
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell- 
> lab.org

Anastasia (Natassa) Gioti
Post-Doc Researcher
Evolutionary Biology Department Uppsala University -Science for Life  
lab, Karolinska Institute Stockholm
anastasia.gioti at ebc.uu.se
anastasia.gioti at scilifelab.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/










From anastasia.gioti at scilifelab.se  Wed May 23 04:07:12 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Wed, 23 May 2012 11:07:12 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
	<03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <1B0770A0-6D14-4336-BC3A-DC24619BC3FE@scilifelab.se>

Hi 
and sorry for the multiple postings. I have a list of models rescued by the nonoverlaping_abinits.fasta  fles (against which i  blasted my missing proteins from the closely related species and further filtered out the dubious hits) and a maker gff3 file, but Carson's script gff3_select won't work, and the reason is that these abinitio models were not promoted into the maker gff3 file, thus they are not there. I refer to the gff3 file generated by gff3_merge script. Am i missing something?
Thank you, 
Anastasia



> 
>>> If you know which ab initio predictions you want to add (I.e. the ab initio promoting scenario I descibed), you can provide those predictions to the use the pred_gff option and then set keep_preds=1 and they will be maintained even without evidence.  Attached is a script that would make selecting those easier.  It take the MAKER generated GFF3 and a list of predictions to keep (one name per line).  These might be the results of a BLAST analysis for example.  It will then return the GFF3 entries for just those models selected.

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From thomas.hackl at uni-wuerzburg.de  Wed May 23 07:01:55 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Wed, 23 May 2012 14:01:55 +0200
Subject: [maker-devel] missing est2genome annotation
Message-ID: <4FBCD1B3.8000102@uni-wuerzburg.de>

Hi,

I used maker to annotate genomic contigs and among other stuff provided 
transcripts from the transcriptome as est evidence. Blast and exonerate 
work fine and produce valid alignments, the alignment files exist in 
theVoid and look very good. Unfortunatly neither the evidence_0.gff nor 
the final .gff carry the corresponding feature annotations.

Any ideas why?

Regards
Thomas

-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From thomas.hackl at uni-wuerzburg.de  Wed May 23 12:14:27 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Wed, 23 May 2012 19:14:27 +0200
Subject: [maker-devel] missing est2genome annotation
In-Reply-To: <4FBCD1B3.8000102@uni-wuerzburg.de>
References: <4FBCD1B3.8000102@uni-wuerzburg.de>
Message-ID: <4FBD1AF3.8020904@uni-wuerzburg.de>

Hi again,

I did some source code digging and caught the following line burying my 
exonerate alignments. I suspect it does so for a very good reason, 
therefore it would help me a lot if someone could explain to me, what is 
going on there.


/lib/GI.pm  l.1473
next if $e->pAh<  $pcov;


Regards
Thomas


Am 23.05.2012 14:01, schrieb Thomas Hackl:
> Hi,
>
> I used maker to annotate genomic contigs and among other stuff 
> provided transcripts from the transcriptome as est evidence. Blast and 
> exonerate work fine and produce valid alignments, the alignment files 
> exist in theVoid and look very good. Unfortunatly neither the 
> evidence_0.gff nor the final .gff carry the corresponding feature 
> annotations.
>
> Any ideas why?
>
> Regards
> Thomas
>


-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 14:30:09 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 12:30:09 -0700
Subject: [maker-devel] Merging gene predictions....
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>

Hi Carson and others,
I am wondering if I can use Maker to merge gene predictions from three gff files. One of the algorithm is 'augustus' which of course i can use it inside Maker. Other two are not part of Maker.

But, in case if I want to pass only the GFFs to Maker and ask it to merge the annotations (when overlap) and pick only annotation that are predicted in 2 out of 3 gffs. Is it possible? I prefer this approach, as we need to run a blast based validation step on predicted features before even try to merge them. Thats another reason why we dont prefer to use the augustus inside maker. 

Thanks,
Gowthaman


From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 16:02:55 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 14:02:55 -0700
Subject: [maker-devel] Merging gene predictions....
In-Reply-To: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>
References: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D8@mail02.sbri.org>

Can i use the following approach Carson?

This is your reply to one of the earlier question:

I've attached a made from scratch drop-in replacement that you can use to do what the old script would have done.  In the current release of MAKER, instead of the gff3_preds2models script users can just give MAKER  a set of predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then leave all other options blank).  The predictions given will the be converted into gene models.

Thanks,
Carson



________________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] On Behalf Of Gowthaman Ramasamy [gowthaman.ramasamy at seattlebiomed.org]
Sent: Thursday, May 24, 2012 12:30 PM
To: Carson Holt; maker-devel at yandell-lab.org
Subject: [maker-devel] Merging gene predictions....

Hi Carson and others,
I am wondering if I can use Maker to merge gene predictions from three gff files. One of the algorithm is 'augustus' which of course i can use it inside Maker. Other two are not part of Maker.

But, in case if I want to pass only the GFFs to Maker and ask it to merge the annotations (when overlap) and pick only annotation that are predicted in 2 out of 3 gffs. Is it possible? I prefer this approach, as we need to run a blast based validation step on predicted features before even try to merge them. Thats another reason why we dont prefer to use the augustus inside maker.

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



From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 16:21:30 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 14:21:30 -0700
Subject: [maker-devel] Merging gene predictions....
In-Reply-To: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D8@mail02.sbri.org>
References: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>,
	<89080953C3D300419AACB6E63A7EEFBA5C8409F8D8@mail02.sbri.org>
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8DA@mail02.sbri.org>

Hi,
I am trying to install MAKER in centOS. I was able to install all the perl deps. and external programs. Perl Build.pl and ./Build Install went with out errors/warnings. I did not enable MPI though.

But, when i start Maker it returs "segmentation fault". 

I have no clue whats going wrong....or where to check for error logs? 

Any help would be appreciated,
Thanks,
gowthaman
_________


From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 16:22:16 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 14:22:16 -0700
Subject: [maker-devel] MAKER installation problem
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8DB@mail02.sbri.org>

Hi,
I am trying to install MAKER in centOS. I was able to install all the perl deps. and external programs. Perl Build.pl and ./Build Install went with out errors/warnings. I did not enable MPI though.

But, when i start Maker it returs "segmentation fault". 

I have no clue whats going wrong....or where to check for error logs? 

Any help would be appreciated,
Thanks,
gowthaman
_________
________________________________________



From bob_freeman at hms.harvard.edu  Fri May 25 11:23:22 2012
From: bob_freeman at hms.harvard.edu (Bob Freeman)
Date: Fri, 25 May 2012 12:23:22 -0400
Subject: [maker-devel] Alternate translation table?
Message-ID: <454CA235-0DB6-451F-97C4-83D32E2E805A@hms.harvard.edu>

Hello all!

Unusual question here: I am running MAKER on a ciliate that uses a non-standard translation table for its translation products. I haven't found an option in the control files that I can change for the for translation of the predicted transcripts. How or where can I go about this?

Tx,
Bob

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
	-- Karen Walker, from Will and Grace





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From carsonhh at gmail.com  Mon May 28 07:43:34 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 08:43:34 -0400
Subject: [maker-devel] Alternate translation table?
In-Reply-To: <454CA235-0DB6-451F-97C4-83D32E2E805A@hms.harvard.edu>
Message-ID: <CBE8E7EF.CAF3%carsonhh@gmail.com>

The alternate translation table is not currently an option.  It's one of
those things that needs to be implemented, but has not been yet.  It's also
not supported by many of the eukaryotic gene predictors MAKER uses.

I could probably get something implemented for you to test in two to three
weeks though (there are a lot of places where the translation table comes
into play).  Let me know.

--Carson



From:  Bob Freeman <bob_freeman at hms.harvard.edu>
Date:  Friday, 25 May, 2012 12:23 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Alternate translation table?

Hello all!

Unusual question here: I am running MAKER on a ciliate that uses a
non-standard translation table for its translation products. I haven't found
an option in the control files that I can change for the for translation of
the predicted transcripts. How or where can I go about this?

Tx,
Bob

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
-- Karen Walker, from Will and Grace





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

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From carsonhh at gmail.com  Mon May 28 08:38:25 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 09:38:25 -0400
Subject: [maker-devel] missing est2genome annotation
In-Reply-To: <4FBD1AF3.8020904@uni-wuerzburg.de>
Message-ID: <CBE8F75D.CB57%carsonhh@gmail.com>

Sorry for the slow reply.  I'm just getting back after traveling.

That's a percent coverage flag.  You can set a percent coverage threshold
in the maker_bopts.ctl file.  Partial high scoring alignments can be
common.  If you only filter by expect score, you would be surprised to see
how many ugly and confusing all the alignments become.

Thanks,
Carson

On 12-05-23 1:14 PM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi again,
>
>I did some source code digging and caught the following line burying my
>exonerate alignments. I suspect it does so for a very good reason,
>therefore it would help me a lot if someone could explain to me, what is
>going on there.
>
>
>/lib/GI.pm  l.1473
>next if $e->pAh<  $pcov;
>
>
>Regards
>Thomas
>
>
>Am 23.05.2012 14:01, schrieb Thomas Hackl:
>> Hi,
>>
>> I used maker to annotate genomic contigs and among other stuff
>> provided transcripts from the transcriptome as est evidence. Blast and
>> exonerate work fine and produce valid alignments, the alignment files
>> exist in theVoid and look very good. Unfortunatly neither the
>> evidence_0.gff nor the final .gff carry the corresponding feature
>> annotations.
>>
>> Any ideas why?
>>
>> Regards
>> Thomas
>>
>
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From seoanezonjic at hotmail.com  Tue May 22 07:55:12 2012
From: seoanezonjic at hotmail.com (p sz)
Date: Tue, 22 May 2012 12:55:12 +0000
Subject: [maker-devel] ipr_update_gff ERROR
Message-ID: <COL119-W282F1F1F211028B1F661C5C7020@phx.gbl>


First, thanks by help me on the lprevious error that I submitted.
I'm still working in the same project and I get a new error. I try interproscan with this commandline:

iprscan_wrap -i parsed_input.all.maker.proteins.fasta -email seoanezonjic at hotmail.com  -format raw

parsed_input.all.maker.proteins.fasta was generated with the tool fasta_merge. I use the output (attached in this email) and a gff file (generated by a normal run of maker, attached in this email) with the ipr_update_gff script of this way:

ipr_update_gff BAC12_Clone_Pt314B2_Lib_Pt_7Ba__organism_Pinus_taeda__0.gff sc_interpro.sh.o109053

And i get this error:
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 15.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 15.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 18.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 18.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 19.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 19.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 48.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 48.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 49.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 49.

The gff file seems updated but i don't know if it works fine or is corrupt
Thanks in advance
 		 	   		  
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From larriba.ed at gmail.com  Fri May 25 11:01:41 2012
From: larriba.ed at gmail.com (Eduardo Larriba)
Date: Fri, 25 May 2012 18:01:41 +0200
Subject: [maker-devel] Consensus gene models
Message-ID: <CADwrZ2XdcZu080yHt7=CreOWbpt791NC8ScB5WVW=NmvN4=Jgw@mail.gmail.com>

Hi Carson and people,
I am working on structural annotation of a filamentous fungus, of which
there is little evidence as EST or Protein. For generate consensus gene  based
on limited evidences to me I used  Marker.
For this I created the files GeneMark prediction-is and SNAP.
I run maker using the EST of my organims (85), along with 5700 EST of the
closed organims. I have made ??predictions with Augustus, and SNAP GeneMark,
with the training files for my organims, in Maker pipeline. Everything works
fine.
My problem is that when I get the consensus sequences of all my contigs,
fasta_merge script (included in Maker), I get different list for each
predictor, as well as when I try to get the gff of all.
They could tell me how I can use Maker consensus for a list of genes? Or I
have to do it manually? There is the possibility that Maker evaluates the
accuracy of each prediction and confirm, so just get a list of the different
predictions?

Thank you very much.


-- 
Eduardo Larriba Tornel
Universidad de Alicante.
Lab. Fitopatolog?a
Dept. Ciencias del Mar y Biolog?a Aplicada
Pabell?n 13.
San Vicente del Raspeig
Tel. 96 590 3400 ext 3280
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From carsonhh at gmail.com  Mon May 28 09:14:22 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 10:14:22 -0400
Subject: [maker-devel] Consensus gene models
In-Reply-To: <CADwrZ2XdcZu080yHt7=CreOWbpt791NC8ScB5WVW=NmvN4=Jgw@mail.gmail.com>
Message-ID: <CBE8FECE.CBA5%carsonhh@gmail.com>

The consensus list is in the maker.proteins.fasta and
maker.transcripts.fasta file.  The predictor specific lists are just for
reference purposes (incase you want to see what the other predictors
produced on their own, i.e. without MAKER's intervention).  The
non-overlapping.fasta file in the same directory will contain consensus
entries for models that were not supported by any evidence and don't overlap
any gene models in the  maker.transcripts.fasta (think of these as the maybe
gene and the maker.transcripts.fasta as the very likely genes).  You can set
keep_preds=1 if you just want MAKER to keep everything with or without
support and just produce consensus (probably ok on a fungus, but I wouldn't
recommend it on other eukayotes because false positive rates will be very
high).

Thanks,
Carson



From:  Eduardo Larriba <larriba.ed at gmail.com>
Date:  Friday, 25 May, 2012 12:01 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Consensus gene models

Hi Carson and people,
I am working on structural annotation of a filamentous fungus, of which
there is little evidence as EST or Protein. For generate consensus gene
based on limited evidences to me I used  Marker.
 For this I created the files GeneMark prediction-is and SNAP.
 I run maker using the EST of my organims (85), along with 5700 EST of the
closed organims. I have made ??predictions with Augustus, and SNAP
GeneMark, with the training files for my organims, in Maker pipeline.
Everything works fine.
 My problem is that when I get the consensus sequences of all my contigs,
fasta_merge script (included in Maker), I get different list for each
predictor, as well as when I try to get the gff of all.
 They could tell me how I can use Maker consensus for a list of genes? Or I
have to do it manually? There is the possibility that Maker evaluates the
accuracy of each prediction and confirm, so just get a list of the different
predictions?

 Thank you very much.


-- 
Eduardo Larriba Tornel
Universidad de Alicante.
Lab. Fitopatolog?a
Dept. Ciencias del Mar y Biolog?a Aplicada
Pabell?n 13. 
San Vicente del Raspeig
Tel. 96 590 3400 ext 3280

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From carsonhh at gmail.com  Mon May 28 09:18:26 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 10:18:26 -0400
Subject: [maker-devel] ipr_update_gff ERROR
In-Reply-To: <COL119-W282F1F1F211028B1F661C5C7020@phx.gbl>
Message-ID: <CBE90090.CBB6%carsonhh@gmail.com>

This error would happen if some results exist in the iprscan output, but
don't match gene entries in the GFF3 file.  If I could see the original
files I can tell you which ones.  This can happen if you combine results
from the non-overlapping.fasta files with the maker.proteins.fasta files for
example.  Models in the non-overlapping.fasta file are not genes in the GFF3
(they are match/match_part enties), so errors happen.

Thanks,
Carson

From:  p sz <seoanezonjic at hotmail.com>
Date:  Tuesday, 22 May, 2012 8:55 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] ipr_update_gff ERROR

First, thanks by help me on the lprevious error that I submitted.
I'm still working in the same project and I get a new error. I try
interproscan with this commandline:

iprscan_wrap -i parsed_input.all.maker.proteins.fasta -email
seoanezonjic at hotmail.com  -format raw

parsed_input.all.maker.proteins.fasta was generated with the tool
fasta_merge. I use the output (attached in this email) and a gff file
(generated by a normal run of maker, attached in this email) with the
ipr_update_gff script of this way:

ipr_update_gff BAC12_Clone_Pt314B2_Lib_Pt_7Ba__organism_Pinus_taeda__0.gff
sc_interpro.sh.o109053

And i get this error:
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 15.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 15.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 18.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 18.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 19.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 19.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 48.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 48.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 49.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 49.

The gff file seems updated but i don't know if it works fine or is corrupt
Thanks in advance
       
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From carsonhh at gmail.com  Tue May 29 07:37:55 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 29 May 2012 08:37:55 -0400
Subject: [maker-devel] can't call method strand on an undefined value
 ERROR: Failed while flattening protein clusters
In-Reply-To: <CAH221bv8rM7w+yOg6AgW9Y9tLHLvivWgGjZFs4e4QLAyuW4pGA@mail.gmail.com>
Message-ID: <CBEA3AC6.CD62%carsonhh@gmail.com>

Use this command to check out the latest unreleased test version, and lt me
know if you still get the error.

Command -->  svn co svn://malachite.genetics.utah.edu/maker/trunk maker

User: yandell_guest
Password: y at ndell_Gu3st

Thanks,
Carson





From:  Scott Geib <smg283 at gmail.com>
Date:  Tuesday, 22 May, 2012 2:42 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] can't call method strand on an undefined value
ERROR: Failed while flattening protein clusters

Hi, 
Using maker 2.24, I am getting the following error (see below) in
protein2genome widget.  I also get the same error with est2genome.  This
happens with my own data (testing on a single scaffold), but not with the
test data supplied with maker (dpp files in data folder).
Scott


Widget::exonerate::protein2genome:
/data0/opt/AlignmentSoftware/exonerate/exonerate-2.2.0-x86_64/bin/exonerate
-q 
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/UniRef90_UPI00019
4D3FC.for.1588546-1589203.9.fasta -t
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.158
8546-1589203.9.fasta -Q protein -T dna -m protein2genome --softmasktarget
--percent 20 --showcigar  >
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.158
8546-1589203.UniRef90_UPI000194D3FC.p_exonerate.9
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 23
 ...processing 1 of 23
 ...processing 2 of 23
 ...processing 3 of 23
 ...processing 4 of 23
 ...processing 5 of 23
 ...processing 6 of 23
 ...processing 7 of 23
 ...processing 8 of 23
 ...processing 9 of 23
 ...processing 10 of 23
 ...processing 11 of 23
 ...processing 12 of 23
 ...processing 13 of 23
 ...processing 14 of 23
 ...processing 15 of 23
 ...processing 16 of 23
 ...processing 17 of 23
 ...processing 18 of 23
 ...processing 19 of 23
 ...processing 20 of 23
 ...processing 21 of 23
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 20
 ...processing 1 of 20
 ...processing 2 of 20
 ...processing 3 of 20
 ...processing 4 of 20
 ...processing 5 of 20
 ...processing 6 of 20
 ...processing 7 of 20
 ...processing 8 of 20
 ...processing 9 of 20
 ...processing 10 of 20
 ...processing 11 of 20
 ...processing 12 of 20
 ...processing 13 of 20
 ...processing 14 of 20
 ...processing 15 of 20
 ...processing 16 of 20
 ...processing 17 of 20
 ...processing 18 of 20
total clusters:2 now processing 0
Can't call method "strand" on an undefined valueERROR: Failed while
flattening protein clusters
ERROR: Chunk failed at level:11, tier_type:2
FAILED CONTIG:scaffold00001

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From bob_freeman at hms.harvard.edu  Tue May 29 11:30:23 2012
From: bob_freeman at hms.harvard.edu (Bob Freeman)
Date: Tue, 29 May 2012 12:30:23 -0400
Subject: [maker-devel] Alternate translation table?
In-Reply-To: <CBE8E7EF.CAF3%carsonhh@gmail.com>
References: <CBE8E7EF.CAF3%carsonhh@gmail.com>
Message-ID: <B198DB2E-A0CC-4A01-843D-59F470E97DC9@hms.harvard.edu>

Thanks, Carson, for the update on this. No need to implement something. I'll keep it simple and translate the collected transcripts using an appropriate translation table.

-Bob

On May 28, 2012, at 8:43 AM, Carson Holt wrote:

> The alternate translation table is not currently an option.  It's one of those things that needs to be implemented, but has not been yet.  It's also not supported by many of the eukaryotic gene predictors MAKER uses.
> 
> I could probably get something implemented for you to test in two to three weeks though (there are a lot of places where the translation table comes into play).  Let me know.
> 
> --Carson
> 
> 
> 
> From: Bob Freeman <bob_freeman at hms.harvard.edu>
> Date: Friday, 25 May, 2012 12:23 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Alternate translation table?
> 
> Hello all!
> 
> Unusual question here: I am running MAKER on a ciliate that uses a non-standard translation table for its translation products. I haven't found an option in the control files that I can change for the for translation of the predicted transcripts. How or where can I go about this?
> 
> Tx,
> Bob
> 
> 
> _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
	-- Karen Walker, from Will and Grace





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From gowthaman.ramasamy at seattlebiomed.org  Tue May 29 16:54:33 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Tue, 29 May 2012 14:54:33 -0700
Subject: [maker-devel] Can maker select a gene model based on #algoritham
	predicted it
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8EB@mail02.sbri.org>

Hi Carson,
Thanks for all the help during the long weekend, in spite of that long drive. I am still trying to imagine that.

I now have maker to consider our own prediction via pred_gff, and use augustus and gene mark (with our training model). And i was able to use altest and protein evidences. Maker happily picks one gene model when there is a overlap between three different predictions. But, when I look at the gff, it seems like it picks a gene model only when there is an est/protein evidence. It leaves out some genes even though, they are predicted by all three algorithms. Of course, keep_pred=1 helps to keep all the models. This kind of leads to over prediction. 

But, I am looking for something in between. And would like to know if that is possible?
1) Pick a gene model if it has an evidence from (est/prot etc...) irrespective of how many algorithms predicted it
2) In the absence of extrinsic evidence (est/prot etc), pick a gene model if that is predicted by at least two algorithms.

Or even simpler:
I have ab-initio predictions from three algorithms, Can I output, those genes that is supported by at least two of them. I care less about exactness of gene boundaries.

Thanks,
Gowthaman

PS: With my recent attempts, i learned couple things about maker/other associated tools that is not documented in gmod-maker wiki. Is it possible/ok if I add contents to it. I am okay with running it by you before making it public.


From carsonhh at gmail.com  Wed May 30 07:54:32 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 30 May 2012 08:54:32 -0400
Subject: [maker-devel] Can maker select a gene model based on
	#algoritham predicted it
In-Reply-To: <89080953C3D300419AACB6E63A7EEFBA5C8409F8EB@mail02.sbri.org>
Message-ID: <CBEB8E25.D097%carsonhh@gmail.com>

It's not an option in exactly the way you are specifying, but there is
something I usually do for annotation that works well.  I run interproscan
or rpsblast on the non_overlapping.proteins.fasta file and select just
those non-overlapping models that have a recognizable protein domain (just
searching the pfam doamin space is more than sufficient).  Then I provide
the selected results to model_gff, and provide the previous maker results
to the maker_gff option with (all reannotation pass options set to 1 and
all analysis options turned off).  This adds models with at least
recognizable domains (as even multiple gene predictors can overpredict in
a similar way).

Attached is a script to help select predictions and upgrade them to models
in GFF3 format.  If you have question let me know.

Thanks,
Carson



On 12-05-29 5:54 PM, "Gowthaman Ramasamy"
<gowthaman.ramasamy at seattlebiomed.org> wrote:

>Hi Carson,
>Thanks for all the help during the long weekend, in spite of that long
>drive. I am still trying to imagine that.
>
>I now have maker to consider our own prediction via pred_gff, and use
>augustus and gene mark (with our training model). And i was able to use
>altest and protein evidences. Maker happily picks one gene model when
>there is a overlap between three different predictions. But, when I look
>at the gff, it seems like it picks a gene model only when there is an
>est/protein evidence. It leaves out some genes even though, they are
>predicted by all three algorithms. Of course, keep_pred=1 helps to keep
>all the models. This kind of leads to over prediction.
>
>But, I am looking for something in between. And would like to know if
>that is possible?
>1) Pick a gene model if it has an evidence from (est/prot etc...)
>irrespective of how many algorithms predicted it
>2) In the absence of extrinsic evidence (est/prot etc), pick a gene model
>if that is predicted by at least two algorithms.
>
>Or even simpler:
>I have ab-initio predictions from three algorithms, Can I output, those
>genes that is supported by at least two of them. I care less about
>exactness of gene boundaries.
>
>Thanks,
>Gowthaman
>
>PS: With my recent attempts, i learned couple things about maker/other
>associated tools that is not documented in gmod-maker wiki. Is it
>possible/ok if I add contents to it. I am okay with running it by you
>before making it public.

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From mikael.durling at slu.se  Thu May 31 07:25:31 2012
From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=)
Date: Thu, 31 May 2012 14:25:31 +0200
Subject: [maker-devel] maker leaving large numbers of defunct zombies
Message-ID: <FBA1F582-5EF0-4D7A-8276-A86DAD5C4C89@slu.se>

Hello,

I've been working lately to set up maker for annotation work on a few fungal genomes. I've got mpi maker up and running now, however, I notice that maker is leaving a lot of <defunct> perl processes behind. This happens to the extent that the process table on the system gets filled up after a few hours run time. Right now the process tree after three hours running looks like this:

    |-sge_execd-+-sge_shepherd---bash---mpirun-+-maker-+-maker
     |           |                              |       `-perl
     |           |                              |-maker-+-maker
     |           |                              |       |-maker---1371*[perl]
     |           |                              |       `-perl
     |           |                              |-maker-+-maker
     |           |                              |       |-maker---1348*[perl]
     |           |                              |       `-perl
     |           |                              |-maker-+-maker
     |           |                              |       |-maker---1384*[perl]
     |           |                              |       `-perl

...and so on for all mpi processes, except for the controlling processes. 

What perl programs is maker calling, that might end up as zombies? I've had a brief look at the source to no avail, but would be happy to dig further with some pointers for where to look.

This is run with the 2.25-beta from the web page, perl 5.16.0 and openmpi 1.4.5. 

Thanks,
Mikael










-------------------------------------
Mikael Brandstr?m Durling, PhD
Assistant Professor

Sveriges lantbruksuniversitet
Swedish University of Agricultural Sciences

Uppsala BioCenter
Dept of Forest Mycology and Plant Pathology
Box 7026, 75007 Uppsala
Visiting address: Almas All? 5
Telefon: 018-671512
mikael.durling at slu.se, www.slu.se/mykopat





From mikael.durling at slu.se  Thu May 31 07:34:30 2012
From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=)
Date: Thu, 31 May 2012 14:34:30 +0200
Subject: [maker-devel] Using GDBM_File instead of DB_File
Message-ID: <B535F29B-D593-44D7-B0C4-D84462957EFB@slu.se>

Hello,

I've been struggling for a few days to get maker up and running with MPI on a debian squeeze system. Compiling a new perl 5.16 exclusively for maker I wound down to that the segfaults came from DB_File. Even by recomiling and updating that module, nothing worked. After checking for dependencies on DB_File in maker, I concluded that the only dependency was through the GI::localize_file, which expects the FastaDB to be instantiated with DB_File. However, FastaDB can run on GDBM_File too. I patched the calls to GI::localize_file in maker to handle the .pag/.dir extensions used by GDBM (below). With this patch applied maker is running for me, even when I have deleted the DB_File module from the perl path and made sure that GDBM_File is installed. My basic question is if there is any other dependency for DB_File which I have missed which may break things?

cheers,
Mikael

--- maker.orig	2012-03-30 15:48:05.000000000 +0200
+++ maker	2012-05-31 10:35:30.253022648 +0200
@@ -512,7 +515,12 @@
 }
 if($size > 1){
     carp "Calling GI::localize_file" if($main::debug);
-    GI::localize_file("$gdbfile.index");
+    if( -f "$gdbfile.index.dir" ){
+	GI::localize_file("$gdbfile.index.dir");
+	GI::localize_file("$gdbfile.index.pag");
+    }else{
+    	GI::localize_file("$gdbfile.index");
+    }
     carp "Calling GI::localize_file" if($main::debug);
     $gdbfile = GI::localize_file($gdbfile);
 }




From carsonhh at gmail.com  Thu May 31 08:04:58 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 31 May 2012 09:04:58 -0400
Subject: [maker-devel] Using GDBM_File instead of DB_File
In-Reply-To: <B535F29B-D593-44D7-B0C4-D84462957EFB@slu.se>
Message-ID: <CBECE3F7.D209%carsonhh@gmail.com>

DB_File is being called by Bio::DB::Fasta.  I can check the object
returned when using GDBM_File instead to see if the index file names are
contained on the object, as I'm just assuming an extension of '.index'.
I'll look around to see if the extension name is assumed anywhere else.

