From help at gmod.org  Wed Mar 10 10:47:38 2010
From: help at gmod.org (Dave Clements, GMOD Help Desk)
Date: Wed, 10 Mar 2010 09:47:38 -0800
Subject: [maker-devel] [Gmod-help] Genome annotation tools
In-Reply-To: <008501cabfdc$7eab3420$7c019c60$@edu>
References: <002201cabfad$2a5dfad0$7f19f070$@edu>
	<20100309132710830.00000002284@arod004-ml3afw61>
	<A0273CC5-331D-44FD-AD49-6B65F34AA04D@nescent.org>
	<008501cabfdc$7eab3420$7c019c60$@edu>
Message-ID: <71ee57c71003100947k7d6dfbe0y3399ed20a28175a@mail.gmail.com>

Dear Ty,

I've forwarded your query on to the MAKER and Ergatis mailing lists.  The
MAKER team can address your question about functional annotation.  Ergatis
is a workflow management system that is also part of GMOD.  If you have a
compute cluster and other types of pipelines to run then you may want to
look at that as well.  (MAKER can also take advantage of a compute cluster.)

Dave C.

On Tue, Mar 9, 2010 at 3:01 PM, Ty Wang <tywang7 at duke.edu> wrote:

>  Dear Sir:
>
>
>
> How are you? I am a bioinformatician working at Duke Sequencing Core
> facility. I work on a lichen genome annotation project. Lichen has two
> genomes, mycobiont and photobiont. We are looking for tools software for
> automated genome annotation in non-model systems. So far, we are interested
> in two software packages specifically (but open to any suggestion). One of
> them is called MAKER recommended by GMOD. The other one is JGI annotation
> pipeline http://www.jsbi.org/journal/GIW06/GIW06P136.pdf. MARKER is good
> at gene structural annotation. And JGI annotation pipeline provides
> additional functional annotation. I could be wrong. What do you think? This
> is my first time working on a genome annotation projection. I would really
> appreciate if you can give me any suggestion or direct me to the right
> person. Looking forward to your reply. Thanks!
>
>
>
> Ty
>
>
>
>
>
>
>



-- 
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/GMOD_Logo_Program
http://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback
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From carson.holt at genetics.utah.edu  Wed Mar 10 11:43:02 2010
From: carson.holt at genetics.utah.edu (Carson Holt)
Date: Wed, 10 Mar 2010 11:43:02 -0700
Subject: [maker-devel] [Gmod-help] Genome annotation tools
In-Reply-To: <71ee57c71003100947k7d6dfbe0y3399ed20a28175a@mail.gmail.com>
Message-ID: <C7BD3646.17B0%carson.holt@genetics.utah.edu>

Yes, you can use MAKER for the structural annotations, and MAKER is compatible with MPICH2.  MAKER also comes with some accessory scripts that assist in adding functional annotations directly to the GFF3 file using InterProScan.  These accessory scripts add InterPro protein domains and GO function categories to each gene model in the GFF3 file automatically.  There is also a simple accessory script that adds putative overall gene function descriptions based on similarity to UniProt/SwissProt genes.

Thanks,
Carson


On 3/10/10 10:47 AM, "Dave Clements, GMOD Help Desk" <help at gmod.org> wrote:

Dear Ty,

I've forwarded your query on to the MAKER and Ergatis mailing lists.  The MAKER team can address your question about functional annotation.  Ergatis is a workflow management system that is also part of GMOD.  If you have a compute cluster and other types of pipelines to run then you may want to look at that as well.  (MAKER can also take advantage of a compute cluster.)

Dave C.

On Tue, Mar 9, 2010 at 3:01 PM, Ty Wang <tywang7 at duke.edu> wrote:
Dear Sir:

How are you? I am a bioinformatician working at Duke Sequencing Core facility. I work on a lichen genome annotation project. Lichen has two genomes, mycobiont and photobiont. We are looking for tools software for automated genome annotation in non-model systems. So far, we are interested in two software packages specifically (but open to any suggestion). One of them is called MAKER recommended by GMOD. The other one is JGI annotation pipeline http://www.jsbi.org/journal/GIW06/GIW06P136.pdf. MARKER is good at gene structural annotation. And JGI annotation pipeline provides additional functional annotation. I could be wrong. What do you think? This is my first time working on a genome annotation projection. I would really appreciate if you can give me any suggestion or direct me to the right person. Looking forward to your reply. Thanks!

