From carsonhh at gmail.com  Mon Jun  1 14:18:12 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 1 Jun 2015 13:18:12 -0600
Subject: [maker-devel] Training Augustus
In-Reply-To: <CAEvDUFDAp1kUorSrv=NCc_=VHO2NkoLXZ06deKHJisjUXFDBXw@mail.gmail.com>
References: <CAEvDUFDAp1kUorSrv=NCc_=VHO2NkoLXZ06deKHJisjUXFDBXw@mail.gmail.com>
Message-ID: <6196307E-7E67-4DA0-8639-E4C0B37A5FDD@gmail.com>

If your using the maker2zff script you can take MAKER results. And filter them.  This produces ZFF.  Then follow the training steps mentioned for SNAP (removing any obvious errors).  Then use this script to convert the ZFF used for SNAP training to an Augustus training file ?> https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl <https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl>

Another thread with more info ?> http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html <http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html>

?Carson



> On May 27, 2015, at 4:57 PM, John Cornelius <jcornel3 at asu.edu> wrote:
> 
>  Hi all, I'm trying to train augustus with a non-model organism, I've run Maker, then trained and run SNAP twice and would now like to run Augustus on the results as well. I've seen the Augustus page on training the program and it mentioned needing a list of 200+ quality gene structures for training, is there a way that I could filter the SNAP results for the highest quality genes to feed into augustus? Thanks.
> 
> -- 
> John Cornelius
> MCB PhD Candidate
> Arizona State University
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150601/046ecbfb/attachment.html>

From panos.ioannidis at gmail.com  Mon Jun  1 14:55:30 2015
From: panos.ioannidis at gmail.com (Panos Ioannidis)
Date: Mon, 1 Jun 2015 21:55:30 +0200
Subject: [maker-devel] new tool for assembly validation
Message-ID: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>

Hello MAKER users,

Our lab has recently developed a new tool for genome/transcriptome assembly
validation called BUSCO (for Benchmarking Universal Single-Copy Orthologs) (
busco.ezlab.org). It works in a way similar to CEGMA, but with certain key
differences.

One of its important features (that actually "pushed" me to write this
post), is that it can train Augustus using the BUSCOs models it identifies
in the genome.

The manuscript is accepted in Bioinformatics and will soon be published,
but you can already download it from the website above and try it.

And please let me know if you have any questions or problems!

Panos
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150601/db26a5d7/attachment.html>

From carsonhh at gmail.com  Mon Jun  1 15:15:54 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 1 Jun 2015 14:15:54 -0600
Subject: [maker-devel] new tool for assembly validation
In-Reply-To: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>
References: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>
Message-ID: <6BAC7138-500F-4273-B141-1657D78F44EA@gmail.com>

Thanks Panos,

I?ve heard good things about BUSCO, in fact someone from the CEGMA/SNAP group recommended we try it instead of CEGMA on a project I?m collaborating on.

Cheers,
Carson


> On Jun 1, 2015, at 1:55 PM, Panos Ioannidis <panos.ioannidis at gmail.com> wrote:
> 
> Hello MAKER users,
> 
> Our lab has recently developed a new tool for genome/transcriptome assembly validation called BUSCO (for Benchmarking Universal Single-Copy Orthologs) (busco.ezlab.org <http://busco.ezlab.org/>). It works in a way similar to CEGMA, but with certain key differences.
> 
> One of its important features (that actually "pushed" me to write this post), is that it can train Augustus using the BUSCOs models it identifies in the genome.
> 
> The manuscript is accepted in Bioinformatics and will soon be published, but you can already download it from the website above and try it.
> 
> And please let me know if you have any questions or problems!
> 
> Panos
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150601/9bdad9a4/attachment.html>

From cjfields at illinois.edu  Mon Jun  1 15:19:39 2015
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 1 Jun 2015 20:19:39 +0000
Subject: [maker-devel] new tool for assembly validation
In-Reply-To: <6BAC7138-500F-4273-B141-1657D78F44EA@gmail.com>
References: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>
	<6BAC7138-500F-4273-B141-1657D78F44EA@gmail.com>
Message-ID: <6C93DB7D-B6B3-4B8F-A796-ECA83A8F386F@illinois.edu>

From Keith Bradnam?s blog:

http://www.acgt.me/blog/2015/5/18/goodbye-cegma-hello-busco

chris

On Jun 1, 2015, at 3:15 PM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:

Thanks Panos,

I?ve heard good things about BUSCO, in fact someone from the CEGMA/SNAP group recommended we try it instead of CEGMA on a project I?m collaborating on.