Thanks,
Carson


On 12-05-31 8:34 AM, "Mikael Brandstr?m Durling" <mikael.durling at slu.se>
wrote:

>Hello,
>
>I've been struggling for a few days to get maker up and running with MPI
>on a debian squeeze system. Compiling a new perl 5.16 exclusively for
>maker I wound down to that the segfaults came from DB_File. Even by
>recomiling and updating that module, nothing worked. After checking for
>dependencies on DB_File in maker, I concluded that the only dependency
>was through the GI::localize_file, which expects the FastaDB to be
>instantiated with DB_File. However, FastaDB can run on GDBM_File too. I
>patched the calls to GI::localize_file in maker to handle the .pag/.dir
>extensions used by GDBM (below). With this patch applied maker is running
>for me, even when I have deleted the DB_File module from the perl path
>and made sure that GDBM_File is installed. My basic question is if there
>is any other dependency for DB_File which I have missed which may break
>things?
>
>cheers,
>Mikael
>
>--- maker.orig	2012-03-30 15:48:05.000000000 +0200
>+++ maker	2012-05-31 10:35:30.253022648 +0200
>@@ -512,7 +515,12 @@
> }
> if($size > 1){
>     carp "Calling GI::localize_file" if($main::debug);
>-    GI::localize_file("$gdbfile.index");
>+    if( -f "$gdbfile.index.dir" ){
>+	GI::localize_file("$gdbfile.index.dir");
>+	GI::localize_file("$gdbfile.index.pag");
>+    }else{
>+    	GI::localize_file("$gdbfile.index");
>+    }
>     carp "Calling GI::localize_file" if($main::debug);
>     $gdbfile = GI::localize_file($gdbfile);
> }
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Thu May 31 08:17:20 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 31 May 2012 09:17:20 -0400
Subject: [maker-devel] maker leaving large numbers of defunct zombies
In-Reply-To: <FBA1F582-5EF0-4D7A-8276-A86DAD5C4C89@slu.se>
Message-ID: <CBECE4F4.D210%carsonhh@gmail.com>

MAKER uses IPC::Open3 to open almost all external applications, including
a helper script called every once in a while that helps check file locks
on NFS.

MAKER then calls waitpid to reap the processes, as IPC::Open3 doesn't
auto-reap.  The only time previously I've seen issues with zombie
accumulation was with MPICH2 when it moved from the MPD process manager to
Hydra.  Hydra had certain broken signal handling issues that I had to bug
the MPICH2 developers about and they fixed it.  It is possible that the
issue you are having may be with OpenMPI or with perl 5.16.  I currently
use perl 5.12.  Perl instituted something called safe signals in either
5.6 or 5.8 and there may be some updates in 5.16 where they've been
changing those around again.

I can try installing a copy of 5.16 to test with and OpenMPI to see if I
can replicate the error.

Thanks,
Carson



On 12-05-31 8:25 AM, "Mikael Brandstr?m Durling" <mikael.durling at slu.se>
wrote:

>Hello,
>
>I've been working lately to set up maker for annotation work on a few
>fungal genomes. I've got mpi maker up and running now, however, I notice
>that maker is leaving a lot of <defunct> perl processes behind. This
>happens to the extent that the process table on the system gets filled up
>after a few hours run time. Right now the process tree after three hours
>running looks like this:
>
>    |-sge_execd-+-sge_shepherd---bash---mpirun-+-maker-+-maker
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1371*[perl]
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1348*[perl]
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1384*[perl]
>     |           |                              |       `-perl
>
>...and so on for all mpi processes, except for the controlling processes.
>
>What perl programs is maker calling, that might end up as zombies? I've
>had a brief look at the source to no avail, but would be happy to dig
>further with some pointers for where to look.
>
>This is run with the 2.25-beta from the web page, perl 5.16.0 and openmpi
>1.4.5. 
>
>Thanks,
>Mikael
>
>
>
>
>
>
>
>
>
>
>-------------------------------------
>Mikael Brandstr?m Durling, PhD
>Assistant Professor
>
>Sveriges lantbruksuniversitet
>Swedish University of Agricultural Sciences
>
>Uppsala BioCenter
>Dept of Forest Mycology and Plant Pathology
>Box 7026, 75007 Uppsala
>Visiting address: Almas All? 5
>Telefon: 018-671512
>mikael.durling at slu.se, www.slu.se/mykopat
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From mikael.durling at slu.se  Thu May 31 08:57:06 2012
From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=)
Date: Thu, 31 May 2012 15:57:06 +0200
Subject: [maker-devel] maker leaving large numbers of defunct zombies
In-Reply-To: <CBECE4F4.D210%carsonhh@gmail.com>
References: <CBECE4F4.D210%carsonhh@gmail.com>
Message-ID: <E779EAA8-C2AC-4362-A3C7-E370777E3D5D@slu.se>

I saw the same problem with the latest MPICH2 using hydra too, so it might boil down to perl/openmpi interactions. I didn't see this problem with the debian supplied perl 5.10, but then I had intermittent segfaults with in DB_File and libpthread. Seemed to be some interaction with the LD_PRELOADed libmpi. That requirement for preloading libmpi was easiest solved by compiling openmpi with --disable-dlopen.

Thanks,
Mikael

31 maj 2012 kl. 15:17 skrev Carson Holt:

> MAKER uses IPC::Open3 to open almost all external applications, including
> a helper script called every once in a while that helps check file locks
> on NFS.
> 
> MAKER then calls waitpid to reap the processes, as IPC::Open3 doesn't
> auto-reap.  The only time previously I've seen issues with zombie
> accumulation was with MPICH2 when it moved from the MPD process manager to
> Hydra.  Hydra had certain broken signal handling issues that I had to bug
> the MPICH2 developers about and they fixed it.  It is possible that the
> issue you are having may be with OpenMPI or with perl 5.16.  I currently
> use perl 5.12.  Perl instituted something called safe signals in either
> 5.6 or 5.8 and there may be some updates in 5.16 where they've been
> changing those around again.
> 
> I can try installing a copy of 5.16 to test with and OpenMPI to see if I
> can replicate the error.
> 
> Thanks,
> Carson
> 
> 
> 
> On 12-05-31 8:25 AM, "Mikael Brandstr?m Durling" <mikael.durling at slu.se>
> wrote:
> 
>> Hello,
>> 
>> I've been working lately to set up maker for annotation work on a few
>> fungal genomes. I've got mpi maker up and running now, however, I notice
>> that maker is leaving a lot of <defunct> perl processes behind. This
>> happens to the extent that the process table on the system gets filled up
>> after a few hours run time. Right now the process tree after three hours
>> running looks like this:
>> 
>>   |-sge_execd-+-sge_shepherd---bash---mpirun-+-maker-+-maker
>>    |           |                              |       `-perl
>>    |           |                              |-maker-+-maker
>>    |           |                              |
>> |-maker---1371*[perl]
>>    |           |                              |       `-perl
>>    |           |                              |-maker-+-maker
>>    |           |                              |
>> |-maker---1348*[perl]
>>    |           |                              |       `-perl
>>    |           |                              |-maker-+-maker
>>    |           |                              |
>> |-maker---1384*[perl]
>>    |           |                              |       `-perl
>> 
>> ...and so on for all mpi processes, except for the controlling processes.
>> 
>> What perl programs is maker calling, that might end up as zombies? I've
>> had a brief look at the source to no avail, but would be happy to dig
>> further with some pointers for where to look.
>> 
>> This is run with the 2.25-beta from the web page, perl 5.16.0 and openmpi
>> 1.4.5. 
>> 
>> Thanks,
>> Mikael
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> -------------------------------------
>> Mikael Brandstr?m Durling, PhD
>> Assistant Professor
>> 
>> Sveriges lantbruksuniversitet
>> Swedish University of Agricultural Sciences
>> 
>> Uppsala BioCenter
>> Dept of Forest Mycology and Plant Pathology
>> Box 7026, 75007 Uppsala
>> Visiting address: Almas All? 5
>> Telefon: 018-671512
>> mikael.durling at slu.se, www.slu.se/mykopat
>> 
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 




From carsonhh at gmail.com  Tue May  1 16:07:47 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 01 May 2012 18:07:47 -0400
Subject: [maker-devel] gff3_preds2models usage question
In-Reply-To: <CANRPJSdHUx_BmAzb+OBLFab02dDtugM9Jf3zsXqjThrKauX29g@mail.gmail.com>
Message-ID: <CBC5D543.C151%carsonhh@gmail.com>

Sorry for the slow response.  The gff3_preds2models script has been
deprecated for some time now (isn't even in the release code anymore), and
the old one won't work with the new library.

I've attached a made from scratch drop-in replacement that you can use to do
what the old script would have done.  In the current release of MAKER,
instead of the gff3_preds2models script users can just give MAKER  a set of
predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then
leave all other options blank).  The predictions given will the be converted
into gene models.

Thanks,
Carson



From:  Walter Eckalbar <weckalba at asu.edu>
Date:  Tuesday, 3 April, 2012 7:28 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] gff3_preds2models usage question

Hello maker developers and users,

I am attempting to use the gff3_preds2models scripts, but running into a few
issues.

Initially, I hit errors that seemed to be fixed by installing CGI and its
dependancies.  However, that during that installation a few tests did fail.
I can provide error logs if that would be helpful, however, I went on to
install and attempt gff3_preds2models anyway.

What I am currently doing is running gff3_merge first, to gather the maker
outputs.  I am doing so with both the -n option on and off.  When providing
the gff3 file with the sequence I get the following error from
gff3_preds2models:

Undefined subroutine &maker::auto_annotator::annotate called at
/Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97,
<GEN16> line 992291.

This seemed to be the same error as that of what someone else saw on these
boards, but I did not see a later email resolving the issue.

I also tried giving it just the gff3 without the sequences at the bottom of
the file and then I get this error:

ERROR: There was a problem in the writing the fasta entry
Either no sequence was given, or there was an error in writing

This leads me to believe I should be using the one with the sequence, but I
am not certain of that.

I see it might be possible to go from maker outputs to chado database then
to gene->mRNA->exon gff3s, but I have not set up my machine for XML or chado
yet, and it does not appear trivial.

Thanks for the help,

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

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From weckalba at asu.edu  Tue May  1 19:33:00 2012
From: weckalba at asu.edu (Walter Eckalbar)
Date: Tue, 1 May 2012 18:33:00 -0700
Subject: [maker-devel] gff3_preds2models usage question
In-Reply-To: <CBC5D543.C151%carsonhh@gmail.com>
References: <CANRPJSdHUx_BmAzb+OBLFab02dDtugM9Jf3zsXqjThrKauX29g@mail.gmail.com>
	<CBC5D543.C151%carsonhh@gmail.com>
Message-ID: <CANRPJSc-EN9jgqW3dJRJmLJ_4SyhavqsOCH+h-031PPtiBHONA@mail.gmail.com>

Hi Carson,

Thanks for the response, even a late one, and thanks for the script.  I'll
certainly be giving that a try.

Walter

On 1 May 2012 15:07, Carson Holt <carsonhh at gmail.com> wrote:

> Sorry for the slow response.  The gff3_preds2models script has been
> deprecated for some time now (isn't even in the release code anymore), and
> the old one won't work with the new library.
>
> I've attached a made from scratch drop-in replacement that you can use to
> do what the old script would have done.  In the current release of MAKER,
> instead of the gff3_preds2models script users can just give MAKER  a set of
> predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then
> leave all other options blank).  The predictions given will the be
> converted into gene models.
>
> Thanks,
> Carson
>
>
>
> From: Walter Eckalbar <weckalba at asu.edu>
> Date: Tuesday, 3 April, 2012 7:28 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] gff3_preds2models usage question
>
> Hello maker developers and users,
>
> I am attempting to use the gff3_preds2models scripts, but running into a
> few issues.
>
> Initially, I hit errors that seemed to be fixed by installing CGI and its
> dependancies.  However, that during that installation a few tests did fail.
>  I can provide error logs if that would be helpful, however, I went on to
> install and attempt gff3_preds2models anyway.
>
> What I am currently doing is running gff3_merge first, to gather the maker
> outputs.  I am doing so with both the -n option on and off.  When providing
> the gff3 file with the sequence I get the following error from
> gff3_preds2models:
>
> Undefined subroutine &maker::auto_annotator::annotate called at
> /Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97,
> <GEN16> line 992291.
>
> This seemed to be the same error as that of what someone else saw on these
> boards, but I did not see a later email resolving the issue.
>
> I also tried giving it just the gff3 without the sequences at the bottom
> of the file and then I get this error:
>
> ERROR: There was a problem in the writing the fasta entry
> Either no sequence was given, or there was an error in writing
>
> This leads me to believe I should be using the one with the sequence, but
> I am not certain of that.
>
> I see it might be possible to go from maker outputs to chado database then
> to gene->mRNA->exon gff3s, but I have not set up my machine for XML or
> chado yet, and it does not appear trivial.
>
> Thanks for the help,
>
> Walter
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From qwang at uwyo.edu  Thu May  3 10:23:16 2012
From: qwang at uwyo.edu (Qiurong Wang)
Date: Thu, 3 May 2012 10:23:16 -0600
Subject: [maker-devel] MAKER download problem
Message-ID: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>

Hi,

I was trying to download MAKER, but I couldn't open the download page.  
Could you please help me to figure out the problem? Thanks a lot!


Qiurong Wang
PhD candidate
Department of Botany
University of Wyoming
Department 3165, 1000 E University Ave. Laramie, Wyoming 82071, USA
Phone: 307-766-2634
Email: qwang at uwyo.edu




From barry.moore at genetics.utah.edu  Thu May  3 11:51:48 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Thu, 3 May 2012 11:51:48 -0600
Subject: [maker-devel] MAKER download problem
In-Reply-To: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>
References: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>
Message-ID: <6B24C00B-6C70-4A40-BA7C-E3AC0C7F5E25@genetics.utah.edu>

Hi all,

The web server hosting the MAKER licensing application and MAKER code distribution was attacked this week.  The University of Utah is currently blocking access to that server from outside University IP space.  We are working hard to move all of the content and web-applications from that machine to a new server and I expect to have the MAKER services restored over the weekend.  This is affecting the ability to submit new licenses for MAKER and to download the MAKER code.  In addition those with existing licenses will need to update their code links for future code updates.  For those of you on campus in Utah or with campus VPN access, the server is running and available.  Updates on the status of the server and details about new links to the MAKER code will be posted to the mailing list soon.

Barry

On May 3, 2012, at 10:23 AM, Qiurong Wang wrote:

> Hi,
> 
> I was trying to download MAKER, but I couldn't open the download page. Could you please help me to figure out the problem? Thanks a lot!
> 
> 
> Qiurong Wang
> PhD candidate
> Department of Botany
> University of Wyoming
> Department 3165, 1000 E University Ave. Laramie, Wyoming 82071, USA
> Phone: 307-766-2634
> Email: qwang at uwyo.edu
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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




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From carsonhh at gmail.com  Thu May  3 12:00:01 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 03 May 2012 14:00:01 -0400
Subject: [maker-devel] MAKER download problem
In-Reply-To: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>
Message-ID: <CBC83F6D.C3B0%carsonhh@gmail.com>

The server hosting the file to download is down temporarily.  I'll put a
copy of MAKER on a separate server and e-mail the link to you.

--Carson



On 12-05-03 12:23 PM, "Qiurong Wang" <qwang at uwyo.edu> wrote:

>Hi,
>
>I was trying to download MAKER, but I couldn't open the download page.
>Could you please help me to figure out the problem? Thanks a lot!
>
>
>Qiurong Wang
>PhD candidate
>Department of Botany
>University of Wyoming
>Department 3165, 1000 E University Ave. Laramie, Wyoming 82071, USA
>Phone: 307-766-2634
>Email: qwang at uwyo.edu
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From cjfields at illinois.edu  Tue May 15 09:01:31 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 15 May 2012 15:01:31 +0000
Subject: [maker-devel] mail list and Trac
Message-ID: <64A6759A-9FD1-4AEE-BCEA-151B0D791ADD@illinois.edu>

Just wanted to point out, I noticed the mail list is not being indexed on Google Groups any more (nothing in May).  Also, any status on Trac?

chris


From barry.moore at genetics.utah.edu  Tue May 15 10:34:29 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 15 May 2012 10:34:29 -0600
Subject: [maker-devel] mail list and Trac
In-Reply-To: <64A6759A-9FD1-4AEE-BCEA-151B0D791ADD@illinois.edu>
References: <64A6759A-9FD1-4AEE-BCEA-151B0D791ADD@illinois.edu>
Message-ID: <C2170DBB-75CB-423D-82E3-C56572B57753@genetics.utah.edu>

Thanks Chris,  I'll check on the Google groups.  The MAKER Trac server was on a server that we had to shut down a couple weeks ago and I had made moving it a lower priority since I didn't think it was getting much use.  I'll get it moved over and bump up the priority on that move since I know someone is looking at it.

B

On May 15, 2012, at 9:01 AM, Fields, Christopher J wrote:

> Just wanted to point out, I noticed the mail list is not being indexed on Google Groups any more (nothing in May).  Also, any status on Trac?
> 
> chris
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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




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From anastasia.gioti at scilifelab.se  Thu May 17 05:27:04 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Thu, 17 May 2012 13:27:04 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
	<03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <4D9922AF-A917-4747-9B7C-CFE9F142D51C@scilifelab.se>

Hi Barry,
Thanks for your detailed instructions. You well understood that I have  
already included the proteins of the closely related species in my  
protein evidence dataset, but still did not get the genes. I have now  
blasted (P) the missing 949 proteins from this species against my  
nonoverlaping_abinits.fasta proteins and have found 618 good hits,  
which i guess I can promote to models using the routine no 2 of your  
last email and Carson's script gff3_select.
I have also looked at the rest of the proteins (331) for which there  
was no model in the nonoverlaping_abinits.fasta. I will try to  
describe 2 examples I looked at in apollo:

1) ab initio models predicted a ~7.5 kb gene covering 3 genes (as  
predicted in the closely related species). Blastx+protein2genome  
similarities were reported for two of these genes, but not for the 3rd  
(the one in the middle). MAKER finally decided to call two genes,  
respecting the blastx+protein2genome evidence, but the 3rd was lost.
I have previously  reported here that MAKER tends to  fuse genes in  
multi-exonic genes and others reported that too, I remember you  
proposed changing a papameter to alter this. To keep in mind for my  
final strategy that i am trying to decide on (for the moment i have  
not rerun MAKER).
For this case, abinitio models do not exist for the gene (in the sense  
that the existing models overlap many genes) and the similarity to the  
protein of the closely related species was not judged sufficient,  
although when i look at a TblastN alignment for this area it looks  
fine to me.

2) Only the 3' end of the gene was called by MAKER, despite blastx  
+protein2genome evidence from the closely related species for the  
entire region. Abinitio models existed as 2 separate genes , one for  
the 3' end region (finally retained by MAKER in a consensus decision I  
guess) and one for the 5' region, but here not all predictors called  
an orf, and finally nothing was called in this region.
In this case, it is a misannotation rather, but which misses a very  
important part of the gene.
I hope my descriptions are clear, otherwise I can provide you the gff  
file of these 2 examples to look by yourself.

I am not very clear about what to do about these 331 cases (which I do  
not know how to look at as well, except for random examples' viwing in  
Apollo). I feel that a second MAKER run would be probably the  
solution, this time providing as pred_gff  the result of a blast  
against the 331. But still, the existing annotations would then have  
to be somehow updated as the new predictions are in conflict with them  
(see example 2). I am a bit confused.
to recap, what would you suggest for the 331 still-missing proteins in  
terms of asessing their profiles n a rather automatic way and in  
inluding them in my annotations without going deep into manual gene  
curation?
Many thnks,
Anastasia
>
> Let me just restate what you've said so that I can be sure that I am  
> correct about what you've already done.  You have run Maker with  
> SNAP, Genemark and Augustus using EST from a closely related species  
> (passed to altest) and protein evidence from other fungi.  You are  
> missing about 1,000 genes compared to the species that provided the  
> EST alignments.  You say their is good evidence that these genes  
> exist from the alignments and I assume by this that you mean the EST/ 
> protein alignments that Maker produced.
>
> 1) Is the closely related fungus annotated and if so have you  
> included it's proteins in the evidence set that you provided to  
> Maker.  If you haven't provided these proteins as evidence to maker  
> then you should do this.  You can re-run maker passing your original  
> models back through like this:
>
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=1
> other_pass=1
>
> #-----Protein Homology Evidence (for best results provide a file for  
> at least one)
> protein=proteins_from_closely_related.fasta
> ## OR it sounds like you've already aligned these with exonerate?
> protein_gff=proteins_from_closely_related_already_aligned.gff
>
> 2) If you've already included those closely related species proteins  
> but still didn't get the 1,000 genes, then take your  
> nonoverlaping_abinits.fasta and blast them directly against your  
> closely related proteins.  Presumably they don't hit too well  
> because if they did they should have been promoted to predictions by  
> Maker the first time, but here you can decide yourself what  
> thresholds to allow to keep the abinit predictions that hit the  
> closely related species proteins.  If you filter you blast hits the  
> way you want and keep the names of the abinit predictions that pass  
> your filter, then use the script Carson attached it it will generate  
> a abinit precidtion GFF file with only the predictions you  
> selected.  You can then pass those predictions back to Maker and  
> force it to keep them and Maker will turn them from predictions  
> (match/match_part) into gene models.
>
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=0
> other_pass=1
>
> #-----Gene Prediction
> snaphmm=
> gmhmm=
> augustus_species=
> fgenesh_par_file=
> pred_gff=ab_init_predictions_rescued_by_blast.gff
>
> keep_preds=1
>
> Barry
>
>>> Thanks,
>>> Carson
>>>
>>> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
>>> Date: Wed, 25 Apr 2012 11:09:36 +0200
>>> To: <maker-devel at yandell-lab.org>
>>> Subject: [maker-devel] Use pass-through system to add missing genes
>>>
>>> Hi,
>>> I  have a set of predicted proteins from the genome of a fungus  
>>> annotated by MAKER  using EST data from a closely related species  
>>> and 3 ab initio predictors  (snap iterativelly trained 3 times,  
>>> genemark trained directly on the assembly and augustus with a  
>>> model from a less closely related species), along with a set of  
>>> fungal proteins. I am missing ~ 1000 proteins when I compare to  
>>> the species i used EST data from, and there is good evidence from  
>>> alignments that these genes exist. The question is how to proceed  
>>> from Blast hits to actual gene models here. The idea would be to  
>>> add these genes to the existing dataset, rather than reannotate  
>>> the genome. I believe that reannotating it without any further  
>>> evidence such as RNA-seq from the species itself would not change  
>>> much,and i d rather stick with actual predictions that i trust and  
>>> have used in subsequent analyses. The 1000 genes I can accept to  
>>> annotate with a less stringent and reliable way than MAKER, I just  
>>> want to add them so that the difference in gene count gets  
>>> corrected.
>>> I was reading the MAKER 2 paper and i was wondering if I can use  
>>> the legacy annotations scheme to do it, by providing GFF3 of the  
>>> alignments between the two species in the regions where genes were  
>>> missed, but as i said, I would not like to reannotate the whole  
>>> genome, and running MAKER2 might cause slight changes that i d  
>>> like to avoid. Is this possible? First, is it possible to provide  
>>> a Gff3 file of specific locations and not the entire genome  
>>> alignment? (I guess so..) Second, how can I tag the existing  
>>> annotations as 'not to be changed' or alternatively, tag the new  
>>> models only? How should I run maker2, with which predictors on and  
>>> which off?
>>> Thanks,
>>> Anastasia
>>>
>>> Anastasia Gioti
>>> Post-doctoral Researcher
>>>
>>> anastasia.gioti at scilifelab.se
>>> anastasia.gioti at ebc.uu.se
>>>
>>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>>>
>>>
>>>
>>> _______________________________________________ maker-devel  
>>> mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> <gff3_select>
>>
>> Anastasia Gioti
>> Post-doctoral Researcher
>>
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/ 
>> Gioti_Anastasia/
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell- 
> lab.org

Anastasia (Natassa) Gioti
Post-Doc Researcher
Evolutionary Biology Department Uppsala University -Science for Life  
lab, Karolinska Institute Stockholm
anastasia.gioti at ebc.uu.se
anastasia.gioti at scilifelab.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/










From yogeshp08 at gmail.com  Tue May 15 10:07:57 2012
From: yogeshp08 at gmail.com (Yogesh)
Date: Tue, 15 May 2012 11:07:57 -0500
Subject: [maker-devel] tblastn Cleanup?
Message-ID: <4478F0B20ED84A85B3C4FE4154F8FAD1@gmail.com>

Hello,

I have a few tblastn alignments with a lot of low quality hits. I have to clean that up. Can you please suggest how Maker pipeline does it? Also can I run it directly on my data without having to go through the whole pipeline?

Thanks,

-Yogesh
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From carsonhh at gmail.com  Fri May 18 08:22:50 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 18 May 2012 10:22:50 -0400
Subject: [maker-devel] tblastn Cleanup?
In-Reply-To: <4478F0B20ED84A85B3C4FE4154F8FAD1@gmail.com>
Message-ID: <CBDBD0A5.C8CD%carsonhh@gmail.com>

There are several things.  I set several filtering options directly on the
BLAST command line.  These are things like maximum intron length, an e-value
filter, and simple repeat filtering (called dust filter in NCBI blast and
seg filter in WUBLAST).

I also run repeat masker over the genome first.  This allows simple and
complex repeats to be removed before running BLAST (otherwise you get many
false alignments).

Last I filter the results based on percent coverage of the hit to the
original database sequence and percent identity.  I think you can set
percent identity as a flag in BLAST, but the percent coverage filter is
being calculated by MAKER, so to do this outside of MAKER would require that
you write your own filtering script to compare the length of the alignment
to the length of the sequence in the database.

I also have an HSP depth overlap filter.  This removes weird low complexity
hits that escape repeatmasking.  They show up as multiple HSPs overlapping
multiple times in the same region (usually very high numbers like 90 HSPs
all 100 bp long in the same region).  I calculate the number of base pairs
in the alignment on the hit then divide by the number of base pairs in the
query alignment.  If it's greater than 3, I throw the hit out.

Thanks,
Carson



From:  Yogesh <yogeshp08 at gmail.com>
Date:  Tuesday, 15 May, 2012 12:07 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] tblastn Cleanup?

 
Hello,

I have a few tblastn alignments with a lot of low quality hits. I have to
clean that up. Can you please suggest how Maker pipeline does it? Also can I
run it directly on my data without having to go through the whole pipeline?