Ty






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From yannick.wurm at unil.ch  Sun Mar 14 12:43:53 2010
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Sun, 14 Mar 2010 19:43:53 +0100
Subject: [maker-devel] maker crash - indexing fasta?
Message-ID: <680060AC-B084-4B33-9D9B-760F566B9572@unil.ch>

Hello,

I'm trying to get maker to work locally.
The test data seems to run correctly.
So then I try running it on my data. 
I have a single 2.8mb scaffold in a fasta file.
I provide a fasta of all ESTs for our organism, and a fasta of uniprot proteins that hit the scaffold. 


The run fails with the following message:
/sfs1/home/frt/ywurm/assemblyValidation/results/2010-03-12/gp9scaffold/maker/Si_gnE.scaffold02061.maker.output/Si_gnE.scaf
fold02061_datastore/Si_gnE.scaffold02061/theVoid.Si_gnE.scaffold02061/Si_gnE.scaffold02061.0.Si_gnE.scaffold02061.Bx.sp_al
l.prots.blastx
deleted:0 hits
cleaning blastx...
 in cluster:shadow cluster...
    i_size:7 j_size:1
 sorting hits in shadow cluster...
... finished.
 i_size:7   current i:0
 i_size:7   current i:1
 i_size:7   current i:2
 i_size:7   current i:3
 i_size:7   current i:4
 i_size:7   current i:5
 i_size:7   current i:6
 in cluster:shadow cluster...
    i_size:0 j_size:0
 sorting hits in shadow cluster...
... finished.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7

WARNING: Cannot find> sp|O00267|SPT5H_HUMAN, trying to re-index the fasta.
stop here:sp|O00267|SPT5H_HUMAN
#----------------------
FATAL: failed!!
#----------------------
ERROR: Fasta index error

ERROR: Failed while doing exonerate of proteins!!

ERROR: Chunk failed at level 14
!!
FAILED CONTIG:Si_gnE.scaffold02061




--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
The contig failed 2 time!!
Maker will not try again!!
The contig will be stored in a fasta file that you can use for debugging.
SeqID: Si_gnE.scaffold02061
Length: 2869475
FASTA: /sfs1/home/frt/ywurm/assemblyValidation/results/2010-03-12/gp9scaffold/maker/Si_gnE.scaffold02061.maker.output/Si_g
nE.scaffold02061_datastore/Si_gnE.scaffold02061/Si_gnE.scaffold02061.died.fasta
#---------------------------------------------------------------------




Maker is now finished!!!
:

I've attached some log files and runinfo in the zip. 
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If any one has a suggestion on how to make things work.... Thanks!!

yannick





--------------------------------------------
          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
   http://www.unil.ch/dee/page28685_fr.html



From carson.holt at genetics.utah.edu  Wed Mar 17 11:48:21 2010
From: carson.holt at genetics.utah.edu (Carson Holt)
Date: Wed, 17 Mar 2010 11:48:21 -0600
Subject: [maker-devel] maker crash - indexing fasta?
In-Reply-To: <680060AC-B084-4B33-9D9B-760F566B9572@unil.ch>
Message-ID: <C7C67205.188C%carson.holt@genetics.utah.edu>

Sorry about the late reply, my mail filters had apparently filtered out this message.  There are two things to check right away.  First make sure you have BioPerl version 1.6 installed.  Indexing errors can occur on version 1.5.  Also rerun your test with the -f option.  The -f option will force MAKER to completely destroy and rebuild old indexes and blast reports before running.  If both of those fail, I can give you pre-release access to MAKER 2.0 which has much more robust indexing of fasta files.

Carson


On 3/14/10 12:43 PM, "Yannick Wurm" <yannick.wurm at unil.ch> wrote:

Hello,

I'm trying to get maker to work locally.
The test data seems to run correctly.
So then I try running it on my data.
I have a single 2.8mb scaffold in a fasta file.
I provide a fasta of all ESTs for our organism, and a fasta of uniprot proteins that hit the scaffold.