Cheers,
Carson


On Jun 1, 2015, at 1:55 PM, Panos Ioannidis <panos.ioannidis at gmail.com<mailto:panos.ioannidis at gmail.com>> wrote:

Hello MAKER users,

Our lab has recently developed a new tool for genome/transcriptome assembly validation called BUSCO (for Benchmarking Universal Single-Copy Orthologs) (busco.ezlab.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__busco.ezlab.org_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=AKkb8CF-lF01USB-JaE2pC35TfJN0Hooxv99KwJ5Pbk&s=RbVHeUwGcQW1WqgFdfRnYPPekTRaFr49a8g_G0Ibj5c&e=>). It works in a way similar to CEGMA, but with certain key differences.

One of its important features (that actually "pushed" me to write this post), is that it can train Augustus using the BUSCOs models it identifies in the genome.

The manuscript is accepted in Bioinformatics and will soon be published, but you can already download it from the website above and try it.

And please let me know if you have any questions or problems!

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

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150601/c3616d22/attachment.html>

From EDUOnline at requentist.eu  Mon Jun  1 16:20:42 2015
From: EDUOnline at requentist.eu (EDU Online)
Date: Mon, 1 Jun 2015 14:20:42 -0700
Subject: [maker-devel] Earn.. a State Issued teaching Credential
Message-ID: <10383881310011211038319418992274255@90rniy3ps.requentist.eu>

An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150601/afd2238a/attachment.html>

From yuejiaxing at gmail.com  Sun Jun  7 15:14:12 2015
From: yuejiaxing at gmail.com (Jia-Xing Yue)
Date: Sun, 7 Jun 2015 22:14:12 +0200
Subject: [maker-devel] ERROR: Failed while gathering ab-init output files
Message-ID: <CAETgyPQuYiE-4FT97k_7a3-bWnYAUVBoNB9UD2RHOG2sFH1jAw@mail.gmail.com>

Hello,

I was trying to run maker (version 2.31.8) for a yeast genome (a
sacharymyceise species). However, I got the following error message:
...
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
preparing masked sequence
preparing ab-inits
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/yjx/Programs/augustus-3.1/bin/augustus --species=saccharomyces
--UTR=off /tmp/maker_Vsb8Io/chrI_pilon.abinit_masked.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_masked.0.saccharomyces.augustus
#-------------------------------#
running  trnascan.
#--------- command -------------#
Widget::trnascan:
/home/yjx/local/bin/tRNAscan-SE -b -q
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0.eukaryotic.trnascan
#-------------------------------#
running  snoscan.
#--------- command -------------#
Widget::snoscan:
/home/yjx/local/bin/snoscan /home/yjx/Programs/snoscan/Sc-all-snos.fa
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0.Sc-all-snos%2Efa.snoscan
#-------------------------------#
gathering ab-init output files

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Did not specify a Query End or Query Begin
STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Root/Root.pm:449
STACK: Bio::Search::HSP::GenericHSP::_query_seq_feature
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/GenericHSP.pm:1525
STACK: Bio::Search::HSP::GenericHSP::query
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/GenericHSP.pm:956
STACK: Bio::Search::HSP::HSPI::start
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/HSPI.pm:503
STACK: PhatHit_utils::add_offset
/home/yjx/Programs/maker/bin/../lib/PhatHit_utils.pm:1462
STACK: GI::parse_abinit_file /home/yjx/Programs/maker/bin/../lib/GI.pm:1199
STACK: Process::MpiChunk::_go
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:1469
STACK: Process::MpiChunk::run
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: Process::MpiTiers::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: /home/yjx/Programs/maker/bin/maker:686
-----------------------------------------------------------
--> rank=NA, hostname=octopus.itc.unipi.it
ERROR: Failed while gathering ab-init output files
ERROR: Chunk failed at level:1, tier_type:2
FAILED CONTIG:chrI_pilon

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:chrI_pilon

examining contents of the fasta file and run log


For this run, I modified the maker_opts.ctl file to specify the genome
sequences, customed EST sequences and customed proteome sequences (all in
fasta format) for the annotation. My setting for gene prediction is as
follows:

#-----Gene Prediction
snaphmm= #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus_species=saccharomyces #Augustus gene prediction species model
fgenesh_par_file= #FGENESH parameter file
pred_gff= #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation
pass-through)
est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
trna=1 #find tRNAs with tRNAscan, 1 = yes, 0 = no
snoscan_rrna=/home/yjx/Programs/snoscan/Sc-all-snos.fa #rRNA file to have
Snoscan find snoRNAs
unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 =
yes, 0 = no


BTW: I've also test maker with the sample data provided with the maker
package (dpp_contig.fasta, dpp_est.fasta and dpp_protein.fasta) and it ran
fine.

Could you help me to figure out what is the cause of this problem? Thanks
in advance!