Thanks,

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

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From smg283 at gmail.com  Tue May 22 00:42:51 2012
From: smg283 at gmail.com (Scott Geib)
Date: Mon, 21 May 2012 20:42:51 -1000
Subject: [maker-devel] can't call method strand on an undefined value ERROR:
 Failed while flattening protein clusters
Message-ID: <CAH221bv8rM7w+yOg6AgW9Y9tLHLvivWgGjZFs4e4QLAyuW4pGA@mail.gmail.com>

Hi,
Using maker 2.24, I am getting the following error (see below) in
protein2genome widget.  I also get the same error with est2genome.  This
happens with my own data (testing on a single scaffold), but not with the
test data supplied with maker (dpp files in data folder).
Scott


Widget::exonerate::protein2genome:
/data0/opt/AlignmentSoftware/exonerate/exonerate-2.2.0-x86_64/bin/exonerate
-q
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/UniRef90_UPI000194D3FC.for.1588546-1589203.9.fasta
-t
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.1588546-1589203.9.fasta
-Q protein -T dna -m protein2genome --softmasktarget  --percent 20
--showcigar  >
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.1588546-1589203.UniRef90_UPI000194D3FC.p_exonerate.9
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 23
 ...processing 1 of 23
 ...processing 2 of 23
 ...processing 3 of 23
 ...processing 4 of 23
 ...processing 5 of 23
 ...processing 6 of 23
 ...processing 7 of 23
 ...processing 8 of 23
 ...processing 9 of 23
 ...processing 10 of 23
 ...processing 11 of 23
 ...processing 12 of 23
 ...processing 13 of 23
 ...processing 14 of 23
 ...processing 15 of 23
 ...processing 16 of 23
 ...processing 17 of 23
 ...processing 18 of 23
 ...processing 19 of 23
 ...processing 20 of 23
 ...processing 21 of 23
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 20
 ...processing 1 of 20
 ...processing 2 of 20
 ...processing 3 of 20
 ...processing 4 of 20
 ...processing 5 of 20
 ...processing 6 of 20
 ...processing 7 of 20
 ...processing 8 of 20
 ...processing 9 of 20
 ...processing 10 of 20
 ...processing 11 of 20
 ...processing 12 of 20
 ...processing 13 of 20
 ...processing 14 of 20
 ...processing 15 of 20
 ...processing 16 of 20
 ...processing 17 of 20
 ...processing 18 of 20
total clusters:2 now processing 0
Can't call method "strand" on an undefined valueERROR: Failed while
flattening protein clusters
ERROR: Chunk failed at level:11, tier_type:2
FAILED CONTIG:scaffold00001
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From anastasia.gioti at scilifelab.se  Tue May 22 07:14:17 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Tue, 22 May 2012 15:14:17 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
	<03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <19E36E3B-6A82-49D5-B0AC-5E521F3E8999@scilifelab.se>

Hi again,
I hav sent an email a few days ago about this thread, and i am not  
sure if you have received it or you still did not have time to look at  
it. In any case, this email was dealing with the fact that some  
proteins were not retrieved in the abinitio models and how to deal  
with it. What I would like to ask here is a few confirmations on how  
to rerun maker for the proteins that were retrieved in the abinitio  
models. i have looked at the Blast results, and have done a series of  
check-ups, so now I am ready to run MAKER again with a list of models  
that I want to retain.
Regarding the following parameters:

1. Do I  set the genome= to nothing here? i.e quote it out? This is in  
the beginning of the control file
#-----Genome (Required for De-Novo Annotation)
genome=#genome sequence file in fasta format
organism_type= #eukaryotic or prokaryotic. Default is eukaryotic

>
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=0
> other_pass=1
>
> #-----Gene Prediction
2. Do i provide again the snap etc models? I am not sure, because i  
thought MAKER would not run ab initio predictors this time (this is  
why I would also quote out the genome file above, as this is not a de  
novo annotation). but if it will, i will then provide the previous  
models i used, except for snap, for which I will generate a new model   
from the gff3 file of the last run (according to snap documentation).  
Am i correct?
> snaphmm=
> gmhmm=
> augustus_species=
> fgenesh_par_file=
> pred_gff=ab_init_predictions_rescued_by_blast.gff
>
> keep_preds=1

Samely, what do i do with repeatmasking etc?
Thanks in adavance,
Anastasia

>
> Barry
>
>>> Thanks,
>>> Carson
>>>
>>> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
>>> Date: Wed, 25 Apr 2012 11:09:36 +0200
>>> To: <maker-devel at yandell-lab.org>
>>> Subject: [maker-devel] Use pass-through system to add missing genes
>>>
>>> Hi,
>>> I  have a set of predicted proteins from the genome of a fungus  
>>> annotated by MAKER  using EST data from a closely related species  
>>> and 3 ab initio predictors  (snap iterativelly trained 3 times,  
>>> genemark trained directly on the assembly and augustus with a  
>>> model from a less closely related species), along with a set of  
>>> fungal proteins. I am missing ~ 1000 proteins when I compare to  
>>> the species i used EST data from, and there is good evidence from  
>>> alignments that these genes exist. The question is how to proceed  
>>> from Blast hits to actual gene models here. The idea would be to  
>>> add these genes to the existing dataset, rather than reannotate  
>>> the genome. I believe that reannotating it without any further  
>>> evidence such as RNA-seq from the species itself would not change  
>>> much,and i d rather stick with actual predictions that i trust and  
>>> have used in subsequent analyses. The 1000 genes I can accept to  
>>> annotate with a less stringent and reliable way than MAKER, I just  
>>> want to add them so that the difference in gene count gets  
>>> corrected.
>>> I was reading the MAKER 2 paper and i was wondering if I can use  
>>> the legacy annotations scheme to do it, by providing GFF3 of the  
>>> alignments between the two species in the regions where genes were  
>>> missed, but as i said, I would not like to reannotate the whole  
>>> genome, and running MAKER2 might cause slight changes that i d  
>>> like to avoid. Is this possible? First, is it possible to provide  
>>> a Gff3 file of specific locations and not the entire genome  
>>> alignment? (I guess so..) Second, how can I tag the existing  
>>> annotations as 'not to be changed' or alternatively, tag the new  
>>> models only? How should I run maker2, with which predictors on and  
>>> which off?
>>> Thanks,
>>> Anastasia
>>>
>>> Anastasia Gioti
>>> Post-doctoral Researcher
>>>
>>> anastasia.gioti at scilifelab.se
>>> anastasia.gioti at ebc.uu.se
>>>
>>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>>>
>>>
>>>
>>> _______________________________________________ maker-devel  
>>> mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> <gff3_select>
>>
>> Anastasia Gioti
>> Post-doctoral Researcher
>>
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/ 
>> Gioti_Anastasia/
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell- 
> lab.org

Anastasia (Natassa) Gioti
Post-Doc Researcher
Evolutionary Biology Department Uppsala University -Science for Life  
lab, Karolinska Institute Stockholm
anastasia.gioti at ebc.uu.se
anastasia.gioti at scilifelab.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/










From anastasia.gioti at scilifelab.se  Wed May 23 03:07:12 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Wed, 23 May 2012 11:07:12 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
	<03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <1B0770A0-6D14-4336-BC3A-DC24619BC3FE@scilifelab.se>

Hi 
and sorry for the multiple postings. I have a list of models rescued by the nonoverlaping_abinits.fasta  fles (against which i  blasted my missing proteins from the closely related species and further filtered out the dubious hits) and a maker gff3 file, but Carson's script gff3_select won't work, and the reason is that these abinitio models were not promoted into the maker gff3 file, thus they are not there. I refer to the gff3 file generated by gff3_merge script. Am i missing something?
Thank you, 
Anastasia



> 
>>> If you know which ab initio predictions you want to add (I.e. the ab initio promoting scenario I descibed), you can provide those predictions to the use the pred_gff option and then set keep_preds=1 and they will be maintained even without evidence.  Attached is a script that would make selecting those easier.  It take the MAKER generated GFF3 and a list of predictions to keep (one name per line).  These might be the results of a BLAST analysis for example.  It will then return the GFF3 entries for just those models selected.

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From thomas.hackl at uni-wuerzburg.de  Wed May 23 06:01:55 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Wed, 23 May 2012 14:01:55 +0200
Subject: [maker-devel] missing est2genome annotation
Message-ID: <4FBCD1B3.8000102@uni-wuerzburg.de>

Hi,

I used maker to annotate genomic contigs and among other stuff provided 
transcripts from the transcriptome as est evidence. Blast and exonerate 
work fine and produce valid alignments, the alignment files exist in 
theVoid and look very good. Unfortunatly neither the evidence_0.gff nor 
the final .gff carry the corresponding feature annotations.

Any ideas why?

Regards
Thomas

-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From thomas.hackl at uni-wuerzburg.de  Wed May 23 11:14:27 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Wed, 23 May 2012 19:14:27 +0200
Subject: [maker-devel] missing est2genome annotation
In-Reply-To: <4FBCD1B3.8000102@uni-wuerzburg.de>
References: <4FBCD1B3.8000102@uni-wuerzburg.de>
Message-ID: <4FBD1AF3.8020904@uni-wuerzburg.de>

Hi again,

I did some source code digging and caught the following line burying my 
exonerate alignments. I suspect it does so for a very good reason, 
therefore it would help me a lot if someone could explain to me, what is 
going on there.


/lib/GI.pm  l.1473
next if $e->pAh<  $pcov;


Regards
Thomas


Am 23.05.2012 14:01, schrieb Thomas Hackl:
> Hi,
>
> I used maker to annotate genomic contigs and among other stuff 
> provided transcripts from the transcriptome as est evidence. Blast and 
> exonerate work fine and produce valid alignments, the alignment files 
> exist in theVoid and look very good. Unfortunatly neither the 
> evidence_0.gff nor the final .gff carry the corresponding feature 
> annotations.
>
> Any ideas why?
>
> Regards
> Thomas
>


-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 13:30:09 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 12:30:09 -0700
Subject: [maker-devel] Merging gene predictions....
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>

Hi Carson and others,
I am wondering if I can use Maker to merge gene predictions from three gff files. One of the algorithm is 'augustus' which of course i can use it inside Maker. Other two are not part of Maker.

But, in case if I want to pass only the GFFs to Maker and ask it to merge the annotations (when overlap) and pick only annotation that are predicted in 2 out of 3 gffs. Is it possible? I prefer this approach, as we need to run a blast based validation step on predicted features before even try to merge them. Thats another reason why we dont prefer to use the augustus inside maker. 

Thanks,
Gowthaman


From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 15:02:55 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 14:02:55 -0700
Subject: [maker-devel] Merging gene predictions....
In-Reply-To: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>
References: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D8@mail02.sbri.org>

Can i use the following approach Carson?

This is your reply to one of the earlier question:

I've attached a made from scratch drop-in replacement that you can use to do what the old script would have done.  In the current release of MAKER, instead of the gff3_preds2models script users can just give MAKER  a set of predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then leave all other options blank).  The predictions given will the be converted into gene models.

Thanks,
Carson



________________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] On Behalf Of Gowthaman Ramasamy [gowthaman.ramasamy at seattlebiomed.org]
Sent: Thursday, May 24, 2012 12:30 PM
To: Carson Holt; maker-devel at yandell-lab.org
Subject: [maker-devel] Merging gene predictions....

Hi Carson and others,
I am wondering if I can use Maker to merge gene predictions from three gff files. One of the algorithm is 'augustus' which of course i can use it inside Maker. Other two are not part of Maker.

But, in case if I want to pass only the GFFs to Maker and ask it to merge the annotations (when overlap) and pick only annotation that are predicted in 2 out of 3 gffs. Is it possible? I prefer this approach, as we need to run a blast based validation step on predicted features before even try to merge them. Thats another reason why we dont prefer to use the augustus inside maker.

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



From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 15:21:30 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 14:21:30 -0700
Subject: [maker-devel] Merging gene predictions....
In-Reply-To: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D8@mail02.sbri.org>
References: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>,
	<89080953C3D300419AACB6E63A7EEFBA5C8409F8D8@mail02.sbri.org>
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8DA@mail02.sbri.org>

Hi,
I am trying to install MAKER in centOS. I was able to install all the perl deps. and external programs. Perl Build.pl and ./Build Install went with out errors/warnings. I did not enable MPI though.

But, when i start Maker it returs "segmentation fault". 

I have no clue whats going wrong....or where to check for error logs? 

Any help would be appreciated,
Thanks,
gowthaman
_________


From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 15:22:16 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 14:22:16 -0700
Subject: [maker-devel] MAKER installation problem
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8DB@mail02.sbri.org>

Hi,
I am trying to install MAKER in centOS. I was able to install all the perl deps. and external programs. Perl Build.pl and ./Build Install went with out errors/warnings. I did not enable MPI though.

But, when i start Maker it returs "segmentation fault". 

I have no clue whats going wrong....or where to check for error logs? 

Any help would be appreciated,
Thanks,
gowthaman
_________
________________________________________



From bob_freeman at hms.harvard.edu  Fri May 25 10:23:22 2012
From: bob_freeman at hms.harvard.edu (Bob Freeman)
Date: Fri, 25 May 2012 12:23:22 -0400
Subject: [maker-devel] Alternate translation table?
Message-ID: <454CA235-0DB6-451F-97C4-83D32E2E805A@hms.harvard.edu>

Hello all!

Unusual question here: I am running MAKER on a ciliate that uses a non-standard translation table for its translation products. I haven't found an option in the control files that I can change for the for translation of the predicted transcripts. How or where can I go about this?

Tx,
Bob

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
	-- Karen Walker, from Will and Grace





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From carsonhh at gmail.com  Mon May 28 06:43:34 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 08:43:34 -0400
Subject: [maker-devel] Alternate translation table?
In-Reply-To: <454CA235-0DB6-451F-97C4-83D32E2E805A@hms.harvard.edu>
Message-ID: <CBE8E7EF.CAF3%carsonhh@gmail.com>

The alternate translation table is not currently an option.  It's one of
those things that needs to be implemented, but has not been yet.  It's also
not supported by many of the eukaryotic gene predictors MAKER uses.

I could probably get something implemented for you to test in two to three
weeks though (there are a lot of places where the translation table comes
into play).  Let me know.

--Carson



From:  Bob Freeman <bob_freeman at hms.harvard.edu>
Date:  Friday, 25 May, 2012 12:23 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Alternate translation table?

Hello all!

Unusual question here: I am running MAKER on a ciliate that uses a
non-standard translation table for its translation products. I haven't found
an option in the control files that I can change for the for translation of
the predicted transcripts. How or where can I go about this?

Tx,
Bob

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
-- Karen Walker, from Will and Grace





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

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From carsonhh at gmail.com  Mon May 28 07:38:25 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 09:38:25 -0400
Subject: [maker-devel] missing est2genome annotation
In-Reply-To: <4FBD1AF3.8020904@uni-wuerzburg.de>
Message-ID: <CBE8F75D.CB57%carsonhh@gmail.com>

Sorry for the slow reply.  I'm just getting back after traveling.

That's a percent coverage flag.  You can set a percent coverage threshold
in the maker_bopts.ctl file.  Partial high scoring alignments can be
common.  If you only filter by expect score, you would be surprised to see
how many ugly and confusing all the alignments become.

Thanks,
Carson

On 12-05-23 1:14 PM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi again,
>
>I did some source code digging and caught the following line burying my
>exonerate alignments. I suspect it does so for a very good reason,
>therefore it would help me a lot if someone could explain to me, what is
>going on there.
>
>
>/lib/GI.pm  l.1473
>next if $e->pAh<  $pcov;
>
>
>Regards
>Thomas
>
>
>Am 23.05.2012 14:01, schrieb Thomas Hackl:
>> Hi,
>>
>> I used maker to annotate genomic contigs and among other stuff
>> provided transcripts from the transcriptome as est evidence. Blast and
>> exonerate work fine and produce valid alignments, the alignment files
>> exist in theVoid and look very good. Unfortunatly neither the
>> evidence_0.gff nor the final .gff carry the corresponding feature
>> annotations.
>>
>> Any ideas why?
>>
>> Regards
>> Thomas
>>
>
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From seoanezonjic at hotmail.com  Tue May 22 06:55:12 2012
From: seoanezonjic at hotmail.com (p sz)
Date: Tue, 22 May 2012 12:55:12 +0000
Subject: [maker-devel] ipr_update_gff ERROR
Message-ID: <COL119-W282F1F1F211028B1F661C5C7020@phx.gbl>


First, thanks by help me on the lprevious error that I submitted.
I'm still working in the same project and I get a new error. I try interproscan with this commandline:

iprscan_wrap -i parsed_input.all.maker.proteins.fasta -email seoanezonjic at hotmail.com  -format raw

parsed_input.all.maker.proteins.fasta was generated with the tool fasta_merge. I use the output (attached in this email) and a gff file (generated by a normal run of maker, attached in this email) with the ipr_update_gff script of this way:

ipr_update_gff BAC12_Clone_Pt314B2_Lib_Pt_7Ba__organism_Pinus_taeda__0.gff sc_interpro.sh.o109053

And i get this error:
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 15.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 15.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 18.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 18.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 19.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 19.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 48.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 48.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 49.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 49.

The gff file seems updated but i don't know if it works fine or is corrupt
Thanks in advance
 		 	   		  
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From larriba.ed at gmail.com  Fri May 25 10:01:41 2012
From: larriba.ed at gmail.com (Eduardo Larriba)
Date: Fri, 25 May 2012 18:01:41 +0200
Subject: [maker-devel] Consensus gene models
Message-ID: <CADwrZ2XdcZu080yHt7=CreOWbpt791NC8ScB5WVW=NmvN4=Jgw@mail.gmail.com>

Hi Carson and people,
I am working on structural annotation of a filamentous fungus, of which
there is little evidence as EST or Protein. For generate consensus gene  based
on limited evidences to me I used  Marker.
For this I created the files GeneMark prediction-is and SNAP.
I run maker using the EST of my organims (85), along with 5700 EST of the
closed organims. I have made ??predictions with Augustus, and SNAP GeneMark,
with the training files for my organims, in Maker pipeline. Everything works
fine.
My problem is that when I get the consensus sequences of all my contigs,
fasta_merge script (included in Maker), I get different list for each
predictor, as well as when I try to get the gff of all.
They could tell me how I can use Maker consensus for a list of genes? Or I
have to do it manually? There is the possibility that Maker evaluates the
accuracy of each prediction and confirm, so just get a list of the different
predictions?

Thank you very much.


-- 
Eduardo Larriba Tornel
Universidad de Alicante.
Lab. Fitopatolog?a
Dept. Ciencias del Mar y Biolog?a Aplicada
Pabell?n 13.
San Vicente del Raspeig
Tel. 96 590 3400 ext 3280
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From carsonhh at gmail.com  Mon May 28 08:14:22 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 10:14:22 -0400
Subject: [maker-devel] Consensus gene models
In-Reply-To: <CADwrZ2XdcZu080yHt7=CreOWbpt791NC8ScB5WVW=NmvN4=Jgw@mail.gmail.com>
Message-ID: <CBE8FECE.CBA5%carsonhh@gmail.com>

The consensus list is in the maker.proteins.fasta and
maker.transcripts.fasta file.  The predictor specific lists are just for
reference purposes (incase you want to see what the other predictors
produced on their own, i.e. without MAKER's intervention).  The
non-overlapping.fasta file in the same directory will contain consensus
entries for models that were not supported by any evidence and don't overlap
any gene models in the  maker.transcripts.fasta (think of these as the maybe
gene and the maker.transcripts.fasta as the very likely genes).  You can set
keep_preds=1 if you just want MAKER to keep everything with or without
support and just produce consensus (probably ok on a fungus, but I wouldn't
recommend it on other eukayotes because false positive rates will be very
high).

Thanks,
Carson



From:  Eduardo Larriba <larriba.ed at gmail.com>
Date:  Friday, 25 May, 2012 12:01 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Consensus gene models

Hi Carson and people,
I am working on structural annotation of a filamentous fungus, of which
there is little evidence as EST or Protein. For generate consensus gene
based on limited evidences to me I used  Marker.
 For this I created the files GeneMark prediction-is and SNAP.
 I run maker using the EST of my organims (85), along with 5700 EST of the
closed organims. I have made ??predictions with Augustus, and SNAP
GeneMark, with the training files for my organims, in Maker pipeline.
Everything works fine.
 My problem is that when I get the consensus sequences of all my contigs,
fasta_merge script (included in Maker), I get different list for each
predictor, as well as when I try to get the gff of all.
 They could tell me how I can use Maker consensus for a list of genes? Or I
have to do it manually? There is the possibility that Maker evaluates the
accuracy of each prediction and confirm, so just get a list of the different
predictions?

 Thank you very much.


-- 
Eduardo Larriba Tornel
Universidad de Alicante.
Lab. Fitopatolog?a
Dept. Ciencias del Mar y Biolog?a Aplicada
Pabell?n 13. 
San Vicente del Raspeig
Tel. 96 590 3400 ext 3280

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http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Mon May 28 08:18:26 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 10:18:26 -0400
Subject: [maker-devel] ipr_update_gff ERROR
In-Reply-To: <COL119-W282F1F1F211028B1F661C5C7020@phx.gbl>
Message-ID: <CBE90090.CBB6%carsonhh@gmail.com>

This error would happen if some results exist in the iprscan output, but
don't match gene entries in the GFF3 file.  If I could see the original
files I can tell you which ones.  This can happen if you combine results
from the non-overlapping.fasta files with the maker.proteins.fasta files for
example.  Models in the non-overlapping.fasta file are not genes in the GFF3
(they are match/match_part enties), so errors happen.

Thanks,
Carson

From:  p sz <seoanezonjic at hotmail.com>
Date:  Tuesday, 22 May, 2012 8:55 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] ipr_update_gff ERROR

First, thanks by help me on the lprevious error that I submitted.
I'm still working in the same project and I get a new error. I try
interproscan with this commandline:

iprscan_wrap -i parsed_input.all.maker.proteins.fasta -email
seoanezonjic at hotmail.com  -format raw

parsed_input.all.maker.proteins.fasta was generated with the tool
fasta_merge. I use the output (attached in this email) and a gff file
(generated by a normal run of maker, attached in this email) with the
ipr_update_gff script of this way:

ipr_update_gff BAC12_Clone_Pt314B2_Lib_Pt_7Ba__organism_Pinus_taeda__0.gff
sc_interpro.sh.o109053

And i get this error:
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 15.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 15.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 18.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 18.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 19.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 19.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 48.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 48.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 49.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 49.

The gff file seems updated but i don't know if it works fine or is corrupt
Thanks in advance
       
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From carsonhh at gmail.com  Tue May 29 06:37:55 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 29 May 2012 08:37:55 -0400
Subject: [maker-devel] can't call method strand on an undefined value
 ERROR: Failed while flattening protein clusters
In-Reply-To: <CAH221bv8rM7w+yOg6AgW9Y9tLHLvivWgGjZFs4e4QLAyuW4pGA@mail.gmail.com>
Message-ID: <CBEA3AC6.CD62%carsonhh@gmail.com>

Use this command to check out the latest unreleased test version, and lt me
know if you still get the error.

Command -->  svn co svn://malachite.genetics.utah.edu/maker/trunk maker

User: yandell_guest
Password: y at ndell_Gu3st

Thanks,
Carson





From:  Scott Geib <smg283 at gmail.com>
Date:  Tuesday, 22 May, 2012 2:42 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] can't call method strand on an undefined value
ERROR: Failed while flattening protein clusters

Hi, 
Using maker 2.24, I am getting the following error (see below) in
protein2genome widget.  I also get the same error with est2genome.  This
happens with my own data (testing on a single scaffold), but not with the
test data supplied with maker (dpp files in data folder).
Scott


Widget::exonerate::protein2genome:
/data0/opt/AlignmentSoftware/exonerate/exonerate-2.2.0-x86_64/bin/exonerate
-q 
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/UniRef90_UPI00019
4D3FC.for.1588546-1589203.9.fasta -t
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.158
8546-1589203.9.fasta -Q protein -T dna -m protein2genome --softmasktarget
--percent 20 --showcigar  >
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.158
8546-1589203.UniRef90_UPI000194D3FC.p_exonerate.9
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 23
 ...processing 1 of 23
 ...processing 2 of 23
 ...processing 3 of 23
 ...processing 4 of 23
 ...processing 5 of 23
 ...processing 6 of 23
 ...processing 7 of 23
 ...processing 8 of 23
 ...processing 9 of 23
 ...processing 10 of 23
 ...processing 11 of 23
 ...processing 12 of 23
 ...processing 13 of 23
 ...processing 14 of 23
 ...processing 15 of 23
 ...processing 16 of 23
 ...processing 17 of 23
 ...processing 18 of 23
 ...processing 19 of 23
 ...processing 20 of 23
 ...processing 21 of 23
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 20
 ...processing 1 of 20
 ...processing 2 of 20
 ...processing 3 of 20
 ...processing 4 of 20
 ...processing 5 of 20
 ...processing 6 of 20
 ...processing 7 of 20
 ...processing 8 of 20
 ...processing 9 of 20
 ...processing 10 of 20
 ...processing 11 of 20
 ...processing 12 of 20
 ...processing 13 of 20
 ...processing 14 of 20
 ...processing 15 of 20
 ...processing 16 of 20
 ...processing 17 of 20
 ...processing 18 of 20
total clusters:2 now processing 0
Can't call method "strand" on an undefined valueERROR: Failed while
flattening protein clusters
ERROR: Chunk failed at level:11, tier_type:2
FAILED CONTIG:scaffold00001

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From bob_freeman at hms.harvard.edu  Tue May 29 10:30:23 2012
From: bob_freeman at hms.harvard.edu (Bob Freeman)
Date: Tue, 29 May 2012 12:30:23 -0400
Subject: [maker-devel] Alternate translation table?
In-Reply-To: <CBE8E7EF.CAF3%carsonhh@gmail.com>
References: <CBE8E7EF.CAF3%carsonhh@gmail.com>
Message-ID: <B198DB2E-A0CC-4A01-843D-59F470E97DC9@hms.harvard.edu>

Thanks, Carson, for the update on this. No need to implement something. I'll keep it simple and translate the collected transcripts using an appropriate translation table.

-Bob

On May 28, 2012, at 8:43 AM, Carson Holt wrote:

> The alternate translation table is not currently an option.  It's one of those things that needs to be implemented, but has not been yet.  It's also not supported by many of the eukaryotic gene predictors MAKER uses.
> 
> I could probably get something implemented for you to test in two to three weeks though (there are a lot of places where the translation table comes into play).  Let me know.
> 
> --Carson
> 
> 
> 
> From: Bob Freeman <bob_freeman at hms.harvard.edu>
> Date: Friday, 25 May, 2012 12:23 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Alternate translation table?
> 
> Hello all!
> 
> Unusual question here: I am running MAKER on a ciliate that uses a non-standard translation table for its translation products. I haven't found an option in the control files that I can change for the for translation of the predicted transcripts. How or where can I go about this?
> 
> Tx,
> Bob
> 
> 
> _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
	-- Karen Walker, from Will and Grace





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From gowthaman.ramasamy at seattlebiomed.org  Tue May 29 15:54:33 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Tue, 29 May 2012 14:54:33 -0700
Subject: [maker-devel] Can maker select a gene model based on #algoritham
	predicted it
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8EB@mail02.sbri.org>

Hi Carson,
Thanks for all the help during the long weekend, in spite of that long drive. I am still trying to imagine that.

I now have maker to consider our own prediction via pred_gff, and use augustus and gene mark (with our training model). And i was able to use altest and protein evidences. Maker happily picks one gene model when there is a overlap between three different predictions. But, when I look at the gff, it seems like it picks a gene model only when there is an est/protein evidence. It leaves out some genes even though, they are predicted by all three algorithms. Of course, keep_pred=1 helps to keep all the models. This kind of leads to over prediction. 

But, I am looking for something in between. And would like to know if that is possible?
1) Pick a gene model if it has an evidence from (est/prot etc...) irrespective of how many algorithms predicted it
2) In the absence of extrinsic evidence (est/prot etc), pick a gene model if that is predicted by at least two algorithms.