The run fails with the following message:
/sfs1/home/frt/ywurm/assemblyValidation/results/2010-03-12/gp9scaffold/maker/Si_gnE.scaffold02061.maker.output/Si_gnE.scaf
fold02061_datastore/Si_gnE.scaffold02061/theVoid.Si_gnE.scaffold02061/Si_gnE.scaffold02061.0.Si_gnE.scaffold02061.Bx.sp_al
l.prots.blastx
deleted:0 hits
cleaning blastx...
 in cluster:shadow cluster...
    i_size:7 j_size:1
 sorting hits in shadow cluster...
... finished.
 i_size:7   current i:0
 i_size:7   current i:1
 i_size:7   current i:2
 i_size:7   current i:3
 i_size:7   current i:4
 i_size:7   current i:5
 i_size:7   current i:6
 in cluster:shadow cluster...
    i_size:0 j_size:0
 sorting hits in shadow cluster...
... finished.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7

WARNING: Cannot find> sp|O00267|SPT5H_HUMAN, trying to re-index the fasta.
stop here:sp|O00267|SPT5H_HUMAN
#----------------------
FATAL: failed!!
#----------------------
ERROR: Fasta index error

ERROR: Failed while doing exonerate of proteins!!

ERROR: Chunk failed at level 14
!!
FAILED CONTIG:Si_gnE.scaffold02061




--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
The contig failed 2 time!!
Maker will not try again!!
The contig will be stored in a fasta file that you can use for debugging.
SeqID: Si_gnE.scaffold02061
Length: 2869475
FASTA: /sfs1/home/frt/ywurm/assemblyValidation/results/2010-03-12/gp9scaffold/maker/Si_gnE.scaffold02061.maker.output/Si_g
nE.scaffold02061_datastore/Si_gnE.scaffold02061/Si_gnE.scaffold02061.died.fasta
#---------------------------------------------------------------------




Maker is now finished!!!
:

I've attached some log files and runinfo in the zip.

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From yannick.wurm at unil.ch  Wed Mar 17 12:13:16 2010
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Wed, 17 Mar 2010 19:13:16 +0100
Subject: [maker-devel] maker crash - indexing fasta?
In-Reply-To: <C7C67205.188C%carson.holt@genetics.utah.edu>
References: <C7C67205.188C%carson.holt@genetics.utah.edu>
Message-ID: <4171FB4A-C5EB-4AD8-A1B6-837D490201FB@unil.ch>

thanks Carson,

looks like I may indeed have a bioperl version problem

I'll keep you posted on how it develops.

Thanks & kind regards,
yannick

On 17 Mar 2010, at 18:48, Carson Holt wrote:

> Sorry about the late reply, my mail filters had apparently filtered out this message.  There are two things to check right away.  First make sure you have BioPerl version 1.6 installed.  Indexing errors can occur on version 1.5.  Also rerun your test with the ?f option.  The ?f option will force MAKER to completely destroy and rebuild old indexes and blast reports before running.  If both of those fail, I can give you pre-release access to MAKER 2.0 which has much more robust indexing of fasta files.
> 
> Carson
> 
> 
> On 3/14/10 12:43 PM, "Yannick Wurm" <yannick.wurm at unil.ch> wrote:
> 
> Hello,
> 
> I'm trying to get maker to work locally.
> The test data seems to run correctly.
> So then I try running it on my data.
> I have a single 2.8mb scaffold in a fasta file.
> I provide a fasta of all ESTs for our organism, and a fasta of uniprot proteins that hit the scaffold.
> 
> 
> The run fails with the following message:
> /sfs1/home/frt/ywurm/assemblyValidation/results/2010-03-12/gp9scaffold/maker/Si_gnE.scaffold02061.maker.output/Si_gnE.scaf
> fold02061_datastore/Si_gnE.scaffold02061/theVoid.Si_gnE.scaffold02061/Si_gnE.scaffold02061.0.Si_gnE.scaffold02061.Bx.sp_al
> l.prots.blastx
> deleted:0 hits
> cleaning blastx...
>  in cluster:shadow cluster...
>     i_size:7 j_size:1
>  sorting hits in shadow cluster...
> ... finished.
>  i_size:7   current i:0
>  i_size:7   current i:1
>  i_size:7   current i:2
>  i_size:7   current i:3
>  i_size:7   current i:4
>  i_size:7   current i:5
>  i_size:7   current i:6
>  in cluster:shadow cluster...
>     i_size:0 j_size:0
>  sorting hits in shadow cluster...
> ... finished.
> cleaning clusters....
> total clusters:1 now processing 0
>  ...processing 0 of 7
>  ...processing 1 of 7
>  ...processing 2 of 7
>  ...processing 3 of 7
>  ...processing 4 of 7
>  ...processing 5 of 7
> 
> WARNING: Cannot find> sp|O00267|SPT5H_HUMAN, trying to re-index the fasta.
> stop here:sp|O00267|SPT5H_HUMAN
> #----------------------
> FATAL: failed!!
> #----------------------
> ERROR: Fasta index error
> 
> ERROR: Failed while doing exonerate of proteins!!
> 
> ERROR: Chunk failed at level 14
> !!
> FAILED CONTIG:Si_gnE.scaffold02061
> 
> 
> 
> 
> --Next Contig--
> 
> Processing run.log file...
> #---------------------------------------------------------------------
> The contig failed 2 time!!
> Maker will not try again!!
> The contig will be stored in a fasta file that you can use for debugging.
> SeqID: Si_gnE.scaffold02061
> Length: 2869475
> FASTA: /sfs1/home/frt/ywurm/assemblyValidation/results/2010-03-12/gp9scaffold/maker/Si_gnE.scaffold02061.maker.output/Si_g
> nE.scaffold02061_datastore/Si_gnE.scaffold02061/Si_gnE.scaffold02061.died.fasta
> #---------------------------------------------------------------------
> 
> 
> 
> 
> Maker is now finished!!!
> :
> 
> I've attached some log files and runinfo in the zip.
> 

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From eugenie.pessia at ens-lyon.fr  Mon Mar 22 07:35:58 2010
From: eugenie.pessia at ens-lyon.fr (=?ISO-8859-1?Q?Eug=E9nie_Pessia?=)
Date: Mon, 22 Mar 2010 14:35:58 +0100
Subject: [maker-devel] non-redundant set of ESTs
Message-ID: <4BA7723E.1070103@ens-lyon.fr>

Dear colleagues,

I am a quite new user of Maker and I have a question concerning the set 
of ESTs that we can provide to Maker.

Indeed, I am annotating a species close to Neurospora crassa. And I have 
got ESTs of my species and of crassa, but both sets have not been 
sequenced in my lab: they are freely available on the internet.
But I don't think these sets are non-redundant. I would even think the 
contrary, seeing the great number of fasta headers they contain (around 
500.000!).

So I would like to know: how much is it important for Maker to predict 
properly genes that the EST set is non-redundant?
And if it really has to be non-redundant, are you aware of a software 
that would easily create this kind of set from the data I have?

I thank you in advance and wish you a nice day,
Eug?nie Pessia


From yannick.wurm at unil.ch  Tue Mar 23 08:51:36 2010
From: yannick.wurm at unil.ch (Yannick Wurm)
Date: Tue, 23 Mar 2010 15:51:36 +0100
Subject: [maker-devel] maker crash - indexing fasta?
In-Reply-To: <C7C67205.188C%carson.holt@genetics.utah.edu>
References: <C7C67205.188C%carson.holt@genetics.utah.edu>
Message-ID: <29A28EF7-5C76-4372-B616-21416C6B890F@unil.ch>

Hi Carson,

upgrading to perl 5.10.1 and bioperl 1.6 did not do the trick, even with the '-f' option.
(all this is on a 64 bit linux machine)

It would thus be great if you could share the prerelease maker 2...

thank you very much,

Yannick




On 17 Mar 2010, at 18:48, Carson Holt wrote:

> Sorry about the late reply, my mail filters had apparently filtered out this message.  There are two things to check right away.  First make sure you have BioPerl version 1.6 installed.  Indexing errors can occur on version 1.5.  Also rerun your test with the ?f option.  The ?f option will force MAKER to completely destroy and rebuild old indexes and blast reports before running.  If both of those fail, I can give you pre-release access to MAKER 2.0 which has much more robust indexing of fasta files.
> 
> Carson
> 
> 
> On 3/14/10 12:43 PM, "Yannick Wurm" <yannick.wurm at unil.ch> wrote:
> 
> Hello,
> 
> I'm trying to get maker to work locally.
> The test data seems to run correctly.
> So then I try running it on my data.
> I have a single 2.8mb scaffold in a fasta file.
> I provide a fasta of all ESTs for our organism, and a fasta of uniprot proteins that hit the scaffold.
> 
> 
> The run fails with the following message:
> /sfs1/home/frt/ywurm/assemblyValidation/results/2010-03-12/gp9scaffold/maker/Si_gnE.scaffold02061.maker.output/Si_gnE.scaf
> fold02061_datastore/Si_gnE.scaffold02061/theVoid.Si_gnE.scaffold02061/Si_gnE.scaffold02061.0.Si_gnE.scaffold02061.Bx.sp_al
> l.prots.blastx
> deleted:0 hits
> cleaning blastx...
>  in cluster:shadow cluster...
>     i_size:7 j_size:1
>  sorting hits in shadow cluster...
> ... finished.
>  i_size:7   current i:0
>  i_size:7   current i:1
>  i_size:7   current i:2
>  i_size:7   current i:3
>  i_size:7   current i:4
>  i_size:7   current i:5
>  i_size:7   current i:6
>  in cluster:shadow cluster...
>     i_size:0 j_size:0
>  sorting hits in shadow cluster...
> ... finished.
> cleaning clusters....
> total clusters:1 now processing 0
>  ...processing 0 of 7
>  ...processing 1 of 7
>  ...processing 2 of 7
>  ...processing 3 of 7
>  ...processing 4 of 7
>  ...processing 5 of 7
> 
> WARNING: Cannot find> sp|O00267|SPT5H_HUMAN, trying to re-index the fasta.
> stop here:sp|O00267|SPT5H_HUMAN
> #----------------------
> FATAL: failed!!
> #----------------------
> ERROR: Fasta index error
> 
> ERROR: Failed while doing exonerate of proteins!!
> 
> ERROR: Chunk failed at level 14
> !!
> FAILED CONTIG:Si_gnE.scaffold02061
> 
> 
> 
> 
> --Next Contig--
> 
> Processing run.log file...
> #---------------------------------------------------------------------
> The contig failed 2 time!!
> Maker will not try again!!
> The contig will be stored in a fasta file that you can use for debugging.
> SeqID: Si_gnE.scaffold02061
> Length: 2869475
> FASTA: /sfs1/home/frt/ywurm/assemblyValidation/results/2010-03-12/gp9scaffold/maker/Si_gnE.scaffold02061.maker.output/Si_g
> nE.scaffold02061_datastore/Si_gnE.scaffold02061/Si_gnE.scaffold02061.died.fasta
> #---------------------------------------------------------------------
> 
> 
> 
> 
> Maker is now finished!!!
> :
> 
> I've attached some log files and runinfo in the zip.
> 



--------------------------------------------
          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
   http://www.unil.ch/dee/page28685_fr.html


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From eugenie.pessia at ens-lyon.fr  Tue Mar 23 11:08:17 2010
From: eugenie.pessia at ens-lyon.fr (=?ISO-8859-1?Q?Eug=E9nie_Pessia?=)
Date: Tue, 23 Mar 2010 18:08:17 +0100
Subject: [maker-devel] error message from GenemarkES
Message-ID: <4BA8F581.1080408@ens-lyon.fr>

Dear colleagues,

I am trying to launch GenemarkES on my species to be able to use it in 
Maker.
However, I got this error message:

running hmm2nt.a2
91 files IN
Can't exec "/home/gegene/bin/GeneMark-ES/make_mat.v3.0.ini.csh": No such 
file or directory at ../../gm_es.pl line 257.
Died at ../../gm_es.pl line 257.