Or even simpler:
I have ab-initio predictions from three algorithms, Can I output, those genes that is supported by at least two of them. I care less about exactness of gene boundaries.

Thanks,
Gowthaman

PS: With my recent attempts, i learned couple things about maker/other associated tools that is not documented in gmod-maker wiki. Is it possible/ok if I add contents to it. I am okay with running it by you before making it public.


From carsonhh at gmail.com  Wed May 30 06:54:32 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 30 May 2012 08:54:32 -0400
Subject: [maker-devel] Can maker select a gene model based on
	#algoritham predicted it
In-Reply-To: <89080953C3D300419AACB6E63A7EEFBA5C8409F8EB@mail02.sbri.org>
Message-ID: <CBEB8E25.D097%carsonhh@gmail.com>

It's not an option in exactly the way you are specifying, but there is
something I usually do for annotation that works well.  I run interproscan
or rpsblast on the non_overlapping.proteins.fasta file and select just
those non-overlapping models that have a recognizable protein domain (just
searching the pfam doamin space is more than sufficient).  Then I provide
the selected results to model_gff, and provide the previous maker results
to the maker_gff option with (all reannotation pass options set to 1 and
all analysis options turned off).  This adds models with at least
recognizable domains (as even multiple gene predictors can overpredict in
a similar way).

Attached is a script to help select predictions and upgrade them to models
in GFF3 format.  If you have question let me know.

Thanks,
Carson



On 12-05-29 5:54 PM, "Gowthaman Ramasamy"
<gowthaman.ramasamy at seattlebiomed.org> wrote:

>Hi Carson,
>Thanks for all the help during the long weekend, in spite of that long
>drive. I am still trying to imagine that.
>
>I now have maker to consider our own prediction via pred_gff, and use
>augustus and gene mark (with our training model). And i was able to use
>altest and protein evidences. Maker happily picks one gene model when
>there is a overlap between three different predictions. But, when I look
>at the gff, it seems like it picks a gene model only when there is an
>est/protein evidence. It leaves out some genes even though, they are
>predicted by all three algorithms. Of course, keep_pred=1 helps to keep
>all the models. This kind of leads to over prediction.
>
>But, I am looking for something in between. And would like to know if
>that is possible?
>1) Pick a gene model if it has an evidence from (est/prot etc...)
>irrespective of how many algorithms predicted it
>2) In the absence of extrinsic evidence (est/prot etc), pick a gene model
>if that is predicted by at least two algorithms.
>
>Or even simpler:
>I have ab-initio predictions from three algorithms, Can I output, those
>genes that is supported by at least two of them. I care less about
>exactness of gene boundaries.
>
>Thanks,
>Gowthaman
>
>PS: With my recent attempts, i learned couple things about maker/other
>associated tools that is not documented in gmod-maker wiki. Is it
>possible/ok if I add contents to it. I am okay with running it by you
>before making it public.

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From mikael.durling at slu.se  Thu May 31 06:25:31 2012
From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=)
Date: Thu, 31 May 2012 14:25:31 +0200
Subject: [maker-devel] maker leaving large numbers of defunct zombies
Message-ID: <FBA1F582-5EF0-4D7A-8276-A86DAD5C4C89@slu.se>

Hello,

I've been working lately to set up maker for annotation work on a few fungal genomes. I've got mpi maker up and running now, however, I notice that maker is leaving a lot of <defunct> perl processes behind. This happens to the extent that the process table on the system gets filled up after a few hours run time. Right now the process tree after three hours running looks like this:

    |-sge_execd-+-sge_shepherd---bash---mpirun-+-maker-+-maker
     |           |                              |       `-perl
     |           |                              |-maker-+-maker
     |           |                              |       |-maker---1371*[perl]
     |           |                              |       `-perl
     |           |                              |-maker-+-maker
     |           |                              |       |-maker---1348*[perl]
     |           |                              |       `-perl
     |           |                              |-maker-+-maker
     |           |                              |       |-maker---1384*[perl]
     |           |                              |       `-perl

...and so on for all mpi processes, except for the controlling processes. 

What perl programs is maker calling, that might end up as zombies? I've had a brief look at the source to no avail, but would be happy to dig further with some pointers for where to look.

This is run with the 2.25-beta from the web page, perl 5.16.0 and openmpi 1.4.5. 

Thanks,
Mikael










-------------------------------------
Mikael Brandstr?m Durling, PhD
Assistant Professor

Sveriges lantbruksuniversitet
Swedish University of Agricultural Sciences

Uppsala BioCenter
Dept of Forest Mycology and Plant Pathology
Box 7026, 75007 Uppsala
Visiting address: Almas All? 5
Telefon: 018-671512
mikael.durling at slu.se, www.slu.se/mykopat





From mikael.durling at slu.se  Thu May 31 06:34:30 2012
From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=)
Date: Thu, 31 May 2012 14:34:30 +0200
Subject: [maker-devel] Using GDBM_File instead of DB_File
Message-ID: <B535F29B-D593-44D7-B0C4-D84462957EFB@slu.se>

Hello,

I've been struggling for a few days to get maker up and running with MPI on a debian squeeze system. Compiling a new perl 5.16 exclusively for maker I wound down to that the segfaults came from DB_File. Even by recomiling and updating that module, nothing worked. After checking for dependencies on DB_File in maker, I concluded that the only dependency was through the GI::localize_file, which expects the FastaDB to be instantiated with DB_File. However, FastaDB can run on GDBM_File too. I patched the calls to GI::localize_file in maker to handle the .pag/.dir extensions used by GDBM (below). With this patch applied maker is running for me, even when I have deleted the DB_File module from the perl path and made sure that GDBM_File is installed. My basic question is if there is any other dependency for DB_File which I have missed which may break things?

cheers,
Mikael

--- maker.orig	2012-03-30 15:48:05.000000000 +0200
+++ maker	2012-05-31 10:35:30.253022648 +0200
@@ -512,7 +515,12 @@
 }
 if($size > 1){
     carp "Calling GI::localize_file" if($main::debug);
-    GI::localize_file("$gdbfile.index");
+    if( -f "$gdbfile.index.dir" ){
+	GI::localize_file("$gdbfile.index.dir");
+	GI::localize_file("$gdbfile.index.pag");
+    }else{
+    	GI::localize_file("$gdbfile.index");
+    }
     carp "Calling GI::localize_file" if($main::debug);
     $gdbfile = GI::localize_file($gdbfile);
 }




From carsonhh at gmail.com  Thu May 31 07:04:58 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 31 May 2012 09:04:58 -0400
Subject: [maker-devel] Using GDBM_File instead of DB_File
In-Reply-To: <B535F29B-D593-44D7-B0C4-D84462957EFB@slu.se>
Message-ID: <CBECE3F7.D209%carsonhh@gmail.com>

DB_File is being called by Bio::DB::Fasta.  I can check the object
returned when using GDBM_File instead to see if the index file names are
contained on the object, as I'm just assuming an extension of '.index'.
I'll look around to see if the extension name is assumed anywhere else.

Thanks,
Carson


On 12-05-31 8:34 AM, "Mikael Brandstr?m Durling" <mikael.durling at slu.se>
wrote:

>Hello,
>
>I've been struggling for a few days to get maker up and running with MPI
>on a debian squeeze system. Compiling a new perl 5.16 exclusively for
>maker I wound down to that the segfaults came from DB_File. Even by
>recomiling and updating that module, nothing worked. After checking for
>dependencies on DB_File in maker, I concluded that the only dependency
>was through the GI::localize_file, which expects the FastaDB to be
>instantiated with DB_File. However, FastaDB can run on GDBM_File too. I
>patched the calls to GI::localize_file in maker to handle the .pag/.dir
>extensions used by GDBM (below). With this patch applied maker is running
>for me, even when I have deleted the DB_File module from the perl path
>and made sure that GDBM_File is installed. My basic question is if there
>is any other dependency for DB_File which I have missed which may break
>things?
>
>cheers,
>Mikael
>
>--- maker.orig	2012-03-30 15:48:05.000000000 +0200
>+++ maker	2012-05-31 10:35:30.253022648 +0200
>@@ -512,7 +515,12 @@
> }
> if($size > 1){
>     carp "Calling GI::localize_file" if($main::debug);
>-    GI::localize_file("$gdbfile.index");
>+    if( -f "$gdbfile.index.dir" ){
>+	GI::localize_file("$gdbfile.index.dir");
>+	GI::localize_file("$gdbfile.index.pag");
>+    }else{
>+    	GI::localize_file("$gdbfile.index");
>+    }
>     carp "Calling GI::localize_file" if($main::debug);
>     $gdbfile = GI::localize_file($gdbfile);
> }
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Thu May 31 07:17:20 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 31 May 2012 09:17:20 -0400
Subject: [maker-devel] maker leaving large numbers of defunct zombies
In-Reply-To: <FBA1F582-5EF0-4D7A-8276-A86DAD5C4C89@slu.se>
Message-ID: <CBECE4F4.D210%carsonhh@gmail.com>

MAKER uses IPC::Open3 to open almost all external applications, including
a helper script called every once in a while that helps check file locks
on NFS.

MAKER then calls waitpid to reap the processes, as IPC::Open3 doesn't
auto-reap.  The only time previously I've seen issues with zombie
accumulation was with MPICH2 when it moved from the MPD process manager to
Hydra.  Hydra had certain broken signal handling issues that I had to bug
the MPICH2 developers about and they fixed it.  It is possible that the
issue you are having may be with OpenMPI or with perl 5.16.  I currently
use perl 5.12.  Perl instituted something called safe signals in either
5.6 or 5.8 and there may be some updates in 5.16 where they've been
changing those around again.

I can try installing a copy of 5.16 to test with and OpenMPI to see if I
can replicate the error.

Thanks,
Carson



On 12-05-31 8:25 AM, "Mikael Brandstr?m Durling" <mikael.durling at slu.se>
wrote:

>Hello,
>
>I've been working lately to set up maker for annotation work on a few
>fungal genomes. I've got mpi maker up and running now, however, I notice
>that maker is leaving a lot of <defunct> perl processes behind. This
>happens to the extent that the process table on the system gets filled up
>after a few hours run time. Right now the process tree after three hours
>running looks like this:
>
>    |-sge_execd-+-sge_shepherd---bash---mpirun-+-maker-+-maker
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1371*[perl]
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1348*[perl]
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1384*[perl]
>     |           |                              |       `-perl
>
>...and so on for all mpi processes, except for the controlling processes.
>
>What perl programs is maker calling, that might end up as zombies? I've
>had a brief look at the source to no avail, but would be happy to dig
>further with some pointers for where to look.
>
>This is run with the 2.25-beta from the web page, perl 5.16.0 and openmpi
>1.4.5. 
>
>Thanks,
>Mikael
>
>
>
>
>
>
>
>
>
>
>-------------------------------------
>Mikael Brandstr?m Durling, PhD
>Assistant Professor
>
>Sveriges lantbruksuniversitet
>Swedish University of Agricultural Sciences
>
>Uppsala BioCenter
>Dept of Forest Mycology and Plant Pathology
>Box 7026, 75007 Uppsala
>Visiting address: Almas All? 5
>Telefon: 018-671512
>mikael.durling at slu.se, www.slu.se/mykopat
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From mikael.durling at slu.se  Thu May 31 07:57:06 2012
From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=)
Date: Thu, 31 May 2012 15:57:06 +0200
Subject: [maker-devel] maker leaving large numbers of defunct zombies
In-Reply-To: <CBECE4F4.D210%carsonhh@gmail.com>
References: <CBECE4F4.D210%carsonhh@gmail.com>
Message-ID: <E779EAA8-C2AC-4362-A3C7-E370777E3D5D@slu.se>

I saw the same problem with the latest MPICH2 using hydra too, so it might boil down to perl/openmpi interactions. I didn't see this problem with the debian supplied perl 5.10, but then I had intermittent segfaults with in DB_File and libpthread. Seemed to be some interaction with the LD_PRELOADed libmpi. That requirement for preloading libmpi was easiest solved by compiling openmpi with --disable-dlopen.

Thanks,
Mikael

31 maj 2012 kl. 15:17 skrev Carson Holt:

> MAKER uses IPC::Open3 to open almost all external applications, including
> a helper script called every once in a while that helps check file locks
> on NFS.
> 
> MAKER then calls waitpid to reap the processes, as IPC::Open3 doesn't
> auto-reap.  The only time previously I've seen issues with zombie
> accumulation was with MPICH2 when it moved from the MPD process manager to
> Hydra.  Hydra had certain broken signal handling issues that I had to bug
> the MPICH2 developers about and they fixed it.  It is possible that the
> issue you are having may be with OpenMPI or with perl 5.16.  I currently
> use perl 5.12.  Perl instituted something called safe signals in either
> 5.6 or 5.8 and there may be some updates in 5.16 where they've been
> changing those around again.
> 
> I can try installing a copy of 5.16 to test with and OpenMPI to see if I
> can replicate the error.
> 
> Thanks,
> Carson
> 
> 
> 
> On 12-05-31 8:25 AM, "Mikael Brandstr?m Durling" <mikael.durling at slu.se>
> wrote:
> 
>> Hello,
>> 
>> I've been working lately to set up maker for annotation work on a few
>> fungal genomes. I've got mpi maker up and running now, however, I notice
>> that maker is leaving a lot of <defunct> perl processes behind. This
>> happens to the extent that the process table on the system gets filled up
>> after a few hours run time. Right now the process tree after three hours
>> running looks like this:
>> 
>>   |-sge_execd-+-sge_shepherd---bash---mpirun-+-maker-+-maker
>>    |           |                              |       `-perl
>>    |           |                              |-maker-+-maker
>>    |           |                              |
>> |-maker---1371*[perl]
>>    |           |                              |       `-perl
>>    |           |                              |-maker-+-maker
>>    |           |                              |
>> |-maker---1348*[perl]
>>    |           |                              |       `-perl
>>    |           |                              |-maker-+-maker
>>    |           |                              |
>> |-maker---1384*[perl]
>>    |           |                              |       `-perl
>> 
>> ...and so on for all mpi processes, except for the controlling processes.
>> 
>> What perl programs is maker calling, that might end up as zombies? I've
>> had a brief look at the source to no avail, but would be happy to dig
>> further with some pointers for where to look.
>> 
>> This is run with the 2.25-beta from the web page, perl 5.16.0 and openmpi
>> 1.4.5. 
>> 
>> Thanks,
>> Mikael
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> -------------------------------------
>> Mikael Brandstr?m Durling, PhD
>> Assistant Professor
>> 
>> Sveriges lantbruksuniversitet
>> Swedish University of Agricultural Sciences
>> 
>> Uppsala BioCenter
>> Dept of Forest Mycology and Plant Pathology
>> Box 7026, 75007 Uppsala
>> Visiting address: Almas All? 5
>> Telefon: 018-671512
>> mikael.durling at slu.se, www.slu.se/mykopat
>> 
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 




From carsonhh at gmail.com  Tue May  1 16:07:47 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 01 May 2012 18:07:47 -0400
Subject: [maker-devel] gff3_preds2models usage question
In-Reply-To: <CANRPJSdHUx_BmAzb+OBLFab02dDtugM9Jf3zsXqjThrKauX29g@mail.gmail.com>
Message-ID: <CBC5D543.C151%carsonhh@gmail.com>

Sorry for the slow response.  The gff3_preds2models script has been
deprecated for some time now (isn't even in the release code anymore), and
the old one won't work with the new library.

I've attached a made from scratch drop-in replacement that you can use to do
what the old script would have done.  In the current release of MAKER,
instead of the gff3_preds2models script users can just give MAKER  a set of
predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then
leave all other options blank).  The predictions given will the be converted
into gene models.

Thanks,
Carson



From:  Walter Eckalbar <weckalba at asu.edu>
Date:  Tuesday, 3 April, 2012 7:28 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] gff3_preds2models usage question

Hello maker developers and users,

I am attempting to use the gff3_preds2models scripts, but running into a few
issues.

Initially, I hit errors that seemed to be fixed by installing CGI and its
dependancies.  However, that during that installation a few tests did fail.
I can provide error logs if that would be helpful, however, I went on to
install and attempt gff3_preds2models anyway.

What I am currently doing is running gff3_merge first, to gather the maker
outputs.  I am doing so with both the -n option on and off.  When providing
the gff3 file with the sequence I get the following error from
gff3_preds2models:

Undefined subroutine &maker::auto_annotator::annotate called at
/Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97,
<GEN16> line 992291.

This seemed to be the same error as that of what someone else saw on these
boards, but I did not see a later email resolving the issue.

I also tried giving it just the gff3 without the sequences at the bottom of
the file and then I get this error:

ERROR: There was a problem in the writing the fasta entry
Either no sequence was given, or there was an error in writing

This leads me to believe I should be using the one with the sequence, but I
am not certain of that.

I see it might be possible to go from maker outputs to chado database then
to gene->mRNA->exon gff3s, but I have not set up my machine for XML or chado
yet, and it does not appear trivial.

Thanks for the help,

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

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From weckalba at asu.edu  Tue May  1 19:33:00 2012
From: weckalba at asu.edu (Walter Eckalbar)
Date: Tue, 1 May 2012 18:33:00 -0700
Subject: [maker-devel] gff3_preds2models usage question
In-Reply-To: <CBC5D543.C151%carsonhh@gmail.com>
References: <CANRPJSdHUx_BmAzb+OBLFab02dDtugM9Jf3zsXqjThrKauX29g@mail.gmail.com>
	<CBC5D543.C151%carsonhh@gmail.com>
Message-ID: <CANRPJSc-EN9jgqW3dJRJmLJ_4SyhavqsOCH+h-031PPtiBHONA@mail.gmail.com>

Hi Carson,

Thanks for the response, even a late one, and thanks for the script.  I'll
certainly be giving that a try.

Walter

On 1 May 2012 15:07, Carson Holt <carsonhh at gmail.com> wrote:

> Sorry for the slow response.  The gff3_preds2models script has been
> deprecated for some time now (isn't even in the release code anymore), and
> the old one won't work with the new library.
>
> I've attached a made from scratch drop-in replacement that you can use to
> do what the old script would have done.  In the current release of MAKER,
> instead of the gff3_preds2models script users can just give MAKER  a set of
> predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then
> leave all other options blank).  The predictions given will the be
> converted into gene models.
>
> Thanks,
> Carson
>
>
>
> From: Walter Eckalbar <weckalba at asu.edu>
> Date: Tuesday, 3 April, 2012 7:28 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] gff3_preds2models usage question
>
> Hello maker developers and users,
>
> I am attempting to use the gff3_preds2models scripts, but running into a
> few issues.
>
> Initially, I hit errors that seemed to be fixed by installing CGI and its
> dependancies.  However, that during that installation a few tests did fail.
>  I can provide error logs if that would be helpful, however, I went on to
> install and attempt gff3_preds2models anyway.
>
> What I am currently doing is running gff3_merge first, to gather the maker
> outputs.  I am doing so with both the -n option on and off.  When providing
> the gff3 file with the sequence I get the following error from
> gff3_preds2models:
>
> Undefined subroutine &maker::auto_annotator::annotate called at
> /Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97,
> <GEN16> line 992291.
>
> This seemed to be the same error as that of what someone else saw on these
> boards, but I did not see a later email resolving the issue.
>
> I also tried giving it just the gff3 without the sequences at the bottom
> of the file and then I get this error:
>
> ERROR: There was a problem in the writing the fasta entry
> Either no sequence was given, or there was an error in writing
>
> This leads me to believe I should be using the one with the sequence, but
> I am not certain of that.
>
> I see it might be possible to go from maker outputs to chado database then
> to gene->mRNA->exon gff3s, but I have not set up my machine for XML or
> chado yet, and it does not appear trivial.
>
> Thanks for the help,
>
> Walter
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From qwang at uwyo.edu  Thu May  3 10:23:16 2012
From: qwang at uwyo.edu (Qiurong Wang)
Date: Thu, 3 May 2012 10:23:16 -0600
Subject: [maker-devel] MAKER download problem
Message-ID: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>

Hi,

I was trying to download MAKER, but I couldn't open the download page.  
Could you please help me to figure out the problem? Thanks a lot!


Qiurong Wang
PhD candidate
Department of Botany
University of Wyoming
Department 3165, 1000 E University Ave. Laramie, Wyoming 82071, USA
Phone: 307-766-2634
Email: qwang at uwyo.edu




From barry.moore at genetics.utah.edu  Thu May  3 11:51:48 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Thu, 3 May 2012 11:51:48 -0600
Subject: [maker-devel] MAKER download problem
In-Reply-To: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>
References: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>
Message-ID: <6B24C00B-6C70-4A40-BA7C-E3AC0C7F5E25@genetics.utah.edu>

Hi all,

The web server hosting the MAKER licensing application and MAKER code distribution was attacked this week.  The University of Utah is currently blocking access to that server from outside University IP space.  We are working hard to move all of the content and web-applications from that machine to a new server and I expect to have the MAKER services restored over the weekend.  This is affecting the ability to submit new licenses for MAKER and to download the MAKER code.  In addition those with existing licenses will need to update their code links for future code updates.  For those of you on campus in Utah or with campus VPN access, the server is running and available.  Updates on the status of the server and details about new links to the MAKER code will be posted to the mailing list soon.

Barry

On May 3, 2012, at 10:23 AM, Qiurong Wang wrote:

> Hi,
> 
> I was trying to download MAKER, but I couldn't open the download page. Could you please help me to figure out the problem? Thanks a lot!
> 
> 
> Qiurong Wang
> PhD candidate
> Department of Botany
> University of Wyoming
> Department 3165, 1000 E University Ave. Laramie, Wyoming 82071, USA
> Phone: 307-766-2634
> Email: qwang at uwyo.edu
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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




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From carsonhh at gmail.com  Thu May  3 12:00:01 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 03 May 2012 14:00:01 -0400
Subject: [maker-devel] MAKER download problem
In-Reply-To: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>
Message-ID: <CBC83F6D.C3B0%carsonhh@gmail.com>

The server hosting the file to download is down temporarily.  I'll put a
copy of MAKER on a separate server and e-mail the link to you.

--Carson



On 12-05-03 12:23 PM, "Qiurong Wang" <qwang at uwyo.edu> wrote:

>Hi,
>
>I was trying to download MAKER, but I couldn't open the download page.
>Could you please help me to figure out the problem? Thanks a lot!
>
>
>Qiurong Wang
>PhD candidate
>Department of Botany
>University of Wyoming
>Department 3165, 1000 E University Ave. Laramie, Wyoming 82071, USA
>Phone: 307-766-2634
>Email: qwang at uwyo.edu
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From cjfields at illinois.edu  Tue May 15 09:01:31 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 15 May 2012 15:01:31 +0000
Subject: [maker-devel] mail list and Trac
Message-ID: <64A6759A-9FD1-4AEE-BCEA-151B0D791ADD@illinois.edu>

Just wanted to point out, I noticed the mail list is not being indexed on Google Groups any more (nothing in May).  Also, any status on Trac?

chris


From barry.moore at genetics.utah.edu  Tue May 15 10:34:29 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 15 May 2012 10:34:29 -0600
Subject: [maker-devel] mail list and Trac
In-Reply-To: <64A6759A-9FD1-4AEE-BCEA-151B0D791ADD@illinois.edu>
References: <64A6759A-9FD1-4AEE-BCEA-151B0D791ADD@illinois.edu>
Message-ID: <C2170DBB-75CB-423D-82E3-C56572B57753@genetics.utah.edu>

Thanks Chris,  I'll check on the Google groups.  The MAKER Trac server was on a server that we had to shut down a couple weeks ago and I had made moving it a lower priority since I didn't think it was getting much use.  I'll get it moved over and bump up the priority on that move since I know someone is looking at it.

B

On May 15, 2012, at 9:01 AM, Fields, Christopher J wrote:

> Just wanted to point out, I noticed the mail list is not being indexed on Google Groups any more (nothing in May).  Also, any status on Trac?
> 
> chris
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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




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From anastasia.gioti at scilifelab.se  Thu May 17 05:27:04 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Thu, 17 May 2012 13:27:04 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
	<03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <4D9922AF-A917-4747-9B7C-CFE9F142D51C@scilifelab.se>

Hi Barry,
Thanks for your detailed instructions. You well understood that I have  
already included the proteins of the closely related species in my  
protein evidence dataset, but still did not get the genes. I have now  
blasted (P) the missing 949 proteins from this species against my  
nonoverlaping_abinits.fasta proteins and have found 618 good hits,  
which i guess I can promote to models using the routine no 2 of your  
last email and Carson's script gff3_select.
I have also looked at the rest of the proteins (331) for which there  
was no model in the nonoverlaping_abinits.fasta. I will try to  
describe 2 examples I looked at in apollo:

1) ab initio models predicted a ~7.5 kb gene covering 3 genes (as  
predicted in the closely related species). Blastx+protein2genome  
similarities were reported for two of these genes, but not for the 3rd  
(the one in the middle). MAKER finally decided to call two genes,  
respecting the blastx+protein2genome evidence, but the 3rd was lost.
I have previously  reported here that MAKER tends to  fuse genes in  
multi-exonic genes and others reported that too, I remember you  
proposed changing a papameter to alter this. To keep in mind for my  
final strategy that i am trying to decide on (for the moment i have  
not rerun MAKER).
For this case, abinitio models do not exist for the gene (in the sense  
that the existing models overlap many genes) and the similarity to the  
protein of the closely related species was not judged sufficient,  
although when i look at a TblastN alignment for this area it looks  
fine to me.

2) Only the 3' end of the gene was called by MAKER, despite blastx  
+protein2genome evidence from the closely related species for the  
entire region. Abinitio models existed as 2 separate genes , one for  
the 3' end region (finally retained by MAKER in a consensus decision I  
guess) and one for the 5' region, but here not all predictors called  
an orf, and finally nothing was called in this region.
In this case, it is a misannotation rather, but which misses a very  
important part of the gene.
I hope my descriptions are clear, otherwise I can provide you the gff  
file of these 2 examples to look by yourself.