Which is strange, because the file make_mat.v3.0.ini.csh exists in my 
/home/gegene/bin/GeneMark-ES/ directory ...

Do you have any idea of what I can do (I am using Linux 32 bits)?

Thanks in advance,
Eug?nie Pessia


From carson.holt at genetics.utah.edu  Tue Mar 23 11:22:33 2010
From: carson.holt at genetics.utah.edu (Carson Holt)
Date: Tue, 23 Mar 2010 11:22:33 -0600
Subject: [maker-devel] error message from GenemarkES
In-Reply-To: <4BA8F581.1080408@ens-lyon.fr>
Message-ID: <C7CE54F9.18F1%carson.holt@genetics.utah.edu>

This might be a better thing to ask one of the GeneMark developers ( borodovsky at gatech.edu ) since so far you are just running GeneMark by itself.  At first glance, it could be that make_mat.v3.0.ini.csh is just not set as executable.

Try typing this into a terminal and then running again:
 chmod +x /home/gegene/bin/GeneMark-ES/make_mat.v3.0.ini.csh

Also run /home/gegene/bin/GeneMark-ES/make_mat.v3.0.ini.csh by itself to see if any errors appear.  When I try running this script without any arguments it just exits without any failures, so at least I know it is working on my machine.  Try the same on your own machine.

Thanks,
Carson


On 3/23/10 11:08 AM, "Eug?nie Pessia" <eugenie.pessia at ens-lyon.fr> wrote:

Dear colleagues,

I am trying to launch GenemarkES on my species to be able to use it in
Maker.
However, I got this error message:

running hmm2nt.a2
91 files IN
Can't exec "/home/gegene/bin/GeneMark-ES/make_mat.v3.0.ini.csh": No such
file or directory at ../../gm_es.pl line 257.
Died at ../../gm_es.pl line 257.

Which is strange, because the file make_mat.v3.0.ini.csh exists in my
/home/gegene/bin/GeneMark-ES/ directory ...

Do you have any idea of what I can do (I am using Linux 32 bits)?

Thanks in advance,
Eug?nie Pessia

_______________________________________________
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 eugenie.pessia at ens-lyon.fr  Mon Mar 29 08:16:11 2010
From: eugenie.pessia at ens-lyon.fr (=?ISO-8859-1?Q?Eug=E9nie_Pessia?=)
Date: Mon, 29 Mar 2010 16:16:11 +0200
Subject: [maker-devel] trouble using Maker
In-Reply-To: <4BA8F581.1080408@ens-lyon.fr>
References: <4BA8F581.1080408@ens-lyon.fr>
Message-ID: <4BB0B62B.6080207@ens-lyon.fr>

Dear Maker community,

Sorry to bother you again but I encountered 2 problems while using Maker 
and I don't understand them

- Apollo : the first time I launched Maker on one of my chromosomes, I 
only used the est2genome option to see if it worked. Then, I had been 
able to open the resulting .gff file with Apollo and to look at the 
genes found by maker. But now that I am running Maker with more options, 
Apollo is not able anymore to open the .gff file: it gets stuck in the 
"load file" window... Do you have any idea why? I join one of my 
maker_opts.ctl so that you can see which options I use
Here is also a link if you want to download one of my .gff files 
obtained: 
http://dl.ens-lyon.fr/bigfilesharing/files/981d3d4ae5de715c0476d0ff8d844ef2/supercont10.1.gff 


- I am having trouble while launching Maker with all the options that 
interest me (see the maker_opts.ctl file). First, half of my 6 species 
on which I launch Maker didn't succeed (Maker died) whereas I am using 
the exact same parameters and files for the 6 and moreover these 6 
species are very close to each other. I have no clue of why.
Second, for the 3 species where Maker succeeded to end, there is only 1 
partial gene that has been found by Genemark. Which is really not much! 
So I think there is a problem with Genemark. I join you the .mod file I 
am using, which I obtained by launching Genemark-ES on Neurospora crassa 
genome.

I thank you in advance for your help and wish you a very nice day,
Eug?nie
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