I am not very clear about what to do about these 331 cases (which I do  
not know how to look at as well, except for random examples' viwing in  
Apollo). I feel that a second MAKER run would be probably the  
solution, this time providing as pred_gff  the result of a blast  
against the 331. But still, the existing annotations would then have  
to be somehow updated as the new predictions are in conflict with them  
(see example 2). I am a bit confused.
to recap, what would you suggest for the 331 still-missing proteins in  
terms of asessing their profiles n a rather automatic way and in  
inluding them in my annotations without going deep into manual gene  
curation?
Many thnks,
Anastasia
>
> Let me just restate what you've said so that I can be sure that I am  
> correct about what you've already done.  You have run Maker with  
> SNAP, Genemark and Augustus using EST from a closely related species  
> (passed to altest) and protein evidence from other fungi.  You are  
> missing about 1,000 genes compared to the species that provided the  
> EST alignments.  You say their is good evidence that these genes  
> exist from the alignments and I assume by this that you mean the EST/ 
> protein alignments that Maker produced.
>
> 1) Is the closely related fungus annotated and if so have you  
> included it's proteins in the evidence set that you provided to  
> Maker.  If you haven't provided these proteins as evidence to maker  
> then you should do this.  You can re-run maker passing your original  
> models back through like this:
>
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=1
> other_pass=1
>
> #-----Protein Homology Evidence (for best results provide a file for  
> at least one)
> protein=proteins_from_closely_related.fasta
> ## OR it sounds like you've already aligned these with exonerate?
> protein_gff=proteins_from_closely_related_already_aligned.gff
>
> 2) If you've already included those closely related species proteins  
> but still didn't get the 1,000 genes, then take your  
> nonoverlaping_abinits.fasta and blast them directly against your  
> closely related proteins.  Presumably they don't hit too well  
> because if they did they should have been promoted to predictions by  
> Maker the first time, but here you can decide yourself what  
> thresholds to allow to keep the abinit predictions that hit the  
> closely related species proteins.  If you filter you blast hits the  
> way you want and keep the names of the abinit predictions that pass  
> your filter, then use the script Carson attached it it will generate  
> a abinit precidtion GFF file with only the predictions you  
> selected.  You can then pass those predictions back to Maker and  
> force it to keep them and Maker will turn them from predictions  
> (match/match_part) into gene models.
>
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=0
> other_pass=1
>
> #-----Gene Prediction
> snaphmm=
> gmhmm=
> augustus_species=
> fgenesh_par_file=
> pred_gff=ab_init_predictions_rescued_by_blast.gff
>
> keep_preds=1
>
> Barry
>
>>> Thanks,
>>> Carson
>>>
>>> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
>>> Date: Wed, 25 Apr 2012 11:09:36 +0200
>>> To: <maker-devel at yandell-lab.org>
>>> Subject: [maker-devel] Use pass-through system to add missing genes
>>>
>>> Hi,
>>> I  have a set of predicted proteins from the genome of a fungus  
>>> annotated by MAKER  using EST data from a closely related species  
>>> and 3 ab initio predictors  (snap iterativelly trained 3 times,  
>>> genemark trained directly on the assembly and augustus with a  
>>> model from a less closely related species), along with a set of  
>>> fungal proteins. I am missing ~ 1000 proteins when I compare to  
>>> the species i used EST data from, and there is good evidence from  
>>> alignments that these genes exist. The question is how to proceed  
>>> from Blast hits to actual gene models here. The idea would be to  
>>> add these genes to the existing dataset, rather than reannotate  
>>> the genome. I believe that reannotating it without any further  
>>> evidence such as RNA-seq from the species itself would not change  
>>> much,and i d rather stick with actual predictions that i trust and  
>>> have used in subsequent analyses. The 1000 genes I can accept to  
>>> annotate with a less stringent and reliable way than MAKER, I just  
>>> want to add them so that the difference in gene count gets  
>>> corrected.
>>> I was reading the MAKER 2 paper and i was wondering if I can use  
>>> the legacy annotations scheme to do it, by providing GFF3 of the  
>>> alignments between the two species in the regions where genes were  
>>> missed, but as i said, I would not like to reannotate the whole  
>>> genome, and running MAKER2 might cause slight changes that i d  
>>> like to avoid. Is this possible? First, is it possible to provide  
>>> a Gff3 file of specific locations and not the entire genome  
>>> alignment? (I guess so..) Second, how can I tag the existing  
>>> annotations as 'not to be changed' or alternatively, tag the new  
>>> models only? How should I run maker2, with which predictors on and  
>>> which off?
>>> Thanks,
>>> Anastasia
>>>
>>> Anastasia Gioti
>>> Post-doctoral Researcher
>>>
>>> anastasia.gioti at scilifelab.se
>>> anastasia.gioti at ebc.uu.se
>>>
>>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>>>
>>>
>>>
>>> _______________________________________________ maker-devel  
>>> mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> <gff3_select>
>>
>> Anastasia Gioti
>> Post-doctoral Researcher
>>
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/ 
>> Gioti_Anastasia/
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell- 
> lab.org

Anastasia (Natassa) Gioti
Post-Doc Researcher
Evolutionary Biology Department Uppsala University -Science for Life  
lab, Karolinska Institute Stockholm
anastasia.gioti at ebc.uu.se
anastasia.gioti at scilifelab.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/










From yogeshp08 at gmail.com  Tue May 15 10:07:57 2012
From: yogeshp08 at gmail.com (Yogesh)
Date: Tue, 15 May 2012 11:07:57 -0500
Subject: [maker-devel] tblastn Cleanup?
Message-ID: <4478F0B20ED84A85B3C4FE4154F8FAD1@gmail.com>

Hello,

I have a few tblastn alignments with a lot of low quality hits. I have to clean that up. Can you please suggest how Maker pipeline does it? Also can I run it directly on my data without having to go through the whole pipeline?

Thanks,

-Yogesh
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From carsonhh at gmail.com  Fri May 18 08:22:50 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 18 May 2012 10:22:50 -0400
Subject: [maker-devel] tblastn Cleanup?
In-Reply-To: <4478F0B20ED84A85B3C4FE4154F8FAD1@gmail.com>
Message-ID: <CBDBD0A5.C8CD%carsonhh@gmail.com>

There are several things.  I set several filtering options directly on the
BLAST command line.  These are things like maximum intron length, an e-value
filter, and simple repeat filtering (called dust filter in NCBI blast and
seg filter in WUBLAST).

I also run repeat masker over the genome first.  This allows simple and
complex repeats to be removed before running BLAST (otherwise you get many
false alignments).

Last I filter the results based on percent coverage of the hit to the
original database sequence and percent identity.  I think you can set
percent identity as a flag in BLAST, but the percent coverage filter is
being calculated by MAKER, so to do this outside of MAKER would require that
you write your own filtering script to compare the length of the alignment
to the length of the sequence in the database.

I also have an HSP depth overlap filter.  This removes weird low complexity
hits that escape repeatmasking.  They show up as multiple HSPs overlapping
multiple times in the same region (usually very high numbers like 90 HSPs
all 100 bp long in the same region).  I calculate the number of base pairs
in the alignment on the hit then divide by the number of base pairs in the
query alignment.  If it's greater than 3, I throw the hit out.

Thanks,
Carson



From:  Yogesh <yogeshp08 at gmail.com>
Date:  Tuesday, 15 May, 2012 12:07 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] tblastn Cleanup?

 
Hello,

I have a few tblastn alignments with a lot of low quality hits. I have to
clean that up. Can you please suggest how Maker pipeline does it? Also can I
run it directly on my data without having to go through the whole pipeline?

Thanks,

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

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From smg283 at gmail.com  Tue May 22 00:42:51 2012
From: smg283 at gmail.com (Scott Geib)
Date: Mon, 21 May 2012 20:42:51 -1000
Subject: [maker-devel] can't call method strand on an undefined value ERROR:
 Failed while flattening protein clusters
Message-ID: <CAH221bv8rM7w+yOg6AgW9Y9tLHLvivWgGjZFs4e4QLAyuW4pGA@mail.gmail.com>

Hi,
Using maker 2.24, I am getting the following error (see below) in
protein2genome widget.  I also get the same error with est2genome.  This
happens with my own data (testing on a single scaffold), but not with the
test data supplied with maker (dpp files in data folder).
Scott


Widget::exonerate::protein2genome:
/data0/opt/AlignmentSoftware/exonerate/exonerate-2.2.0-x86_64/bin/exonerate
-q
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/UniRef90_UPI000194D3FC.for.1588546-1589203.9.fasta
-t
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.1588546-1589203.9.fasta
-Q protein -T dna -m protein2genome --softmasktarget  --percent 20
--showcigar  >
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.1588546-1589203.UniRef90_UPI000194D3FC.p_exonerate.9
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 23
 ...processing 1 of 23
 ...processing 2 of 23
 ...processing 3 of 23
 ...processing 4 of 23
 ...processing 5 of 23
 ...processing 6 of 23
 ...processing 7 of 23
 ...processing 8 of 23
 ...processing 9 of 23
 ...processing 10 of 23
 ...processing 11 of 23
 ...processing 12 of 23
 ...processing 13 of 23
 ...processing 14 of 23
 ...processing 15 of 23
 ...processing 16 of 23
 ...processing 17 of 23
 ...processing 18 of 23
 ...processing 19 of 23
 ...processing 20 of 23
 ...processing 21 of 23
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 20
 ...processing 1 of 20
 ...processing 2 of 20
 ...processing 3 of 20
 ...processing 4 of 20
 ...processing 5 of 20
 ...processing 6 of 20
 ...processing 7 of 20
 ...processing 8 of 20
 ...processing 9 of 20
 ...processing 10 of 20
 ...processing 11 of 20
 ...processing 12 of 20
 ...processing 13 of 20
 ...processing 14 of 20
 ...processing 15 of 20
 ...processing 16 of 20
 ...processing 17 of 20
 ...processing 18 of 20
total clusters:2 now processing 0
Can't call method "strand" on an undefined valueERROR: Failed while
flattening protein clusters
ERROR: Chunk failed at level:11, tier_type:2
FAILED CONTIG:scaffold00001
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From anastasia.gioti at scilifelab.se  Tue May 22 07:14:17 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Tue, 22 May 2012 15:14:17 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
	<03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <19E36E3B-6A82-49D5-B0AC-5E521F3E8999@scilifelab.se>

Hi again,
I hav sent an email a few days ago about this thread, and i am not  
sure if you have received it or you still did not have time to look at  
it. In any case, this email was dealing with the fact that some  
proteins were not retrieved in the abinitio models and how to deal  
with it. What I would like to ask here is a few confirmations on how  
to rerun maker for the proteins that were retrieved in the abinitio  
models. i have looked at the Blast results, and have done a series of  
check-ups, so now I am ready to run MAKER again with a list of models  
that I want to retain.
Regarding the following parameters:

1. Do I  set the genome= to nothing here? i.e quote it out? This is in  
the beginning of the control file
#-----Genome (Required for De-Novo Annotation)
genome=#genome sequence file in fasta format
organism_type= #eukaryotic or prokaryotic. Default is eukaryotic

>
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=0
> other_pass=1
>
> #-----Gene Prediction
2. Do i provide again the snap etc models? I am not sure, because i  
thought MAKER would not run ab initio predictors this time (this is  
why I would also quote out the genome file above, as this is not a de  
novo annotation). but if it will, i will then provide the previous  
models i used, except for snap, for which I will generate a new model   
from the gff3 file of the last run (according to snap documentation).  
Am i correct?
> snaphmm=
> gmhmm=
> augustus_species=
> fgenesh_par_file=
> pred_gff=ab_init_predictions_rescued_by_blast.gff
>
> keep_preds=1

Samely, what do i do with repeatmasking etc?
Thanks in adavance,
Anastasia

>
> Barry
>
>>> Thanks,
>>> Carson
>>>
>>> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
>>> Date: Wed, 25 Apr 2012 11:09:36 +0200
>>> To: <maker-devel at yandell-lab.org>
>>> Subject: [maker-devel] Use pass-through system to add missing genes
>>>
>>> Hi,
>>> I  have a set of predicted proteins from the genome of a fungus  
>>> annotated by MAKER  using EST data from a closely related species  
>>> and 3 ab initio predictors  (snap iterativelly trained 3 times,  
>>> genemark trained directly on the assembly and augustus with a  
>>> model from a less closely related species), along with a set of  
>>> fungal proteins. I am missing ~ 1000 proteins when I compare to  
>>> the species i used EST data from, and there is good evidence from  
>>> alignments that these genes exist. The question is how to proceed  
>>> from Blast hits to actual gene models here. The idea would be to  
>>> add these genes to the existing dataset, rather than reannotate  
>>> the genome. I believe that reannotating it without any further  
>>> evidence such as RNA-seq from the species itself would not change  
>>> much,and i d rather stick with actual predictions that i trust and  
>>> have used in subsequent analyses. The 1000 genes I can accept to  
>>> annotate with a less stringent and reliable way than MAKER, I just  
>>> want to add them so that the difference in gene count gets  
>>> corrected.
>>> I was reading the MAKER 2 paper and i was wondering if I can use  
>>> the legacy annotations scheme to do it, by providing GFF3 of the  
>>> alignments between the two species in the regions where genes were  
>>> missed, but as i said, I would not like to reannotate the whole  
>>> genome, and running MAKER2 might cause slight changes that i d  
>>> like to avoid. Is this possible? First, is it possible to provide  
>>> a Gff3 file of specific locations and not the entire genome  
>>> alignment? (I guess so..) Second, how can I tag the existing  
>>> annotations as 'not to be changed' or alternatively, tag the new  
>>> models only? How should I run maker2, with which predictors on and  
>>> which off?
>>> Thanks,
>>> Anastasia
>>>
>>> Anastasia Gioti
>>> Post-doctoral Researcher
>>>
>>> anastasia.gioti at scilifelab.se
>>> anastasia.gioti at ebc.uu.se
>>>
>>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>>>
>>>
>>>
>>> _______________________________________________ maker-devel  
>>> mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> <gff3_select>
>>
>> Anastasia Gioti
>> Post-doctoral Researcher
>>
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/ 
>> Gioti_Anastasia/
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell- 
> lab.org

Anastasia (Natassa) Gioti
Post-Doc Researcher
Evolutionary Biology Department Uppsala University -Science for Life  
lab, Karolinska Institute Stockholm
anastasia.gioti at ebc.uu.se
anastasia.gioti at scilifelab.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/










From anastasia.gioti at scilifelab.se  Wed May 23 03:07:12 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Wed, 23 May 2012 11:07:12 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
	<03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <1B0770A0-6D14-4336-BC3A-DC24619BC3FE@scilifelab.se>

Hi 
and sorry for the multiple postings. I have a list of models rescued by the nonoverlaping_abinits.fasta  fles (against which i  blasted my missing proteins from the closely related species and further filtered out the dubious hits) and a maker gff3 file, but Carson's script gff3_select won't work, and the reason is that these abinitio models were not promoted into the maker gff3 file, thus they are not there. I refer to the gff3 file generated by gff3_merge script. Am i missing something?
Thank you, 
Anastasia



> 
>>> If you know which ab initio predictions you want to add (I.e. the ab initio promoting scenario I descibed), you can provide those predictions to the use the pred_gff option and then set keep_preds=1 and they will be maintained even without evidence.  Attached is a script that would make selecting those easier.  It take the MAKER generated GFF3 and a list of predictions to keep (one name per line).  These might be the results of a BLAST analysis for example.  It will then return the GFF3 entries for just those models selected.

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From thomas.hackl at uni-wuerzburg.de  Wed May 23 06:01:55 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Wed, 23 May 2012 14:01:55 +0200
Subject: [maker-devel] missing est2genome annotation
Message-ID: <4FBCD1B3.8000102@uni-wuerzburg.de>

Hi,

I used maker to annotate genomic contigs and among other stuff provided 
transcripts from the transcriptome as est evidence. Blast and exonerate 
work fine and produce valid alignments, the alignment files exist in 
theVoid and look very good. Unfortunatly neither the evidence_0.gff nor 
the final .gff carry the corresponding feature annotations.

Any ideas why?

Regards
Thomas

-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From thomas.hackl at uni-wuerzburg.de  Wed May 23 11:14:27 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Wed, 23 May 2012 19:14:27 +0200
Subject: [maker-devel] missing est2genome annotation
In-Reply-To: <4FBCD1B3.8000102@uni-wuerzburg.de>
References: <4FBCD1B3.8000102@uni-wuerzburg.de>
Message-ID: <4FBD1AF3.8020904@uni-wuerzburg.de>

Hi again,

I did some source code digging and caught the following line burying my 
exonerate alignments. I suspect it does so for a very good reason, 
therefore it would help me a lot if someone could explain to me, what is 
going on there.


/lib/GI.pm  l.1473
next if $e->pAh<  $pcov;


Regards
Thomas


Am 23.05.2012 14:01, schrieb Thomas Hackl:
> Hi,
>
> I used maker to annotate genomic contigs and among other stuff 
> provided transcripts from the transcriptome as est evidence. Blast and 
> exonerate work fine and produce valid alignments, the alignment files 
> exist in theVoid and look very good. Unfortunatly neither the 
> evidence_0.gff nor the final .gff carry the corresponding feature 
> annotations.
>
> Any ideas why?
>
> Regards
> Thomas
>


-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 13:30:09 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 12:30:09 -0700
Subject: [maker-devel] Merging gene predictions....
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>

Hi Carson and others,
I am wondering if I can use Maker to merge gene predictions from three gff files. One of the algorithm is 'augustus' which of course i can use it inside Maker. Other two are not part of Maker.

But, in case if I want to pass only the GFFs to Maker and ask it to merge the annotations (when overlap) and pick only annotation that are predicted in 2 out of 3 gffs. Is it possible? I prefer this approach, as we need to run a blast based validation step on predicted features before even try to merge them. Thats another reason why we dont prefer to use the augustus inside maker. 

Thanks,
Gowthaman


From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 15:02:55 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 14:02:55 -0700
Subject: [maker-devel] Merging gene predictions....
In-Reply-To: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>
References: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D8@mail02.sbri.org>

Can i use the following approach Carson?

This is your reply to one of the earlier question:

I've attached a made from scratch drop-in replacement that you can use to do what the old script would have done.  In the current release of MAKER, instead of the gff3_preds2models script users can just give MAKER  a set of predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then leave all other options blank).  The predictions given will the be converted into gene models.

Thanks,
Carson



________________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] On Behalf Of Gowthaman Ramasamy [gowthaman.ramasamy at seattlebiomed.org]
Sent: Thursday, May 24, 2012 12:30 PM
To: Carson Holt; maker-devel at yandell-lab.org
Subject: [maker-devel] Merging gene predictions....

Hi Carson and others,
I am wondering if I can use Maker to merge gene predictions from three gff files. One of the algorithm is 'augustus' which of course i can use it inside Maker. Other two are not part of Maker.

But, in case if I want to pass only the GFFs to Maker and ask it to merge the annotations (when overlap) and pick only annotation that are predicted in 2 out of 3 gffs. Is it possible? I prefer this approach, as we need to run a blast based validation step on predicted features before even try to merge them. Thats another reason why we dont prefer to use the augustus inside maker.

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



From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 15:21:30 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 14:21:30 -0700
Subject: [maker-devel] Merging gene predictions....
In-Reply-To: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D8@mail02.sbri.org>
References: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>,
	<89080953C3D300419AACB6E63A7EEFBA5C8409F8D8@mail02.sbri.org>
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8DA@mail02.sbri.org>

Hi,
I am trying to install MAKER in centOS. I was able to install all the perl deps. and external programs. Perl Build.pl and ./Build Install went with out errors/warnings. I did not enable MPI though.

But, when i start Maker it returs "segmentation fault". 

I have no clue whats going wrong....or where to check for error logs? 

Any help would be appreciated,
Thanks,
gowthaman
_________


From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 15:22:16 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 14:22:16 -0700
Subject: [maker-devel] MAKER installation problem
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8DB@mail02.sbri.org>

Hi,
I am trying to install MAKER in centOS. I was able to install all the perl deps. and external programs. Perl Build.pl and ./Build Install went with out errors/warnings. I did not enable MPI though.

But, when i start Maker it returs "segmentation fault". 

I have no clue whats going wrong....or where to check for error logs? 

Any help would be appreciated,
Thanks,
gowthaman
_________
________________________________________



From bob_freeman at hms.harvard.edu  Fri May 25 10:23:22 2012
From: bob_freeman at hms.harvard.edu (Bob Freeman)
Date: Fri, 25 May 2012 12:23:22 -0400
Subject: [maker-devel] Alternate translation table?
Message-ID: <454CA235-0DB6-451F-97C4-83D32E2E805A@hms.harvard.edu>

Hello all!

Unusual question here: I am running MAKER on a ciliate that uses a non-standard translation table for its translation products. I haven't found an option in the control files that I can change for the for translation of the predicted transcripts. How or where can I go about this?

Tx,
Bob

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
	-- Karen Walker, from Will and Grace





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From carsonhh at gmail.com  Mon May 28 06:43:34 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 08:43:34 -0400
Subject: [maker-devel] Alternate translation table?
In-Reply-To: <454CA235-0DB6-451F-97C4-83D32E2E805A@hms.harvard.edu>
Message-ID: <CBE8E7EF.CAF3%carsonhh@gmail.com>

The alternate translation table is not currently an option.  It's one of
those things that needs to be implemented, but has not been yet.  It's also
not supported by many of the eukaryotic gene predictors MAKER uses.

I could probably get something implemented for you to test in two to three
weeks though (there are a lot of places where the translation table comes
into play).  Let me know.

--Carson



From:  Bob Freeman <bob_freeman at hms.harvard.edu>
Date:  Friday, 25 May, 2012 12:23 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Alternate translation table?

Hello all!

Unusual question here: I am running MAKER on a ciliate that uses a
non-standard translation table for its translation products. I haven't found
an option in the control files that I can change for the for translation of
the predicted transcripts. How or where can I go about this?

Tx,
Bob

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
-- Karen Walker, from Will and Grace





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

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From carsonhh at gmail.com  Mon May 28 07:38:25 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 09:38:25 -0400
Subject: [maker-devel] missing est2genome annotation
In-Reply-To: <4FBD1AF3.8020904@uni-wuerzburg.de>
Message-ID: <CBE8F75D.CB57%carsonhh@gmail.com>

Sorry for the slow reply.  I'm just getting back after traveling.

That's a percent coverage flag.  You can set a percent coverage threshold
in the maker_bopts.ctl file.  Partial high scoring alignments can be
common.  If you only filter by expect score, you would be surprised to see
how many ugly and confusing all the alignments become.

Thanks,
Carson

On 12-05-23 1:14 PM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi again,
>
>I did some source code digging and caught the following line burying my
>exonerate alignments. I suspect it does so for a very good reason,
>therefore it would help me a lot if someone could explain to me, what is
>going on there.
>
>
>/lib/GI.pm  l.1473
>next if $e->pAh<  $pcov;
>
>
>Regards
>Thomas
>
>
>Am 23.05.2012 14:01, schrieb Thomas Hackl:
>> Hi,
>>
>> I used maker to annotate genomic contigs and among other stuff
>> provided transcripts from the transcriptome as est evidence. Blast and
>> exonerate work fine and produce valid alignments, the alignment files
>> exist in theVoid and look very good. Unfortunatly neither the
>> evidence_0.gff nor the final .gff carry the corresponding feature
>> annotations.
>>
>> Any ideas why?
>>
>> Regards
>> Thomas
>>
>
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From seoanezonjic at hotmail.com  Tue May 22 06:55:12 2012
From: seoanezonjic at hotmail.com (p sz)
Date: Tue, 22 May 2012 12:55:12 +0000
Subject: [maker-devel] ipr_update_gff ERROR
Message-ID: <COL119-W282F1F1F211028B1F661C5C7020@phx.gbl>


First, thanks by help me on the lprevious error that I submitted.
I'm still working in the same project and I get a new error. I try interproscan with this commandline:

iprscan_wrap -i parsed_input.all.maker.proteins.fasta -email seoanezonjic at hotmail.com  -format raw

parsed_input.all.maker.proteins.fasta was generated with the tool fasta_merge. I use the output (attached in this email) and a gff file (generated by a normal run of maker, attached in this email) with the ipr_update_gff script of this way:

ipr_update_gff BAC12_Clone_Pt314B2_Lib_Pt_7Ba__organism_Pinus_taeda__0.gff sc_interpro.sh.o109053

And i get this error:
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 15.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 15.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 18.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 18.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 19.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 19.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 48.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 48.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 49.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 49.

The gff file seems updated but i don't know if it works fine or is corrupt
Thanks in advance
 		 	   		  
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From larriba.ed at gmail.com  Fri May 25 10:01:41 2012
From: larriba.ed at gmail.com (Eduardo Larriba)
Date: Fri, 25 May 2012 18:01:41 +0200
Subject: [maker-devel] Consensus gene models
Message-ID: <CADwrZ2XdcZu080yHt7=CreOWbpt791NC8ScB5WVW=NmvN4=Jgw@mail.gmail.com>

Hi Carson and people,
I am working on structural annotation of a filamentous fungus, of which
there is little evidence as EST or Protein. For generate consensus gene  based
on limited evidences to me I used  Marker.
For this I created the files GeneMark prediction-is and SNAP.
I run maker using the EST of my organims (85), along with 5700 EST of the
closed organims. I have made ??predictions with Augustus, and SNAP GeneMark,
with the training files for my organims, in Maker pipeline. Everything works
fine.
My problem is that when I get the consensus sequences of all my contigs,
fasta_merge script (included in Maker), I get different list for each
predictor, as well as when I try to get the gff of all.
They could tell me how I can use Maker consensus for a list of genes? Or I
have to do it manually? There is the possibility that Maker evaluates the
accuracy of each prediction and confirm, so just get a list of the different
predictions?

Thank you very much.


-- 
Eduardo Larriba Tornel
Universidad de Alicante.
Lab. Fitopatolog?a
Dept. Ciencias del Mar y Biolog?a Aplicada
Pabell?n 13.
San Vicente del Raspeig
Tel. 96 590 3400 ext 3280
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From carsonhh at gmail.com  Mon May 28 08:14:22 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 10:14:22 -0400
Subject: [maker-devel] Consensus gene models
In-Reply-To: <CADwrZ2XdcZu080yHt7=CreOWbpt791NC8ScB5WVW=NmvN4=Jgw@mail.gmail.com>
Message-ID: <CBE8FECE.CBA5%carsonhh@gmail.com>

The consensus list is in the maker.proteins.fasta and
maker.transcripts.fasta file.  The predictor specific lists are just for
reference purposes (incase you want to see what the other predictors
produced on their own, i.e. without MAKER's intervention).  The
non-overlapping.fasta file in the same directory will contain consensus
entries for models that were not supported by any evidence and don't overlap
any gene models in the  maker.transcripts.fasta (think of these as the maybe
gene and the maker.transcripts.fasta as the very likely genes).  You can set
keep_preds=1 if you just want MAKER to keep everything with or without
support and just produce consensus (probably ok on a fungus, but I wouldn't
recommend it on other eukayotes because false positive rates will be very
high).

Thanks,
Carson



From:  Eduardo Larriba <larriba.ed at gmail.com>
Date:  Friday, 25 May, 2012 12:01 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Consensus gene models

Hi Carson and people,
I am working on structural annotation of a filamentous fungus, of which
there is little evidence as EST or Protein. For generate consensus gene
based on limited evidences to me I used  Marker.
 For this I created the files GeneMark prediction-is and SNAP.
 I run maker using the EST of my organims (85), along with 5700 EST of the
closed organims. I have made ??predictions with Augustus, and SNAP
GeneMark, with the training files for my organims, in Maker pipeline.
Everything works fine.
 My problem is that when I get the consensus sequences of all my contigs,
fasta_merge script (included in Maker), I get different list for each
predictor, as well as when I try to get the gff of all.
 They could tell me how I can use Maker consensus for a list of genes? Or I
have to do it manually? There is the possibility that Maker evaluates the
accuracy of each prediction and confirm, so just get a list of the different
predictions?

 Thank you very much.


-- 
Eduardo Larriba Tornel
Universidad de Alicante.
Lab. Fitopatolog?a
Dept. Ciencias del Mar y Biolog?a Aplicada
Pabell?n 13. 
San Vicente del Raspeig
Tel. 96 590 3400 ext 3280

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From carsonhh at gmail.com  Mon May 28 08:18:26 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 10:18:26 -0400
Subject: [maker-devel] ipr_update_gff ERROR
In-Reply-To: <COL119-W282F1F1F211028B1F661C5C7020@phx.gbl>
Message-ID: <CBE90090.CBB6%carsonhh@gmail.com>

This error would happen if some results exist in the iprscan output, but
don't match gene entries in the GFF3 file.  If I could see the original
files I can tell you which ones.  This can happen if you combine results
from the non-overlapping.fasta files with the maker.proteins.fasta files for
example.  Models in the non-overlapping.fasta file are not genes in the GFF3
(they are match/match_part enties), so errors happen.

Thanks,
Carson

From:  p sz <seoanezonjic at hotmail.com>
Date:  Tuesday, 22 May, 2012 8:55 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] ipr_update_gff ERROR

First, thanks by help me on the lprevious error that I submitted.
I'm still working in the same project and I get a new error. I try
interproscan with this commandline:

iprscan_wrap -i parsed_input.all.maker.proteins.fasta -email
seoanezonjic at hotmail.com  -format raw

parsed_input.all.maker.proteins.fasta was generated with the tool
fasta_merge. I use the output (attached in this email) and a gff file
(generated by a normal run of maker, attached in this email) with the
ipr_update_gff script of this way:

ipr_update_gff BAC12_Clone_Pt314B2_Lib_Pt_7Ba__organism_Pinus_taeda__0.gff
sc_interpro.sh.o109053

And i get this error:
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 15.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 15.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 18.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 18.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 19.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 19.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 48.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 48.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 49.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 49.

The gff file seems updated but i don't know if it works fine or is corrupt
Thanks in advance
       
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From carsonhh at gmail.com  Tue May 29 06:37:55 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 29 May 2012 08:37:55 -0400
Subject: [maker-devel] can't call method strand on an undefined value
 ERROR: Failed while flattening protein clusters
In-Reply-To: <CAH221bv8rM7w+yOg6AgW9Y9tLHLvivWgGjZFs4e4QLAyuW4pGA@mail.gmail.com>
Message-ID: <CBEA3AC6.CD62%carsonhh@gmail.com>

Use this command to check out the latest unreleased test version, and lt me
know if you still get the error.

Command -->  svn co svn://malachite.genetics.utah.edu/maker/trunk maker

User: yandell_guest
Password: y at ndell_Gu3st

Thanks,
Carson





From:  Scott Geib <smg283 at gmail.com>
Date:  Tuesday, 22 May, 2012 2:42 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] can't call method strand on an undefined value
ERROR: Failed while flattening protein clusters

Hi, 
Using maker 2.24, I am getting the following error (see below) in
protein2genome widget.  I also get the same error with est2genome.  This
happens with my own data (testing on a single scaffold), but not with the
test data supplied with maker (dpp files in data folder).
Scott


Widget::exonerate::protein2genome:
/data0/opt/AlignmentSoftware/exonerate/exonerate-2.2.0-x86_64/bin/exonerate
-q 
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/UniRef90_UPI00019
4D3FC.for.1588546-1589203.9.fasta -t
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.158
8546-1589203.9.fasta -Q protein -T dna -m protein2genome --softmasktarget
--percent 20 --showcigar  >
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.158
8546-1589203.UniRef90_UPI000194D3FC.p_exonerate.9
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 23
 ...processing 1 of 23
 ...processing 2 of 23
 ...processing 3 of 23
 ...processing 4 of 23
 ...processing 5 of 23
 ...processing 6 of 23
 ...processing 7 of 23
 ...processing 8 of 23
 ...processing 9 of 23
 ...processing 10 of 23
 ...processing 11 of 23
 ...processing 12 of 23
 ...processing 13 of 23
 ...processing 14 of 23
 ...processing 15 of 23
 ...processing 16 of 23
 ...processing 17 of 23
 ...processing 18 of 23
 ...processing 19 of 23
 ...processing 20 of 23
 ...processing 21 of 23
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 20
 ...processing 1 of 20
 ...processing 2 of 20
 ...processing 3 of 20
 ...processing 4 of 20
 ...processing 5 of 20
 ...processing 6 of 20
 ...processing 7 of 20
 ...processing 8 of 20
 ...processing 9 of 20
 ...processing 10 of 20
 ...processing 11 of 20
 ...processing 12 of 20
 ...processing 13 of 20
 ...processing 14 of 20
 ...processing 15 of 20
 ...processing 16 of 20
 ...processing 17 of 20
 ...processing 18 of 20
total clusters:2 now processing 0
Can't call method "strand" on an undefined valueERROR: Failed while
flattening protein clusters
ERROR: Chunk failed at level:11, tier_type:2
FAILED CONTIG:scaffold00001

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From bob_freeman at hms.harvard.edu  Tue May 29 10:30:23 2012
From: bob_freeman at hms.harvard.edu (Bob Freeman)
Date: Tue, 29 May 2012 12:30:23 -0400
Subject: [maker-devel] Alternate translation table?
In-Reply-To: <CBE8E7EF.CAF3%carsonhh@gmail.com>
References: <CBE8E7EF.CAF3%carsonhh@gmail.com>
Message-ID: <B198DB2E-A0CC-4A01-843D-59F470E97DC9@hms.harvard.edu>

Thanks, Carson, for the update on this. No need to implement something. I'll keep it simple and translate the collected transcripts using an appropriate translation table.

-Bob

On May 28, 2012, at 8:43 AM, Carson Holt wrote:

> The alternate translation table is not currently an option.  It's one of those things that needs to be implemented, but has not been yet.  It's also not supported by many of the eukaryotic gene predictors MAKER uses.
> 
> I could probably get something implemented for you to test in two to three weeks though (there are a lot of places where the translation table comes into play).  Let me know.
> 
> --Carson
> 
> 
> 
> From: Bob Freeman <bob_freeman at hms.harvard.edu>
> Date: Friday, 25 May, 2012 12:23 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Alternate translation table?
> 
> Hello all!
> 
> Unusual question here: I am running MAKER on a ciliate that uses a non-standard translation table for its translation products. I haven't found an option in the control files that I can change for the for translation of the predicted transcripts. How or where can I go about this?
> 
> Tx,
> Bob
> 
> 
> _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
	-- Karen Walker, from Will and Grace





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From gowthaman.ramasamy at seattlebiomed.org  Tue May 29 15:54:33 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Tue, 29 May 2012 14:54:33 -0700
Subject: [maker-devel] Can maker select a gene model based on #algoritham
	predicted it
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8EB@mail02.sbri.org>

Hi Carson,
Thanks for all the help during the long weekend, in spite of that long drive. I am still trying to imagine that.

I now have maker to consider our own prediction via pred_gff, and use augustus and gene mark (with our training model). And i was able to use altest and protein evidences. Maker happily picks one gene model when there is a overlap between three different predictions. But, when I look at the gff, it seems like it picks a gene model only when there is an est/protein evidence. It leaves out some genes even though, they are predicted by all three algorithms. Of course, keep_pred=1 helps to keep all the models. This kind of leads to over prediction. 

But, I am looking for something in between. And would like to know if that is possible?
1) Pick a gene model if it has an evidence from (est/prot etc...) irrespective of how many algorithms predicted it
2) In the absence of extrinsic evidence (est/prot etc), pick a gene model if that is predicted by at least two algorithms.

Or even simpler:
I have ab-initio predictions from three algorithms, Can I output, those genes that is supported by at least two of them. I care less about exactness of gene boundaries.

Thanks,
Gowthaman

PS: With my recent attempts, i learned couple things about maker/other associated tools that is not documented in gmod-maker wiki. Is it possible/ok if I add contents to it. I am okay with running it by you before making it public.


From carsonhh at gmail.com  Wed May 30 06:54:32 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 30 May 2012 08:54:32 -0400
Subject: [maker-devel] Can maker select a gene model based on
	#algoritham predicted it
In-Reply-To: <89080953C3D300419AACB6E63A7EEFBA5C8409F8EB@mail02.sbri.org>
Message-ID: <CBEB8E25.D097%carsonhh@gmail.com>

It's not an option in exactly the way you are specifying, but there is
something I usually do for annotation that works well.  I run interproscan
or rpsblast on the non_overlapping.proteins.fasta file and select just
those non-overlapping models that have a recognizable protein domain (just
searching the pfam doamin space is more than sufficient).  Then I provide
the selected results to model_gff, and provide the previous maker results
to the maker_gff option with (all reannotation pass options set to 1 and
all analysis options turned off).  This adds models with at least
recognizable domains (as even multiple gene predictors can overpredict in
a similar way).

Attached is a script to help select predictions and upgrade them to models
in GFF3 format.  If you have question let me know.

Thanks,
Carson



On 12-05-29 5:54 PM, "Gowthaman Ramasamy"
<gowthaman.ramasamy at seattlebiomed.org> wrote:

>Hi Carson,
>Thanks for all the help during the long weekend, in spite of that long
>drive. I am still trying to imagine that.
>
>I now have maker to consider our own prediction via pred_gff, and use
>augustus and gene mark (with our training model). And i was able to use
>altest and protein evidences. Maker happily picks one gene model when
>there is a overlap between three different predictions. But, when I look
>at the gff, it seems like it picks a gene model only when there is an
>est/protein evidence. It leaves out some genes even though, they are
>predicted by all three algorithms. Of course, keep_pred=1 helps to keep
>all the models. This kind of leads to over prediction.
>
>But, I am looking for something in between. And would like to know if
>that is possible?
>1) Pick a gene model if it has an evidence from (est/prot etc...)
>irrespective of how many algorithms predicted it
>2) In the absence of extrinsic evidence (est/prot etc), pick a gene model
>if that is predicted by at least two algorithms.
>
>Or even simpler:
>I have ab-initio predictions from three algorithms, Can I output, those
>genes that is supported by at least two of them. I care less about
>exactness of gene boundaries.
>
>Thanks,
>Gowthaman
>
>PS: With my recent attempts, i learned couple things about maker/other
>associated tools that is not documented in gmod-maker wiki. Is it
>possible/ok if I add contents to it. I am okay with running it by you
>before making it public.

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From mikael.durling at slu.se  Thu May 31 06:25:31 2012
From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=)
Date: Thu, 31 May 2012 14:25:31 +0200
Subject: [maker-devel] maker leaving large numbers of defunct zombies
Message-ID: <FBA1F582-5EF0-4D7A-8276-A86DAD5C4C89@slu.se>

Hello,

I've been working lately to set up maker for annotation work on a few fungal genomes. I've got mpi maker up and running now, however, I notice that maker is leaving a lot of <defunct> perl processes behind. This happens to the extent that the process table on the system gets filled up after a few hours run time. Right now the process tree after three hours running looks like this:

    |-sge_execd-+-sge_shepherd---bash---mpirun-+-maker-+-maker
     |           |                              |       `-perl
     |           |                              |-maker-+-maker
     |           |                              |       |-maker---1371*[perl]
     |           |                              |       `-perl
     |           |                              |-maker-+-maker
     |           |                              |       |-maker---1348*[perl]
     |           |                              |       `-perl
     |           |                              |-maker-+-maker
     |           |                              |       |-maker---1384*[perl]
     |           |                              |       `-perl

...and so on for all mpi processes, except for the controlling processes. 

What perl programs is maker calling, that might end up as zombies? I've had a brief look at the source to no avail, but would be happy to dig further with some pointers for where to look.

This is run with the 2.25-beta from the web page, perl 5.16.0 and openmpi 1.4.5. 

Thanks,
Mikael










-------------------------------------
Mikael Brandstr?m Durling, PhD
Assistant Professor

Sveriges lantbruksuniversitet
Swedish University of Agricultural Sciences

Uppsala BioCenter
Dept of Forest Mycology and Plant Pathology
Box 7026, 75007 Uppsala
Visiting address: Almas All? 5
Telefon: 018-671512
mikael.durling at slu.se, www.slu.se/mykopat





From mikael.durling at slu.se  Thu May 31 06:34:30 2012
From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=)
Date: Thu, 31 May 2012 14:34:30 +0200
Subject: [maker-devel] Using GDBM_File instead of DB_File
Message-ID: <B535F29B-D593-44D7-B0C4-D84462957EFB@slu.se>

Hello,

I've been struggling for a few days to get maker up and running with MPI on a debian squeeze system. Compiling a new perl 5.16 exclusively for maker I wound down to that the segfaults came from DB_File. Even by recomiling and updating that module, nothing worked. After checking for dependencies on DB_File in maker, I concluded that the only dependency was through the GI::localize_file, which expects the FastaDB to be instantiated with DB_File. However, FastaDB can run on GDBM_File too. I patched the calls to GI::localize_file in maker to handle the .pag/.dir extensions used by GDBM (below). With this patch applied maker is running for me, even when I have deleted the DB_File module from the perl path and made sure that GDBM_File is installed. My basic question is if there is any other dependency for DB_File which I have missed which may break things?

cheers,
Mikael

--- maker.orig	2012-03-30 15:48:05.000000000 +0200
+++ maker	2012-05-31 10:35:30.253022648 +0200
@@ -512,7 +515,12 @@
 }
 if($size > 1){
     carp "Calling GI::localize_file" if($main::debug);
-    GI::localize_file("$gdbfile.index");
+    if( -f "$gdbfile.index.dir" ){
+	GI::localize_file("$gdbfile.index.dir");
+	GI::localize_file("$gdbfile.index.pag");
+    }else{
+    	GI::localize_file("$gdbfile.index");
+    }
     carp "Calling GI::localize_file" if($main::debug);
     $gdbfile = GI::localize_file($gdbfile);
 }




From carsonhh at gmail.com  Thu May 31 07:04:58 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 31 May 2012 09:04:58 -0400
Subject: [maker-devel] Using GDBM_File instead of DB_File
In-Reply-To: <B535F29B-D593-44D7-B0C4-D84462957EFB@slu.se>
Message-ID: <CBECE3F7.D209%carsonhh@gmail.com>

DB_File is being called by Bio::DB::Fasta.  I can check the object
returned when using GDBM_File instead to see if the index file names are
contained on the object, as I'm just assuming an extension of '.index'.
I'll look around to see if the extension name is assumed anywhere else.

Thanks,
Carson


On 12-05-31 8:34 AM, "Mikael Brandstr?m Durling" <mikael.durling at slu.se>
wrote:

>Hello,
>
>I've been struggling for a few days to get maker up and running with MPI
>on a debian squeeze system. Compiling a new perl 5.16 exclusively for
>maker I wound down to that the segfaults came from DB_File. Even by
>recomiling and updating that module, nothing worked. After checking for
>dependencies on DB_File in maker, I concluded that the only dependency
>was through the GI::localize_file, which expects the FastaDB to be
>instantiated with DB_File. However, FastaDB can run on GDBM_File too. I
>patched the calls to GI::localize_file in maker to handle the .pag/.dir
>extensions used by GDBM (below). With this patch applied maker is running
>for me, even when I have deleted the DB_File module from the perl path
>and made sure that GDBM_File is installed. My basic question is if there
>is any other dependency for DB_File which I have missed which may break
>things?
>
>cheers,
>Mikael
>
>--- maker.orig	2012-03-30 15:48:05.000000000 +0200
>+++ maker	2012-05-31 10:35:30.253022648 +0200
>@@ -512,7 +515,12 @@
> }
> if($size > 1){
>     carp "Calling GI::localize_file" if($main::debug);
>-    GI::localize_file("$gdbfile.index");
>+    if( -f "$gdbfile.index.dir" ){
>+	GI::localize_file("$gdbfile.index.dir");
>+	GI::localize_file("$gdbfile.index.pag");
>+    }else{
>+    	GI::localize_file("$gdbfile.index");
>+    }
>     carp "Calling GI::localize_file" if($main::debug);
>     $gdbfile = GI::localize_file($gdbfile);
> }
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Thu May 31 07:17:20 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 31 May 2012 09:17:20 -0400
Subject: [maker-devel] maker leaving large numbers of defunct zombies
In-Reply-To: <FBA1F582-5EF0-4D7A-8276-A86DAD5C4C89@slu.se>
Message-ID: <CBECE4F4.D210%carsonhh@gmail.com>

MAKER uses IPC::Open3 to open almost all external applications, including
a helper script called every once in a while that helps check file locks
on NFS.

MAKER then calls waitpid to reap the processes, as IPC::Open3 doesn't
auto-reap.  The only time previously I've seen issues with zombie
accumulation was with MPICH2 when it moved from the MPD process manager to
Hydra.  Hydra had certain broken signal handling issues that I had to bug
the MPICH2 developers about and they fixed it.  It is possible that the
issue you are having may be with OpenMPI or with perl 5.16.  I currently
use perl 5.12.  Perl instituted something called safe signals in either
5.6 or 5.8 and there may be some updates in 5.16 where they've been
changing those around again.

I can try installing a copy of 5.16 to test with and OpenMPI to see if I
can replicate the error.

Thanks,
Carson



On 12-05-31 8:25 AM, "Mikael Brandstr?m Durling" <mikael.durling at slu.se>
wrote:

>Hello,
>
>I've been working lately to set up maker for annotation work on a few
>fungal genomes. I've got mpi maker up and running now, however, I notice
>that maker is leaving a lot of <defunct> perl processes behind. This
>happens to the extent that the process table on the system gets filled up
>after a few hours run time. Right now the process tree after three hours
>running looks like this:
>
>    |-sge_execd-+-sge_shepherd---bash---mpirun-+-maker-+-maker
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1371*[perl]
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1348*[perl]
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1384*[perl]
>     |           |                              |       `-perl
>
>...and so on for all mpi processes, except for the controlling processes.
>
>What perl programs is maker calling, that might end up as zombies? I've
>had a brief look at the source to no avail, but would be happy to dig
>further with some pointers for where to look.
>
>This is run with the 2.25-beta from the web page, perl 5.16.0 and openmpi
>1.4.5. 
>
>Thanks,
>Mikael
>
>
>
>
>
>
>
>
>
>
>-------------------------------------
>Mikael Brandstr?m Durling, PhD
>Assistant Professor
>
>Sveriges lantbruksuniversitet
>Swedish University of Agricultural Sciences
>
>Uppsala BioCenter
>Dept of Forest Mycology and Plant Pathology
>Box 7026, 75007 Uppsala
>Visiting address: Almas All? 5
>Telefon: 018-671512
>mikael.durling at slu.se, www.slu.se/mykopat
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From mikael.durling at slu.se  Thu May 31 07:57:06 2012
From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=)
Date: Thu, 31 May 2012 15:57:06 +0200
Subject: [maker-devel] maker leaving large numbers of defunct zombies
In-Reply-To: <CBECE4F4.D210%carsonhh@gmail.com>
References: <CBECE4F4.D210%carsonhh@gmail.com>
Message-ID: <E779EAA8-C2AC-4362-A3C7-E370777E3D5D@slu.se>

I saw the same problem with the latest MPICH2 using hydra too, so it might boil down to perl/openmpi interactions. I didn't see this problem with the debian supplied perl 5.10, but then I had intermittent segfaults with in DB_File and libpthread. Seemed to be some interaction with the LD_PRELOADed libmpi. That requirement for preloading libmpi was easiest solved by compiling openmpi with --disable-dlopen.

Thanks,
Mikael

31 maj 2012 kl. 15:17 skrev Carson Holt:

> MAKER uses IPC::Open3 to open almost all external applications, including
> a helper script called every once in a while that helps check file locks
> on NFS.
> 
> MAKER then calls waitpid to reap the processes, as IPC::Open3 doesn't
> auto-reap.  The only time previously I've seen issues with zombie
> accumulation was with MPICH2 when it moved from the MPD process manager to
> Hydra.  Hydra had certain broken signal handling issues that I had to bug
> the MPICH2 developers about and they fixed it.  It is possible that the
> issue you are having may be with OpenMPI or with perl 5.16.  I currently
> use perl 5.12.  Perl instituted something called safe signals in either
> 5.6 or 5.8 and there may be some updates in 5.16 where they've been
> changing those around again.
> 
> I can try installing a copy of 5.16 to test with and OpenMPI to see if I
> can replicate the error.
> 
> Thanks,
> Carson
> 
> 
> 
> On 12-05-31 8:25 AM, "Mikael Brandstr?m Durling" <mikael.durling at slu.se>
> wrote:
> 
>> Hello,
>> 
>> I've been working lately to set up maker for annotation work on a few
>> fungal genomes. I've got mpi maker up and running now, however, I notice
>> that maker is leaving a lot of <defunct> perl processes behind. This
>> happens to the extent that the process table on the system gets filled up
>> after a few hours run time. Right now the process tree after three hours
>> running looks like this:
>> 
>>   |-sge_execd-+-sge_shepherd---bash---mpirun-+-maker-+-maker
>>    |           |                              |       `-perl
>>    |           |                              |-maker-+-maker
>>    |           |                              |
>> |-maker---1371*[perl]
>>    |           |                              |       `-perl
>>    |           |                              |-maker-+-maker
>>    |           |                              |
>> |-maker---1348*[perl]
>>    |           |                              |       `-perl
>>    |           |                              |-maker-+-maker
>>    |           |                              |
>> |-maker---1384*[perl]
>>    |           |                              |       `-perl
>> 
>> ...and so on for all mpi processes, except for the controlling processes.
>> 
>> What perl programs is maker calling, that might end up as zombies? I've
>> had a brief look at the source to no avail, but would be happy to dig
>> further with some pointers for where to look.
>> 
>> This is run with the 2.25-beta from the web page, perl 5.16.0 and openmpi
>> 1.4.5. 
>> 
>> Thanks,
>> Mikael
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> -------------------------------------
>> Mikael Brandstr?m Durling, PhD
>> Assistant Professor
>> 
>> Sveriges lantbruksuniversitet
>> Swedish University of Agricultural Sciences
>> 
>> Uppsala BioCenter
>> Dept of Forest Mycology and Plant Pathology
>> Box 7026, 75007 Uppsala
>> Visiting address: Almas All? 5
>> Telefon: 018-671512
>> mikael.durling at slu.se, www.slu.se/mykopat
>> 
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 




From carsonhh at gmail.com  Tue May  1 16:07:47 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 01 May 2012 18:07:47 -0400
Subject: [maker-devel] gff3_preds2models usage question
In-Reply-To: <CANRPJSdHUx_BmAzb+OBLFab02dDtugM9Jf3zsXqjThrKauX29g@mail.gmail.com>
Message-ID: <CBC5D543.C151%carsonhh@gmail.com>

Sorry for the slow response.  The gff3_preds2models script has been
deprecated for some time now (isn't even in the release code anymore), and
the old one won't work with the new library.

I've attached a made from scratch drop-in replacement that you can use to do
what the old script would have done.  In the current release of MAKER,
instead of the gff3_preds2models script users can just give MAKER  a set of
predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then
leave all other options blank).  The predictions given will the be converted
into gene models.

Thanks,
Carson



From:  Walter Eckalbar <weckalba at asu.edu>
Date:  Tuesday, 3 April, 2012 7:28 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] gff3_preds2models usage question

Hello maker developers and users,

I am attempting to use the gff3_preds2models scripts, but running into a few
issues.

Initially, I hit errors that seemed to be fixed by installing CGI and its
dependancies.  However, that during that installation a few tests did fail.
I can provide error logs if that would be helpful, however, I went on to
install and attempt gff3_preds2models anyway.

What I am currently doing is running gff3_merge first, to gather the maker
outputs.  I am doing so with both the -n option on and off.  When providing
the gff3 file with the sequence I get the following error from
gff3_preds2models:

Undefined subroutine &maker::auto_annotator::annotate called at
/Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97,
<GEN16> line 992291.

This seemed to be the same error as that of what someone else saw on these
boards, but I did not see a later email resolving the issue.

I also tried giving it just the gff3 without the sequences at the bottom of
the file and then I get this error:

ERROR: There was a problem in the writing the fasta entry
Either no sequence was given, or there was an error in writing

This leads me to believe I should be using the one with the sequence, but I
am not certain of that.

I see it might be possible to go from maker outputs to chado database then
to gene->mRNA->exon gff3s, but I have not set up my machine for XML or chado
yet, and it does not appear trivial.

Thanks for the help,

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

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From weckalba at asu.edu  Tue May  1 19:33:00 2012
From: weckalba at asu.edu (Walter Eckalbar)
Date: Tue, 1 May 2012 18:33:00 -0700
Subject: [maker-devel] gff3_preds2models usage question
In-Reply-To: <CBC5D543.C151%carsonhh@gmail.com>
References: <CANRPJSdHUx_BmAzb+OBLFab02dDtugM9Jf3zsXqjThrKauX29g@mail.gmail.com>
	<CBC5D543.C151%carsonhh@gmail.com>
Message-ID: <CANRPJSc-EN9jgqW3dJRJmLJ_4SyhavqsOCH+h-031PPtiBHONA@mail.gmail.com>

Hi Carson,

Thanks for the response, even a late one, and thanks for the script.  I'll
certainly be giving that a try.

Walter

On 1 May 2012 15:07, Carson Holt <carsonhh at gmail.com> wrote:

> Sorry for the slow response.  The gff3_preds2models script has been
> deprecated for some time now (isn't even in the release code anymore), and
> the old one won't work with the new library.
>
> I've attached a made from scratch drop-in replacement that you can use to
> do what the old script would have done.  In the current release of MAKER,
> instead of the gff3_preds2models script users can just give MAKER  a set of
> predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then
> leave all other options blank).  The predictions given will the be
> converted into gene models.
>
> Thanks,
> Carson
>
>
>
> From: Walter Eckalbar <weckalba at asu.edu>
> Date: Tuesday, 3 April, 2012 7:28 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] gff3_preds2models usage question
>
> Hello maker developers and users,
>
> I am attempting to use the gff3_preds2models scripts, but running into a
> few issues.
>
> Initially, I hit errors that seemed to be fixed by installing CGI and its
> dependancies.  However, that during that installation a few tests did fail.
>  I can provide error logs if that would be helpful, however, I went on to
> install and attempt gff3_preds2models anyway.
>
> What I am currently doing is running gff3_merge first, to gather the maker
> outputs.  I am doing so with both the -n option on and off.  When providing
> the gff3 file with the sequence I get the following error from
> gff3_preds2models:
>
> Undefined subroutine &maker::auto_annotator::annotate called at
> /Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97,
> <GEN16> line 992291.
>
> This seemed to be the same error as that of what someone else saw on these
> boards, but I did not see a later email resolving the issue.
>
> I also tried giving it just the gff3 without the sequences at the bottom
> of the file and then I get this error:
>
> ERROR: There was a problem in the writing the fasta entry
> Either no sequence was given, or there was an error in writing
>
> This leads me to believe I should be using the one with the sequence, but
> I am not certain of that.
>
> I see it might be possible to go from maker outputs to chado database then
> to gene->mRNA->exon gff3s, but I have not set up my machine for XML or
> chado yet, and it does not appear trivial.
>
> Thanks for the help,
>
> Walter
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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From qwang at uwyo.edu  Thu May  3 10:23:16 2012
From: qwang at uwyo.edu (Qiurong Wang)
Date: Thu, 3 May 2012 10:23:16 -0600
Subject: [maker-devel] MAKER download problem
Message-ID: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>

Hi,

I was trying to download MAKER, but I couldn't open the download page.  
Could you please help me to figure out the problem? Thanks a lot!


Qiurong Wang
PhD candidate
Department of Botany
University of Wyoming
Department 3165, 1000 E University Ave. Laramie, Wyoming 82071, USA
Phone: 307-766-2634
Email: qwang at uwyo.edu




From barry.moore at genetics.utah.edu  Thu May  3 11:51:48 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Thu, 3 May 2012 11:51:48 -0600
Subject: [maker-devel] MAKER download problem
In-Reply-To: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>
References: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>
Message-ID: <6B24C00B-6C70-4A40-BA7C-E3AC0C7F5E25@genetics.utah.edu>

Hi all,

The web server hosting the MAKER licensing application and MAKER code distribution was attacked this week.  The University of Utah is currently blocking access to that server from outside University IP space.  We are working hard to move all of the content and web-applications from that machine to a new server and I expect to have the MAKER services restored over the weekend.  This is affecting the ability to submit new licenses for MAKER and to download the MAKER code.  In addition those with existing licenses will need to update their code links for future code updates.  For those of you on campus in Utah or with campus VPN access, the server is running and available.  Updates on the status of the server and details about new links to the MAKER code will be posted to the mailing list soon.

Barry

On May 3, 2012, at 10:23 AM, Qiurong Wang wrote:

> Hi,
> 
> I was trying to download MAKER, but I couldn't open the download page. Could you please help me to figure out the problem? Thanks a lot!
> 
> 
> Qiurong Wang
> PhD candidate
> Department of Botany
> University of Wyoming
> Department 3165, 1000 E University Ave. Laramie, Wyoming 82071, USA
> Phone: 307-766-2634
> Email: qwang at uwyo.edu
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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




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From carsonhh at gmail.com  Thu May  3 12:00:01 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 03 May 2012 14:00:01 -0400
Subject: [maker-devel] MAKER download problem
In-Reply-To: <8754B55D-C119-4A7C-9594-BEAEAD3BB939@uwyo.edu>
Message-ID: <CBC83F6D.C3B0%carsonhh@gmail.com>

The server hosting the file to download is down temporarily.  I'll put a
copy of MAKER on a separate server and e-mail the link to you.

--Carson



On 12-05-03 12:23 PM, "Qiurong Wang" <qwang at uwyo.edu> wrote:

>Hi,
>
>I was trying to download MAKER, but I couldn't open the download page.
>Could you please help me to figure out the problem? Thanks a lot!
>
>
>Qiurong Wang
>PhD candidate
>Department of Botany
>University of Wyoming
>Department 3165, 1000 E University Ave. Laramie, Wyoming 82071, USA
>Phone: 307-766-2634
>Email: qwang at uwyo.edu
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From cjfields at illinois.edu  Tue May 15 09:01:31 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 15 May 2012 15:01:31 +0000
Subject: [maker-devel] mail list and Trac
Message-ID: <64A6759A-9FD1-4AEE-BCEA-151B0D791ADD@illinois.edu>

Just wanted to point out, I noticed the mail list is not being indexed on Google Groups any more (nothing in May).  Also, any status on Trac?

chris


From barry.moore at genetics.utah.edu  Tue May 15 10:34:29 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 15 May 2012 10:34:29 -0600
Subject: [maker-devel] mail list and Trac
In-Reply-To: <64A6759A-9FD1-4AEE-BCEA-151B0D791ADD@illinois.edu>
References: <64A6759A-9FD1-4AEE-BCEA-151B0D791ADD@illinois.edu>
Message-ID: <C2170DBB-75CB-423D-82E3-C56572B57753@genetics.utah.edu>

Thanks Chris,  I'll check on the Google groups.  The MAKER Trac server was on a server that we had to shut down a couple weeks ago and I had made moving it a lower priority since I didn't think it was getting much use.  I'll get it moved over and bump up the priority on that move since I know someone is looking at it.

B

On May 15, 2012, at 9:01 AM, Fields, Christopher J wrote:

> Just wanted to point out, I noticed the mail list is not being indexed on Google Groups any more (nothing in May).  Also, any status on Trac?
> 
> chris
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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




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From anastasia.gioti at scilifelab.se  Thu May 17 05:27:04 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Thu, 17 May 2012 13:27:04 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
	<03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <4D9922AF-A917-4747-9B7C-CFE9F142D51C@scilifelab.se>

Hi Barry,
Thanks for your detailed instructions. You well understood that I have  
already included the proteins of the closely related species in my  
protein evidence dataset, but still did not get the genes. I have now  
blasted (P) the missing 949 proteins from this species against my  
nonoverlaping_abinits.fasta proteins and have found 618 good hits,  
which i guess I can promote to models using the routine no 2 of your  
last email and Carson's script gff3_select.
I have also looked at the rest of the proteins (331) for which there  
was no model in the nonoverlaping_abinits.fasta. I will try to  
describe 2 examples I looked at in apollo:

1) ab initio models predicted a ~7.5 kb gene covering 3 genes (as  
predicted in the closely related species). Blastx+protein2genome  
similarities were reported for two of these genes, but not for the 3rd  
(the one in the middle). MAKER finally decided to call two genes,  
respecting the blastx+protein2genome evidence, but the 3rd was lost.
I have previously  reported here that MAKER tends to  fuse genes in  
multi-exonic genes and others reported that too, I remember you  
proposed changing a papameter to alter this. To keep in mind for my  
final strategy that i am trying to decide on (for the moment i have  
not rerun MAKER).
For this case, abinitio models do not exist for the gene (in the sense  
that the existing models overlap many genes) and the similarity to the  
protein of the closely related species was not judged sufficient,  
although when i look at a TblastN alignment for this area it looks  
fine to me.

2) Only the 3' end of the gene was called by MAKER, despite blastx  
+protein2genome evidence from the closely related species for the  
entire region. Abinitio models existed as 2 separate genes , one for  
the 3' end region (finally retained by MAKER in a consensus decision I  
guess) and one for the 5' region, but here not all predictors called  
an orf, and finally nothing was called in this region.
In this case, it is a misannotation rather, but which misses a very  
important part of the gene.
I hope my descriptions are clear, otherwise I can provide you the gff  
file of these 2 examples to look by yourself.

I am not very clear about what to do about these 331 cases (which I do  
not know how to look at as well, except for random examples' viwing in  
Apollo). I feel that a second MAKER run would be probably the  
solution, this time providing as pred_gff  the result of a blast  
against the 331. But still, the existing annotations would then have  
to be somehow updated as the new predictions are in conflict with them  
(see example 2). I am a bit confused.
to recap, what would you suggest for the 331 still-missing proteins in  
terms of asessing their profiles n a rather automatic way and in  
inluding them in my annotations without going deep into manual gene  
curation?
Many thnks,
Anastasia
>
> Let me just restate what you've said so that I can be sure that I am  
> correct about what you've already done.  You have run Maker with  
> SNAP, Genemark and Augustus using EST from a closely related species  
> (passed to altest) and protein evidence from other fungi.  You are  
> missing about 1,000 genes compared to the species that provided the  
> EST alignments.  You say their is good evidence that these genes  
> exist from the alignments and I assume by this that you mean the EST/ 
> protein alignments that Maker produced.
>
> 1) Is the closely related fungus annotated and if so have you  
> included it's proteins in the evidence set that you provided to  
> Maker.  If you haven't provided these proteins as evidence to maker  
> then you should do this.  You can re-run maker passing your original  
> models back through like this:
>
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=1
> other_pass=1
>
> #-----Protein Homology Evidence (for best results provide a file for  
> at least one)
> protein=proteins_from_closely_related.fasta
> ## OR it sounds like you've already aligned these with exonerate?
> protein_gff=proteins_from_closely_related_already_aligned.gff
>
> 2) If you've already included those closely related species proteins  
> but still didn't get the 1,000 genes, then take your  
> nonoverlaping_abinits.fasta and blast them directly against your  
> closely related proteins.  Presumably they don't hit too well  
> because if they did they should have been promoted to predictions by  
> Maker the first time, but here you can decide yourself what  
> thresholds to allow to keep the abinit predictions that hit the  
> closely related species proteins.  If you filter you blast hits the  
> way you want and keep the names of the abinit predictions that pass  
> your filter, then use the script Carson attached it it will generate  
> a abinit precidtion GFF file with only the predictions you  
> selected.  You can then pass those predictions back to Maker and  
> force it to keep them and Maker will turn them from predictions  
> (match/match_part) into gene models.
>
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=0
> other_pass=1
>
> #-----Gene Prediction
> snaphmm=
> gmhmm=
> augustus_species=
> fgenesh_par_file=
> pred_gff=ab_init_predictions_rescued_by_blast.gff
>
> keep_preds=1
>
> Barry
>
>>> Thanks,
>>> Carson
>>>
>>> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
>>> Date: Wed, 25 Apr 2012 11:09:36 +0200
>>> To: <maker-devel at yandell-lab.org>
>>> Subject: [maker-devel] Use pass-through system to add missing genes
>>>
>>> Hi,
>>> I  have a set of predicted proteins from the genome of a fungus  
>>> annotated by MAKER  using EST data from a closely related species  
>>> and 3 ab initio predictors  (snap iterativelly trained 3 times,  
>>> genemark trained directly on the assembly and augustus with a  
>>> model from a less closely related species), along with a set of  
>>> fungal proteins. I am missing ~ 1000 proteins when I compare to  
>>> the species i used EST data from, and there is good evidence from  
>>> alignments that these genes exist. The question is how to proceed  
>>> from Blast hits to actual gene models here. The idea would be to  
>>> add these genes to the existing dataset, rather than reannotate  
>>> the genome. I believe that reannotating it without any further  
>>> evidence such as RNA-seq from the species itself would not change  
>>> much,and i d rather stick with actual predictions that i trust and  
>>> have used in subsequent analyses. The 1000 genes I can accept to  
>>> annotate with a less stringent and reliable way than MAKER, I just  
>>> want to add them so that the difference in gene count gets  
>>> corrected.
>>> I was reading the MAKER 2 paper and i was wondering if I can use  
>>> the legacy annotations scheme to do it, by providing GFF3 of the  
>>> alignments between the two species in the regions where genes were  
>>> missed, but as i said, I would not like to reannotate the whole  
>>> genome, and running MAKER2 might cause slight changes that i d  
>>> like to avoid. Is this possible? First, is it possible to provide  
>>> a Gff3 file of specific locations and not the entire genome  
>>> alignment? (I guess so..) Second, how can I tag the existing  
>>> annotations as 'not to be changed' or alternatively, tag the new  
>>> models only? How should I run maker2, with which predictors on and  
>>> which off?
>>> Thanks,
>>> Anastasia
>>>
>>> Anastasia Gioti
>>> Post-doctoral Researcher
>>>
>>> anastasia.gioti at scilifelab.se
>>> anastasia.gioti at ebc.uu.se
>>>
>>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>>>
>>>
>>>
>>> _______________________________________________ maker-devel  
>>> mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> <gff3_select>
>>
>> Anastasia Gioti
>> Post-doctoral Researcher
>>
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/ 
>> Gioti_Anastasia/
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell- 
> lab.org

Anastasia (Natassa) Gioti
Post-Doc Researcher
Evolutionary Biology Department Uppsala University -Science for Life  
lab, Karolinska Institute Stockholm
anastasia.gioti at ebc.uu.se
anastasia.gioti at scilifelab.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/










From yogeshp08 at gmail.com  Tue May 15 10:07:57 2012
From: yogeshp08 at gmail.com (Yogesh)
Date: Tue, 15 May 2012 11:07:57 -0500
Subject: [maker-devel] tblastn Cleanup?
Message-ID: <4478F0B20ED84A85B3C4FE4154F8FAD1@gmail.com>

Hello,

I have a few tblastn alignments with a lot of low quality hits. I have to clean that up. Can you please suggest how Maker pipeline does it? Also can I run it directly on my data without having to go through the whole pipeline?

Thanks,

-Yogesh
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From carsonhh at gmail.com  Fri May 18 08:22:50 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 18 May 2012 10:22:50 -0400
Subject: [maker-devel] tblastn Cleanup?
In-Reply-To: <4478F0B20ED84A85B3C4FE4154F8FAD1@gmail.com>
Message-ID: <CBDBD0A5.C8CD%carsonhh@gmail.com>

There are several things.  I set several filtering options directly on the
BLAST command line.  These are things like maximum intron length, an e-value
filter, and simple repeat filtering (called dust filter in NCBI blast and
seg filter in WUBLAST).

I also run repeat masker over the genome first.  This allows simple and
complex repeats to be removed before running BLAST (otherwise you get many
false alignments).

Last I filter the results based on percent coverage of the hit to the
original database sequence and percent identity.  I think you can set
percent identity as a flag in BLAST, but the percent coverage filter is
being calculated by MAKER, so to do this outside of MAKER would require that
you write your own filtering script to compare the length of the alignment
to the length of the sequence in the database.

I also have an HSP depth overlap filter.  This removes weird low complexity
hits that escape repeatmasking.  They show up as multiple HSPs overlapping
multiple times in the same region (usually very high numbers like 90 HSPs
all 100 bp long in the same region).  I calculate the number of base pairs
in the alignment on the hit then divide by the number of base pairs in the
query alignment.  If it's greater than 3, I throw the hit out.

Thanks,
Carson



From:  Yogesh <yogeshp08 at gmail.com>
Date:  Tuesday, 15 May, 2012 12:07 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] tblastn Cleanup?

 
Hello,

I have a few tblastn alignments with a lot of low quality hits. I have to
clean that up. Can you please suggest how Maker pipeline does it? Also can I
run it directly on my data without having to go through the whole pipeline?

Thanks,

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

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From smg283 at gmail.com  Tue May 22 00:42:51 2012
From: smg283 at gmail.com (Scott Geib)
Date: Mon, 21 May 2012 20:42:51 -1000
Subject: [maker-devel] can't call method strand on an undefined value ERROR:
 Failed while flattening protein clusters
Message-ID: <CAH221bv8rM7w+yOg6AgW9Y9tLHLvivWgGjZFs4e4QLAyuW4pGA@mail.gmail.com>

Hi,
Using maker 2.24, I am getting the following error (see below) in
protein2genome widget.  I also get the same error with est2genome.  This
happens with my own data (testing on a single scaffold), but not with the
test data supplied with maker (dpp files in data folder).
Scott


Widget::exonerate::protein2genome:
/data0/opt/AlignmentSoftware/exonerate/exonerate-2.2.0-x86_64/bin/exonerate
-q
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/UniRef90_UPI000194D3FC.for.1588546-1589203.9.fasta
-t
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.1588546-1589203.9.fasta
-Q protein -T dna -m protein2genome --softmasktarget  --percent 20
--showcigar  >
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.1588546-1589203.UniRef90_UPI000194D3FC.p_exonerate.9
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 23
 ...processing 1 of 23
 ...processing 2 of 23
 ...processing 3 of 23
 ...processing 4 of 23
 ...processing 5 of 23
 ...processing 6 of 23
 ...processing 7 of 23
 ...processing 8 of 23
 ...processing 9 of 23
 ...processing 10 of 23
 ...processing 11 of 23
 ...processing 12 of 23
 ...processing 13 of 23
 ...processing 14 of 23
 ...processing 15 of 23
 ...processing 16 of 23
 ...processing 17 of 23
 ...processing 18 of 23
 ...processing 19 of 23
 ...processing 20 of 23
 ...processing 21 of 23
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 20
 ...processing 1 of 20
 ...processing 2 of 20
 ...processing 3 of 20
 ...processing 4 of 20
 ...processing 5 of 20
 ...processing 6 of 20
 ...processing 7 of 20
 ...processing 8 of 20
 ...processing 9 of 20
 ...processing 10 of 20
 ...processing 11 of 20
 ...processing 12 of 20
 ...processing 13 of 20
 ...processing 14 of 20
 ...processing 15 of 20
 ...processing 16 of 20
 ...processing 17 of 20
 ...processing 18 of 20
total clusters:2 now processing 0
Can't call method "strand" on an undefined valueERROR: Failed while
flattening protein clusters
ERROR: Chunk failed at level:11, tier_type:2
FAILED CONTIG:scaffold00001
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From anastasia.gioti at scilifelab.se  Tue May 22 07:14:17 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Tue, 22 May 2012 15:14:17 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
	<03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <19E36E3B-6A82-49D5-B0AC-5E521F3E8999@scilifelab.se>

Hi again,
I hav sent an email a few days ago about this thread, and i am not  
sure if you have received it or you still did not have time to look at  
it. In any case, this email was dealing with the fact that some  
proteins were not retrieved in the abinitio models and how to deal  
with it. What I would like to ask here is a few confirmations on how  
to rerun maker for the proteins that were retrieved in the abinitio  
models. i have looked at the Blast results, and have done a series of  
check-ups, so now I am ready to run MAKER again with a list of models  
that I want to retain.
Regarding the following parameters:

1. Do I  set the genome= to nothing here? i.e quote it out? This is in  
the beginning of the control file
#-----Genome (Required for De-Novo Annotation)
genome=#genome sequence file in fasta format
organism_type= #eukaryotic or prokaryotic. Default is eukaryotic

>
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=0
> other_pass=1
>
> #-----Gene Prediction
2. Do i provide again the snap etc models? I am not sure, because i  
thought MAKER would not run ab initio predictors this time (this is  
why I would also quote out the genome file above, as this is not a de  
novo annotation). but if it will, i will then provide the previous  
models i used, except for snap, for which I will generate a new model   
from the gff3 file of the last run (according to snap documentation).  
Am i correct?
> snaphmm=
> gmhmm=
> augustus_species=
> fgenesh_par_file=
> pred_gff=ab_init_predictions_rescued_by_blast.gff
>
> keep_preds=1

Samely, what do i do with repeatmasking etc?
Thanks in adavance,
Anastasia

>
> Barry
>
>>> Thanks,
>>> Carson
>>>
>>> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
>>> Date: Wed, 25 Apr 2012 11:09:36 +0200
>>> To: <maker-devel at yandell-lab.org>
>>> Subject: [maker-devel] Use pass-through system to add missing genes
>>>
>>> Hi,
>>> I  have a set of predicted proteins from the genome of a fungus  
>>> annotated by MAKER  using EST data from a closely related species  
>>> and 3 ab initio predictors  (snap iterativelly trained 3 times,  
>>> genemark trained directly on the assembly and augustus with a  
>>> model from a less closely related species), along with a set of  
>>> fungal proteins. I am missing ~ 1000 proteins when I compare to  
>>> the species i used EST data from, and there is good evidence from  
>>> alignments that these genes exist. The question is how to proceed  
>>> from Blast hits to actual gene models here. The idea would be to  
>>> add these genes to the existing dataset, rather than reannotate  
>>> the genome. I believe that reannotating it without any further  
>>> evidence such as RNA-seq from the species itself would not change  
>>> much,and i d rather stick with actual predictions that i trust and  
>>> have used in subsequent analyses. The 1000 genes I can accept to  
>>> annotate with a less stringent and reliable way than MAKER, I just  
>>> want to add them so that the difference in gene count gets  
>>> corrected.
>>> I was reading the MAKER 2 paper and i was wondering if I can use  
>>> the legacy annotations scheme to do it, by providing GFF3 of the  
>>> alignments between the two species in the regions where genes were  
>>> missed, but as i said, I would not like to reannotate the whole  
>>> genome, and running MAKER2 might cause slight changes that i d  
>>> like to avoid. Is this possible? First, is it possible to provide  
>>> a Gff3 file of specific locations and not the entire genome  
>>> alignment? (I guess so..) Second, how can I tag the existing  
>>> annotations as 'not to be changed' or alternatively, tag the new  
>>> models only? How should I run maker2, with which predictors on and  
>>> which off?
>>> Thanks,
>>> Anastasia
>>>
>>> Anastasia Gioti
>>> Post-doctoral Researcher
>>>
>>> anastasia.gioti at scilifelab.se
>>> anastasia.gioti at ebc.uu.se
>>>
>>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>>>
>>>
>>>
>>> _______________________________________________ maker-devel  
>>> mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> <gff3_select>
>>
>> Anastasia Gioti
>> Post-doctoral Researcher
>>
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/ 
>> Gioti_Anastasia/
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell- 
> lab.org

Anastasia (Natassa) Gioti
Post-Doc Researcher
Evolutionary Biology Department Uppsala University -Science for Life  
lab, Karolinska Institute Stockholm
anastasia.gioti at ebc.uu.se
anastasia.gioti at scilifelab.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/










From anastasia.gioti at scilifelab.se  Wed May 23 03:07:12 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Wed, 23 May 2012 11:07:12 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
	<03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <1B0770A0-6D14-4336-BC3A-DC24619BC3FE@scilifelab.se>

Hi 
and sorry for the multiple postings. I have a list of models rescued by the nonoverlaping_abinits.fasta  fles (against which i  blasted my missing proteins from the closely related species and further filtered out the dubious hits) and a maker gff3 file, but Carson's script gff3_select won't work, and the reason is that these abinitio models were not promoted into the maker gff3 file, thus they are not there. I refer to the gff3 file generated by gff3_merge script. Am i missing something?
Thank you, 
Anastasia



> 
>>> If you know which ab initio predictions you want to add (I.e. the ab initio promoting scenario I descibed), you can provide those predictions to the use the pred_gff option and then set keep_preds=1 and they will be maintained even without evidence.  Attached is a script that would make selecting those easier.  It take the MAKER generated GFF3 and a list of predictions to keep (one name per line).  These might be the results of a BLAST analysis for example.  It will then return the GFF3 entries for just those models selected.

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From thomas.hackl at uni-wuerzburg.de  Wed May 23 06:01:55 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Wed, 23 May 2012 14:01:55 +0200
Subject: [maker-devel] missing est2genome annotation
Message-ID: <4FBCD1B3.8000102@uni-wuerzburg.de>

Hi,

I used maker to annotate genomic contigs and among other stuff provided 
transcripts from the transcriptome as est evidence. Blast and exonerate 
work fine and produce valid alignments, the alignment files exist in 
theVoid and look very good. Unfortunatly neither the evidence_0.gff nor 
the final .gff carry the corresponding feature annotations.

Any ideas why?

Regards
Thomas

-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From thomas.hackl at uni-wuerzburg.de  Wed May 23 11:14:27 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Wed, 23 May 2012 19:14:27 +0200
Subject: [maker-devel] missing est2genome annotation
In-Reply-To: <4FBCD1B3.8000102@uni-wuerzburg.de>
References: <4FBCD1B3.8000102@uni-wuerzburg.de>
Message-ID: <4FBD1AF3.8020904@uni-wuerzburg.de>

Hi again,

I did some source code digging and caught the following line burying my 
exonerate alignments. I suspect it does so for a very good reason, 
therefore it would help me a lot if someone could explain to me, what is 
going on there.


/lib/GI.pm  l.1473
next if $e->pAh<  $pcov;


Regards
Thomas


Am 23.05.2012 14:01, schrieb Thomas Hackl:
> Hi,
>
> I used maker to annotate genomic contigs and among other stuff 
> provided transcripts from the transcriptome as est evidence. Blast and 
> exonerate work fine and produce valid alignments, the alignment files 
> exist in theVoid and look very good. Unfortunatly neither the 
> evidence_0.gff nor the final .gff carry the corresponding feature 
> annotations.
>
> Any ideas why?
>
> Regards
> Thomas
>


-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 13:30:09 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 12:30:09 -0700
Subject: [maker-devel] Merging gene predictions....
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>

Hi Carson and others,
I am wondering if I can use Maker to merge gene predictions from three gff files. One of the algorithm is 'augustus' which of course i can use it inside Maker. Other two are not part of Maker.

But, in case if I want to pass only the GFFs to Maker and ask it to merge the annotations (when overlap) and pick only annotation that are predicted in 2 out of 3 gffs. Is it possible? I prefer this approach, as we need to run a blast based validation step on predicted features before even try to merge them. Thats another reason why we dont prefer to use the augustus inside maker. 

Thanks,
Gowthaman


From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 15:02:55 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 14:02:55 -0700
Subject: [maker-devel] Merging gene predictions....
In-Reply-To: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>
References: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D8@mail02.sbri.org>

Can i use the following approach Carson?

This is your reply to one of the earlier question:

I've attached a made from scratch drop-in replacement that you can use to do what the old script would have done.  In the current release of MAKER, instead of the gff3_preds2models script users can just give MAKER  a set of predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then leave all other options blank).  The predictions given will the be converted into gene models.

Thanks,
Carson



________________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] On Behalf Of Gowthaman Ramasamy [gowthaman.ramasamy at seattlebiomed.org]
Sent: Thursday, May 24, 2012 12:30 PM
To: Carson Holt; maker-devel at yandell-lab.org
Subject: [maker-devel] Merging gene predictions....

Hi Carson and others,
I am wondering if I can use Maker to merge gene predictions from three gff files. One of the algorithm is 'augustus' which of course i can use it inside Maker. Other two are not part of Maker.

But, in case if I want to pass only the GFFs to Maker and ask it to merge the annotations (when overlap) and pick only annotation that are predicted in 2 out of 3 gffs. Is it possible? I prefer this approach, as we need to run a blast based validation step on predicted features before even try to merge them. Thats another reason why we dont prefer to use the augustus inside maker.

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



From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 15:21:30 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 14:21:30 -0700
Subject: [maker-devel] Merging gene predictions....
In-Reply-To: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D8@mail02.sbri.org>
References: <89080953C3D300419AACB6E63A7EEFBA5C8409F8D6@mail02.sbri.org>,
	<89080953C3D300419AACB6E63A7EEFBA5C8409F8D8@mail02.sbri.org>
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8DA@mail02.sbri.org>

Hi,
I am trying to install MAKER in centOS. I was able to install all the perl deps. and external programs. Perl Build.pl and ./Build Install went with out errors/warnings. I did not enable MPI though.

But, when i start Maker it returs "segmentation fault". 

I have no clue whats going wrong....or where to check for error logs? 

Any help would be appreciated,
Thanks,
gowthaman
_________


From gowthaman.ramasamy at seattlebiomed.org  Thu May 24 15:22:16 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Thu, 24 May 2012 14:22:16 -0700
Subject: [maker-devel] MAKER installation problem
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8DB@mail02.sbri.org>

Hi,
I am trying to install MAKER in centOS. I was able to install all the perl deps. and external programs. Perl Build.pl and ./Build Install went with out errors/warnings. I did not enable MPI though.

But, when i start Maker it returs "segmentation fault". 

I have no clue whats going wrong....or where to check for error logs? 

Any help would be appreciated,
Thanks,
gowthaman
_________
________________________________________



From bob_freeman at hms.harvard.edu  Fri May 25 10:23:22 2012
From: bob_freeman at hms.harvard.edu (Bob Freeman)
Date: Fri, 25 May 2012 12:23:22 -0400
Subject: [maker-devel] Alternate translation table?
Message-ID: <454CA235-0DB6-451F-97C4-83D32E2E805A@hms.harvard.edu>

Hello all!

Unusual question here: I am running MAKER on a ciliate that uses a non-standard translation table for its translation products. I haven't found an option in the control files that I can change for the for translation of the predicted transcripts. How or where can I go about this?

Tx,
Bob

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
	-- Karen Walker, from Will and Grace





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From carsonhh at gmail.com  Mon May 28 06:43:34 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 08:43:34 -0400
Subject: [maker-devel] Alternate translation table?
In-Reply-To: <454CA235-0DB6-451F-97C4-83D32E2E805A@hms.harvard.edu>
Message-ID: <CBE8E7EF.CAF3%carsonhh@gmail.com>

The alternate translation table is not currently an option.  It's one of
those things that needs to be implemented, but has not been yet.  It's also
not supported by many of the eukaryotic gene predictors MAKER uses.

I could probably get something implemented for you to test in two to three
weeks though (there are a lot of places where the translation table comes
into play).  Let me know.

--Carson



From:  Bob Freeman <bob_freeman at hms.harvard.edu>
Date:  Friday, 25 May, 2012 12:23 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Alternate translation table?

Hello all!

Unusual question here: I am running MAKER on a ciliate that uses a
non-standard translation table for its translation products. I haven't found
an option in the control files that I can change for the for translation of
the predicted transcripts. How or where can I go about this?

Tx,
Bob

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
-- Karen Walker, from Will and Grace





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

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From carsonhh at gmail.com  Mon May 28 07:38:25 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 09:38:25 -0400
Subject: [maker-devel] missing est2genome annotation
In-Reply-To: <4FBD1AF3.8020904@uni-wuerzburg.de>
Message-ID: <CBE8F75D.CB57%carsonhh@gmail.com>

Sorry for the slow reply.  I'm just getting back after traveling.

That's a percent coverage flag.  You can set a percent coverage threshold
in the maker_bopts.ctl file.  Partial high scoring alignments can be
common.  If you only filter by expect score, you would be surprised to see
how many ugly and confusing all the alignments become.

Thanks,
Carson

On 12-05-23 1:14 PM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi again,
>
>I did some source code digging and caught the following line burying my
>exonerate alignments. I suspect it does so for a very good reason,
>therefore it would help me a lot if someone could explain to me, what is
>going on there.
>
>
>/lib/GI.pm  l.1473
>next if $e->pAh<  $pcov;
>
>
>Regards
>Thomas
>
>
>Am 23.05.2012 14:01, schrieb Thomas Hackl:
>> Hi,
>>
>> I used maker to annotate genomic contigs and among other stuff
>> provided transcripts from the transcriptome as est evidence. Blast and
>> exonerate work fine and produce valid alignments, the alignment files
>> exist in theVoid and look very good. Unfortunatly neither the
>> evidence_0.gff nor the final .gff carry the corresponding feature
>> annotations.
>>
>> Any ideas why?
>>
>> Regards
>> Thomas
>>
>
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From seoanezonjic at hotmail.com  Tue May 22 06:55:12 2012
From: seoanezonjic at hotmail.com (p sz)
Date: Tue, 22 May 2012 12:55:12 +0000
Subject: [maker-devel] ipr_update_gff ERROR
Message-ID: <COL119-W282F1F1F211028B1F661C5C7020@phx.gbl>


First, thanks by help me on the lprevious error that I submitted.
I'm still working in the same project and I get a new error. I try interproscan with this commandline:

iprscan_wrap -i parsed_input.all.maker.proteins.fasta -email seoanezonjic at hotmail.com  -format raw

parsed_input.all.maker.proteins.fasta was generated with the tool fasta_merge. I use the output (attached in this email) and a gff file (generated by a normal run of maker, attached in this email) with the ipr_update_gff script of this way:

ipr_update_gff BAC12_Clone_Pt314B2_Lib_Pt_7Ba__organism_Pinus_taeda__0.gff sc_interpro.sh.o109053

And i get this error:
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 179, <$IN> line 15.
Use of uninitialized value $gene_id in hash element at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 181, <$IN> line 15.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 18.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 18.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 19.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 19.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 48.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 48.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 49.
Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 49.

The gff file seems updated but i don't know if it works fine or is corrupt
Thanks in advance
 		 	   		  
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From larriba.ed at gmail.com  Fri May 25 10:01:41 2012
From: larriba.ed at gmail.com (Eduardo Larriba)
Date: Fri, 25 May 2012 18:01:41 +0200
Subject: [maker-devel] Consensus gene models
Message-ID: <CADwrZ2XdcZu080yHt7=CreOWbpt791NC8ScB5WVW=NmvN4=Jgw@mail.gmail.com>

Hi Carson and people,
I am working on structural annotation of a filamentous fungus, of which
there is little evidence as EST or Protein. For generate consensus gene  based
on limited evidences to me I used  Marker.
For this I created the files GeneMark prediction-is and SNAP.
I run maker using the EST of my organims (85), along with 5700 EST of the
closed organims. I have made ??predictions with Augustus, and SNAP GeneMark,
with the training files for my organims, in Maker pipeline. Everything works
fine.
My problem is that when I get the consensus sequences of all my contigs,
fasta_merge script (included in Maker), I get different list for each
predictor, as well as when I try to get the gff of all.
They could tell me how I can use Maker consensus for a list of genes? Or I
have to do it manually? There is the possibility that Maker evaluates the
accuracy of each prediction and confirm, so just get a list of the different
predictions?

Thank you very much.


-- 
Eduardo Larriba Tornel
Universidad de Alicante.
Lab. Fitopatolog?a
Dept. Ciencias del Mar y Biolog?a Aplicada
Pabell?n 13.
San Vicente del Raspeig
Tel. 96 590 3400 ext 3280
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From carsonhh at gmail.com  Mon May 28 08:14:22 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 10:14:22 -0400
Subject: [maker-devel] Consensus gene models
In-Reply-To: <CADwrZ2XdcZu080yHt7=CreOWbpt791NC8ScB5WVW=NmvN4=Jgw@mail.gmail.com>
Message-ID: <CBE8FECE.CBA5%carsonhh@gmail.com>

The consensus list is in the maker.proteins.fasta and
maker.transcripts.fasta file.  The predictor specific lists are just for
reference purposes (incase you want to see what the other predictors
produced on their own, i.e. without MAKER's intervention).  The
non-overlapping.fasta file in the same directory will contain consensus
entries for models that were not supported by any evidence and don't overlap
any gene models in the  maker.transcripts.fasta (think of these as the maybe
gene and the maker.transcripts.fasta as the very likely genes).  You can set
keep_preds=1 if you just want MAKER to keep everything with or without
support and just produce consensus (probably ok on a fungus, but I wouldn't
recommend it on other eukayotes because false positive rates will be very
high).

Thanks,
Carson



From:  Eduardo Larriba <larriba.ed at gmail.com>
Date:  Friday, 25 May, 2012 12:01 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Consensus gene models

Hi Carson and people,
I am working on structural annotation of a filamentous fungus, of which
there is little evidence as EST or Protein. For generate consensus gene
based on limited evidences to me I used  Marker.
 For this I created the files GeneMark prediction-is and SNAP.
 I run maker using the EST of my organims (85), along with 5700 EST of the
closed organims. I have made ??predictions with Augustus, and SNAP
GeneMark, with the training files for my organims, in Maker pipeline.
Everything works fine.
 My problem is that when I get the consensus sequences of all my contigs,
fasta_merge script (included in Maker), I get different list for each
predictor, as well as when I try to get the gff of all.
 They could tell me how I can use Maker consensus for a list of genes? Or I
have to do it manually? There is the possibility that Maker evaluates the
accuracy of each prediction and confirm, so just get a list of the different
predictions?

 Thank you very much.


-- 
Eduardo Larriba Tornel
Universidad de Alicante.
Lab. Fitopatolog?a
Dept. Ciencias del Mar y Biolog?a Aplicada
Pabell?n 13. 
San Vicente del Raspeig
Tel. 96 590 3400 ext 3280

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

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From carsonhh at gmail.com  Mon May 28 08:18:26 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 28 May 2012 10:18:26 -0400
Subject: [maker-devel] ipr_update_gff ERROR
In-Reply-To: <COL119-W282F1F1F211028B1F661C5C7020@phx.gbl>
Message-ID: <CBE90090.CBB6%carsonhh@gmail.com>

This error would happen if some results exist in the iprscan output, but
don't match gene entries in the GFF3 file.  If I could see the original
files I can tell you which ones.  This can happen if you combine results
from the non-overlapping.fasta files with the maker.proteins.fasta files for
example.  Models in the non-overlapping.fasta file are not genes in the GFF3
(they are match/match_part enties), so errors happen.

Thanks,
Carson

From:  p sz <seoanezonjic at hotmail.com>
Date:  Tuesday, 22 May, 2012 8:55 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] ipr_update_gff ERROR

First, thanks by help me on the lprevious error that I submitted.
I'm still working in the same project and I get a new error. I try
interproscan with this commandline:

iprscan_wrap -i parsed_input.all.maker.proteins.fasta -email
seoanezonjic at hotmail.com  -format raw

parsed_input.all.maker.proteins.fasta was generated with the tool
fasta_merge. I use the output (attached in this email) and a gff file
(generated by a normal run of maker, attached in this email) with the
ipr_update_gff script of this way:

ipr_update_gff BAC12_Clone_Pt314B2_Lib_Pt_7Ba__organism_Pinus_taeda__0.gff
sc_interpro.sh.o109053

And i get this error:
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 15.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 15.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 18.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 18.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 19.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 19.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 48.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 48.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 49.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 49.

The gff file seems updated but i don't know if it works fine or is corrupt
Thanks in advance
       
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From carsonhh at gmail.com  Tue May 29 06:37:55 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 29 May 2012 08:37:55 -0400
Subject: [maker-devel] can't call method strand on an undefined value
 ERROR: Failed while flattening protein clusters
In-Reply-To: <CAH221bv8rM7w+yOg6AgW9Y9tLHLvivWgGjZFs4e4QLAyuW4pGA@mail.gmail.com>
Message-ID: <CBEA3AC6.CD62%carsonhh@gmail.com>

Use this command to check out the latest unreleased test version, and lt me
know if you still get the error.

Command -->  svn co svn://malachite.genetics.utah.edu/maker/trunk maker

User: yandell_guest
Password: y at ndell_Gu3st

Thanks,
Carson





From:  Scott Geib <smg283 at gmail.com>
Date:  Tuesday, 22 May, 2012 2:42 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] can't call method strand on an undefined value
ERROR: Failed while flattening protein clusters

Hi, 
Using maker 2.24, I am getting the following error (see below) in
protein2genome widget.  I also get the same error with est2genome.  This
happens with my own data (testing on a single scaffold), but not with the
test data supplied with maker (dpp files in data folder).
Scott


Widget::exonerate::protein2genome:
/data0/opt/AlignmentSoftware/exonerate/exonerate-2.2.0-x86_64/bin/exonerate
-q 
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/UniRef90_UPI00019
4D3FC.for.1588546-1589203.9.fasta -t
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.158
8546-1589203.9.fasta -Q protein -T dna -m protein2genome --softmasktarget
--percent 20 --showcigar  >
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.158
8546-1589203.UniRef90_UPI000194D3FC.p_exonerate.9
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 23
 ...processing 1 of 23
 ...processing 2 of 23
 ...processing 3 of 23
 ...processing 4 of 23
 ...processing 5 of 23
 ...processing 6 of 23
 ...processing 7 of 23
 ...processing 8 of 23
 ...processing 9 of 23
 ...processing 10 of 23
 ...processing 11 of 23
 ...processing 12 of 23
 ...processing 13 of 23
 ...processing 14 of 23
 ...processing 15 of 23
 ...processing 16 of 23
 ...processing 17 of 23
 ...processing 18 of 23
 ...processing 19 of 23
 ...processing 20 of 23
 ...processing 21 of 23
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 20
 ...processing 1 of 20
 ...processing 2 of 20
 ...processing 3 of 20
 ...processing 4 of 20
 ...processing 5 of 20
 ...processing 6 of 20
 ...processing 7 of 20
 ...processing 8 of 20
 ...processing 9 of 20
 ...processing 10 of 20
 ...processing 11 of 20
 ...processing 12 of 20
 ...processing 13 of 20
 ...processing 14 of 20
 ...processing 15 of 20
 ...processing 16 of 20
 ...processing 17 of 20
 ...processing 18 of 20
total clusters:2 now processing 0
Can't call method "strand" on an undefined valueERROR: Failed while
flattening protein clusters
ERROR: Chunk failed at level:11, tier_type:2
FAILED CONTIG:scaffold00001

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From bob_freeman at hms.harvard.edu  Tue May 29 10:30:23 2012
From: bob_freeman at hms.harvard.edu (Bob Freeman)
Date: Tue, 29 May 2012 12:30:23 -0400
Subject: [maker-devel] Alternate translation table?
In-Reply-To: <CBE8E7EF.CAF3%carsonhh@gmail.com>
References: <CBE8E7EF.CAF3%carsonhh@gmail.com>
Message-ID: <B198DB2E-A0CC-4A01-843D-59F470E97DC9@hms.harvard.edu>

Thanks, Carson, for the update on this. No need to implement something. I'll keep it simple and translate the collected transcripts using an appropriate translation table.

-Bob

On May 28, 2012, at 8:43 AM, Carson Holt wrote:

> The alternate translation table is not currently an option.  It's one of those things that needs to be implemented, but has not been yet.  It's also not supported by many of the eukaryotic gene predictors MAKER uses.
> 
> I could probably get something implemented for you to test in two to three weeks though (there are a lot of places where the translation table comes into play).  Let me know.
> 
> --Carson
> 
> 
> 
> From: Bob Freeman <bob_freeman at hms.harvard.edu>
> Date: Friday, 25 May, 2012 12:23 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Alternate translation table?
> 
> Hello all!
> 
> Unusual question here: I am running MAKER on a ciliate that uses a non-standard translation table for its translation products. I haven't found an option in the control files that I can change for the for translation of the predicted transcripts. How or where can I go about this?
> 
> Tx,
> Bob
> 
> 
> _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
	-- Karen Walker, from Will and Grace





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From gowthaman.ramasamy at seattlebiomed.org  Tue May 29 15:54:33 2012
From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy)
Date: Tue, 29 May 2012 14:54:33 -0700
Subject: [maker-devel] Can maker select a gene model based on #algoritham
	predicted it
Message-ID: <89080953C3D300419AACB6E63A7EEFBA5C8409F8EB@mail02.sbri.org>

Hi Carson,
Thanks for all the help during the long weekend, in spite of that long drive. I am still trying to imagine that.

I now have maker to consider our own prediction via pred_gff, and use augustus and gene mark (with our training model). And i was able to use altest and protein evidences. Maker happily picks one gene model when there is a overlap between three different predictions. But, when I look at the gff, it seems like it picks a gene model only when there is an est/protein evidence. It leaves out some genes even though, they are predicted by all three algorithms. Of course, keep_pred=1 helps to keep all the models. This kind of leads to over prediction. 

But, I am looking for something in between. And would like to know if that is possible?
1) Pick a gene model if it has an evidence from (est/prot etc...) irrespective of how many algorithms predicted it
2) In the absence of extrinsic evidence (est/prot etc), pick a gene model if that is predicted by at least two algorithms.

Or even simpler:
I have ab-initio predictions from three algorithms, Can I output, those genes that is supported by at least two of them. I care less about exactness of gene boundaries.

Thanks,
Gowthaman

PS: With my recent attempts, i learned couple things about maker/other associated tools that is not documented in gmod-maker wiki. Is it possible/ok if I add contents to it. I am okay with running it by you before making it public.


From carsonhh at gmail.com  Wed May 30 06:54:32 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 30 May 2012 08:54:32 -0400
Subject: [maker-devel] Can maker select a gene model based on
	#algoritham predicted it
In-Reply-To: <89080953C3D300419AACB6E63A7EEFBA5C8409F8EB@mail02.sbri.org>
Message-ID: <CBEB8E25.D097%carsonhh@gmail.com>

It's not an option in exactly the way you are specifying, but there is
something I usually do for annotation that works well.  I run interproscan
or rpsblast on the non_overlapping.proteins.fasta file and select just
those non-overlapping models that have a recognizable protein domain (just
searching the pfam doamin space is more than sufficient).  Then I provide
the selected results to model_gff, and provide the previous maker results
to the maker_gff option with (all reannotation pass options set to 1 and
all analysis options turned off).  This adds models with at least
recognizable domains (as even multiple gene predictors can overpredict in
a similar way).

Attached is a script to help select predictions and upgrade them to models
in GFF3 format.  If you have question let me know.

Thanks,
Carson



On 12-05-29 5:54 PM, "Gowthaman Ramasamy"
<gowthaman.ramasamy at seattlebiomed.org> wrote:

>Hi Carson,
>Thanks for all the help during the long weekend, in spite of that long
>drive. I am still trying to imagine that.
>
>I now have maker to consider our own prediction via pred_gff, and use
>augustus and gene mark (with our training model). And i was able to use
>altest and protein evidences. Maker happily picks one gene model when
>there is a overlap between three different predictions. But, when I look
>at the gff, it seems like it picks a gene model only when there is an
>est/protein evidence. It leaves out some genes even though, they are
>predicted by all three algorithms. Of course, keep_pred=1 helps to keep
>all the models. This kind of leads to over prediction.
>
>But, I am looking for something in between. And would like to know if
>that is possible?
>1) Pick a gene model if it has an evidence from (est/prot etc...)
>irrespective of how many algorithms predicted it
>2) In the absence of extrinsic evidence (est/prot etc), pick a gene model
>if that is predicted by at least two algorithms.
>
>Or even simpler:
>I have ab-initio predictions from three algorithms, Can I output, those
>genes that is supported by at least two of them. I care less about
>exactness of gene boundaries.
>
>Thanks,
>Gowthaman
>
>PS: With my recent attempts, i learned couple things about maker/other
>associated tools that is not documented in gmod-maker wiki. Is it
>possible/ok if I add contents to it. I am okay with running it by you
>before making it public.

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From mikael.durling at slu.se  Thu May 31 06:25:31 2012
From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=)
Date: Thu, 31 May 2012 14:25:31 +0200
Subject: [maker-devel] maker leaving large numbers of defunct zombies
Message-ID: <FBA1F582-5EF0-4D7A-8276-A86DAD5C4C89@slu.se>

Hello,

I've been working lately to set up maker for annotation work on a few fungal genomes. I've got mpi maker up and running now, however, I notice that maker is leaving a lot of <defunct> perl processes behind. This happens to the extent that the process table on the system gets filled up after a few hours run time. Right now the process tree after three hours running looks like this:

    |-sge_execd-+-sge_shepherd---bash---mpirun-+-maker-+-maker
     |           |                              |       `-perl
     |           |                              |-maker-+-maker
     |           |                              |       |-maker---1371*[perl]
     |           |                              |       `-perl
     |           |                              |-maker-+-maker
     |           |                              |       |-maker---1348*[perl]
     |           |                              |       `-perl
     |           |                              |-maker-+-maker
     |           |                              |       |-maker---1384*[perl]
     |           |                              |       `-perl

...and so on for all mpi processes, except for the controlling processes. 

What perl programs is maker calling, that might end up as zombies? I've had a brief look at the source to no avail, but would be happy to dig further with some pointers for where to look.

This is run with the 2.25-beta from the web page, perl 5.16.0 and openmpi 1.4.5. 

Thanks,
Mikael










-------------------------------------
Mikael Brandstr?m Durling, PhD
Assistant Professor

Sveriges lantbruksuniversitet
Swedish University of Agricultural Sciences

Uppsala BioCenter
Dept of Forest Mycology and Plant Pathology
Box 7026, 75007 Uppsala
Visiting address: Almas All? 5
Telefon: 018-671512
mikael.durling at slu.se, www.slu.se/mykopat





From mikael.durling at slu.se  Thu May 31 06:34:30 2012
From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=)
Date: Thu, 31 May 2012 14:34:30 +0200
Subject: [maker-devel] Using GDBM_File instead of DB_File
Message-ID: <B535F29B-D593-44D7-B0C4-D84462957EFB@slu.se>

Hello,

I've been struggling for a few days to get maker up and running with MPI on a debian squeeze system. Compiling a new perl 5.16 exclusively for maker I wound down to that the segfaults came from DB_File. Even by recomiling and updating that module, nothing worked. After checking for dependencies on DB_File in maker, I concluded that the only dependency was through the GI::localize_file, which expects the FastaDB to be instantiated with DB_File. However, FastaDB can run on GDBM_File too. I patched the calls to GI::localize_file in maker to handle the .pag/.dir extensions used by GDBM (below). With this patch applied maker is running for me, even when I have deleted the DB_File module from the perl path and made sure that GDBM_File is installed. My basic question is if there is any other dependency for DB_File which I have missed which may break things?

cheers,
Mikael

--- maker.orig	2012-03-30 15:48:05.000000000 +0200
+++ maker	2012-05-31 10:35:30.253022648 +0200
@@ -512,7 +515,12 @@
 }
 if($size > 1){
     carp "Calling GI::localize_file" if($main::debug);
-    GI::localize_file("$gdbfile.index");
+    if( -f "$gdbfile.index.dir" ){
+	GI::localize_file("$gdbfile.index.dir");
+	GI::localize_file("$gdbfile.index.pag");
+    }else{
+    	GI::localize_file("$gdbfile.index");
+    }
     carp "Calling GI::localize_file" if($main::debug);
     $gdbfile = GI::localize_file($gdbfile);
 }




From carsonhh at gmail.com  Thu May 31 07:04:58 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 31 May 2012 09:04:58 -0400
Subject: [maker-devel] Using GDBM_File instead of DB_File
In-Reply-To: <B535F29B-D593-44D7-B0C4-D84462957EFB@slu.se>
Message-ID: <CBECE3F7.D209%carsonhh@gmail.com>

DB_File is being called by Bio::DB::Fasta.  I can check the object
returned when using GDBM_File instead to see if the index file names are
contained on the object, as I'm just assuming an extension of '.index'.
I'll look around to see if the extension name is assumed anywhere else.

Thanks,
Carson


On 12-05-31 8:34 AM, "Mikael Brandstr?m Durling" <mikael.durling at slu.se>
wrote:

>Hello,
>
>I've been struggling for a few days to get maker up and running with MPI
>on a debian squeeze system. Compiling a new perl 5.16 exclusively for
>maker I wound down to that the segfaults came from DB_File. Even by
>recomiling and updating that module, nothing worked. After checking for
>dependencies on DB_File in maker, I concluded that the only dependency
>was through the GI::localize_file, which expects the FastaDB to be
>instantiated with DB_File. However, FastaDB can run on GDBM_File too. I
>patched the calls to GI::localize_file in maker to handle the .pag/.dir
>extensions used by GDBM (below). With this patch applied maker is running
>for me, even when I have deleted the DB_File module from the perl path
>and made sure that GDBM_File is installed. My basic question is if there
>is any other dependency for DB_File which I have missed which may break
>things?
>
>cheers,
>Mikael
>
>--- maker.orig	2012-03-30 15:48:05.000000000 +0200
>+++ maker	2012-05-31 10:35:30.253022648 +0200
>@@ -512,7 +515,12 @@
> }
> if($size > 1){
>     carp "Calling GI::localize_file" if($main::debug);
>-    GI::localize_file("$gdbfile.index");
>+    if( -f "$gdbfile.index.dir" ){
>+	GI::localize_file("$gdbfile.index.dir");
>+	GI::localize_file("$gdbfile.index.pag");
>+    }else{
>+    	GI::localize_file("$gdbfile.index");
>+    }
>     carp "Calling GI::localize_file" if($main::debug);
>     $gdbfile = GI::localize_file($gdbfile);
> }
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Thu May 31 07:17:20 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 31 May 2012 09:17:20 -0400
Subject: [maker-devel] maker leaving large numbers of defunct zombies
In-Reply-To: <FBA1F582-5EF0-4D7A-8276-A86DAD5C4C89@slu.se>
Message-ID: <CBECE4F4.D210%carsonhh@gmail.com>

MAKER uses IPC::Open3 to open almost all external applications, including
a helper script called every once in a while that helps check file locks
on NFS.

MAKER then calls waitpid to reap the processes, as IPC::Open3 doesn't
auto-reap.  The only time previously I've seen issues with zombie
accumulation was with MPICH2 when it moved from the MPD process manager to
Hydra.  Hydra had certain broken signal handling issues that I had to bug
the MPICH2 developers about and they fixed it.  It is possible that the
issue you are having may be with OpenMPI or with perl 5.16.  I currently
use perl 5.12.  Perl instituted something called safe signals in either
5.6 or 5.8 and there may be some updates in 5.16 where they've been
changing those around again.

I can try installing a copy of 5.16 to test with and OpenMPI to see if I
can replicate the error.

Thanks,
Carson



On 12-05-31 8:25 AM, "Mikael Brandstr?m Durling" <mikael.durling at slu.se>
wrote:

>Hello,
>
>I've been working lately to set up maker for annotation work on a few
>fungal genomes. I've got mpi maker up and running now, however, I notice
>that maker is leaving a lot of <defunct> perl processes behind. This
>happens to the extent that the process table on the system gets filled up
>after a few hours run time. Right now the process tree after three hours
>running looks like this:
>
>    |-sge_execd-+-sge_shepherd---bash---mpirun-+-maker-+-maker
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1371*[perl]
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1348*[perl]
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1384*[perl]
>     |           |                              |       `-perl
>
>...and so on for all mpi processes, except for the controlling processes.
>
>What perl programs is maker calling, that might end up as zombies? I've
>had a brief look at the source to no avail, but would be happy to dig
>further with some pointers for where to look.
>
>This is run with the 2.25-beta from the web page, perl 5.16.0 and openmpi
>1.4.5. 
>
>Thanks,
>Mikael
>
>
>
>
>
>
>
>
>
>
>-------------------------------------
>Mikael Brandstr?m Durling, PhD
>Assistant Professor
>
>Sveriges lantbruksuniversitet
>Swedish University of Agricultural Sciences
>
>Uppsala BioCenter
>Dept of Forest Mycology and Plant Pathology
>Box 7026, 75007 Uppsala
>Visiting address: Almas All? 5
>Telefon: 018-671512
>mikael.durling at slu.se, www.slu.se/mykopat
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From mikael.durling at slu.se  Thu May 31 07:57:06 2012
From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=)
Date: Thu, 31 May 2012 15:57:06 +0200
Subject: [maker-devel] maker leaving large numbers of defunct zombies
In-Reply-To: <CBECE4F4.D210%carsonhh@gmail.com>
References: <CBECE4F4.D210%carsonhh@gmail.com>
Message-ID: <E779EAA8-C2AC-4362-A3C7-E370777E3D5D@slu.se>

I saw the same problem with the latest MPICH2 using hydra too, so it might boil down to perl/openmpi interactions. I didn't see this problem with the debian supplied perl 5.10, but then I had intermittent segfaults with in DB_File and libpthread. Seemed to be some interaction with the LD_PRELOADed libmpi. That requirement for preloading libmpi was easiest solved by compiling openmpi with --disable-dlopen.

Thanks,
Mikael

31 maj 2012 kl. 15:17 skrev Carson Holt:

> MAKER uses IPC::Open3 to open almost all external applications, including
> a helper script called every once in a while that helps check file locks
> on NFS.
> 
> MAKER then calls waitpid to reap the processes, as IPC::Open3 doesn't
> auto-reap.  The only time previously I've seen issues with zombie
> accumulation was with MPICH2 when it moved from the MPD process manager to
> Hydra.  Hydra had certain broken signal handling issues that I had to bug
> the MPICH2 developers about and they fixed it.  It is possible that the
> issue you are having may be with OpenMPI or with perl 5.16.  I currently
> use perl 5.12.  Perl instituted something called safe signals in either
> 5.6 or 5.8 and there may be some updates in 5.16 where they've been
> changing those around again.
> 
> I can try installing a copy of 5.16 to test with and OpenMPI to see if I
> can replicate the error.
> 
> Thanks,
> Carson
> 
> 
> 
> On 12-05-31 8:25 AM, "Mikael Brandstr?m Durling" <mikael.durling at slu.se>
> wrote:
> 
>> Hello,
>> 
>> I've been working lately to set up maker for annotation work on a few
>> fungal genomes. I've got mpi maker up and running now, however, I notice
>> that maker is leaving a lot of <defunct> perl processes behind. This
>> happens to the extent that the process table on the system gets filled up
>> after a few hours run time. Right now the process tree after three hours
>> running looks like this:
>> 
>>   |-sge_execd-+-sge_shepherd---bash---mpirun-+-maker-+-maker
>>    |           |                              |       `-perl
>>    |           |                              |-maker-+-maker
>>    |           |                              |
>> |-maker---1371*[perl]
>>    |           |                              |       `-perl
>>    |           |                              |-maker-+-maker
>>    |           |                              |
>> |-maker---1348*[perl]
>>    |           |                              |       `-perl
>>    |           |                              |-maker-+-maker
>>    |           |                              |
>> |-maker---1384*[perl]
>>    |           |                              |       `-perl
>> 
>> ...and so on for all mpi processes, except for the controlling processes.
>> 
>> What perl programs is maker calling, that might end up as zombies? I've
>> had a brief look at the source to no avail, but would be happy to dig
>> further with some pointers for where to look.
>> 
>> This is run with the 2.25-beta from the web page, perl 5.16.0 and openmpi
>> 1.4.5. 
>> 
>> Thanks,
>> Mikael
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> -------------------------------------
>> Mikael Brandstr?m Durling, PhD
>> Assistant Professor
>> 
>> Sveriges lantbruksuniversitet
>> Swedish University of Agricultural Sciences
>> 
>> Uppsala BioCenter
>> Dept of Forest Mycology and Plant Pathology
>> Box 7026, 75007 Uppsala
>> Visiting address: Almas All? 5
>> Telefon: 018-671512
>> mikael.durling at slu.se, www.slu.se/mykopat
>> 
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
>