Best,
Jia-Xing
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150607/5a7fd72a/attachment.html>

From aaronmck at uw.edu  Tue Jun  9 00:13:26 2015
From: aaronmck at uw.edu (Aaron McKenna)
Date: Mon, 8 Jun 2015 22:13:26 -0700
Subject: [maker-devel] Trouble with gmhmme3 setup
Message-ID: <CANy9vOJ6hbq7-WbMZEjcFRk+23EMWCGnd+wdQdjres2phcmYAg@mail.gmail.com>

Hi Maker-dev list,

I've just started with the Maker2 pipeline, but I seem to be stuck at the
gmhmme3 part.   The install script says this is optional:

**(OPTIONAL COMPONENTS)

1. Augustus 2.0 or higher. Download from
http://bioinf.uni-greifswald.de/augustus/
2. GeneMark-ES. Download from http://exon.biology.gatech.edu
...

but if don't list a path in my exe file I get:

ERROR: You have failed to provide a value for 'gmhmme3' in the control
files.

If I do provide a link to the latest (GeneMark.hmm eukaryotic, version
3.48) version I get the following error a little later in the run:

error in file format, /tmp/neZlIonRi_/4rlZBFukur_mod
ERROR: GeneMark Failed
--> rank=NA, hostname=parvati.grid.gs.washington.edu
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2

Has anyone seen this before?  Thanks for any info you have.

- Aaron
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150608/b7ed7ca5/attachment.html>

From carsonhh at gmail.com  Tue Jun  9 11:50:57 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 9 Jun 2015 10:50:57 -0600
Subject: [maker-devel] Trouble with gmhmme3 setup
In-Reply-To: <CANy9vOJ6hbq7-WbMZEjcFRk+23EMWCGnd+wdQdjres2phcmYAg@mail.gmail.com>
References: <CANy9vOJ6hbq7-WbMZEjcFRk+23EMWCGnd+wdQdjres2phcmYAg@mail.gmail.com>
Message-ID: <E7288876-FF0C-4F8B-8E2A-BB910FFC022E@gmail.com>

Use the gmhmme3 and probuild executable bundled with the GeneMark-ES / ET v.4.29 download (not the GeneMark.hmm eukaryotic download). Also make sure you have set up the gm_key according to the install instructions for the package.  You can also test out the validity of the *.mod file you are trying to run with by running gmhmme3 manually once on the command line.

Thanks,
Carson


> On Jun 8, 2015, at 11:13 PM, Aaron McKenna <aaronmck at uw.edu> wrote:
> 
> Hi Maker-dev list,
> 
> I've just started with the Maker2 pipeline, but I seem to be stuck at the gmhmme3 part.   The install script says this is optional:
> 
> **(OPTIONAL COMPONENTS)
> 
> 1. Augustus 2.0 or higher. Download from http://bioinf.uni-greifswald.de/augustus/ <http://bioinf.uni-greifswald.de/augustus/>
> 2. GeneMark-ES. Download from http://exon.biology.gatech.edu <http://exon.biology.gatech.edu/>
> ...
> 
> but if don't list a path in my exe file I get:
> 
> ERROR: You have failed to provide a value for 'gmhmme3' in the control files.
> 
> If I do provide a link to the latest (GeneMark.hmm eukaryotic, version 3.48) version I get the following error a little later in the run:
> 
> error in file format, /tmp/neZlIonRi_/4rlZBFukur_mod
> ERROR: GeneMark Failed
> --> rank=NA, hostname=parvati.grid.gs.washington.edu <http://parvati.grid.gs.washington.edu/>
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:0, tier_type:2
> 
> Has anyone seen this before?  Thanks for any info you have.
> 
> - Aaron
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150609/75502ffc/attachment.html>

From adanowitz8 at gmail.com  Thu Jun 11 16:44:59 2015
From: adanowitz8 at gmail.com (Ann Danowitz)
Date: Thu, 11 Jun 2015 14:44:59 -0700
Subject: [maker-devel] Maker 2.31 fails with MPI.pm
Message-ID: <CAOramcsgnduh00kMWa6uRn3m_rWBTvW35mo0j7Skf0TCgwZwLA@mail.gmail.com>

Hello Yandell maker gurus,

Installed Maker 2.31 with MPICH2 .
No errors with Build.PL and Build install
==============================================================================
STATUS MAKER v2.31.8
==============================================================================
PERL Dependencies: VERIFIED
External Programs: VERIFIED
External C Libraries: VERIFIED
MPI SUPPORT: ENABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE: CONFIGURATION OK

but with the following command, maker fails:

dcopetti at bam:/opt/bam_processing/Dario/MAKER_mpi[4:21pm]> mpiexec -n 20
/opt/maker/bin/maker maker_opts_wg_bam_mpi.ctl maker_bopts_wg_bam_mpi.ctl
maker_exe_wg_bam_mpi.ctl

 at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 236.
--> rank=NA, hostname=bam.genome.arizona.edu
    ...propagated at /usr/local/share/perl5/Inline/C.pm line 772.
--> rank=NA, hostname=bam.genome.arizona.edu
 at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 256.
    Parallel::Application::MPI::_bind("/usr/lib64/openmpi/bin/mpicc",
"/usr/include", "/opt/maker/bin/../perl", "") called at
/opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 213
    Parallel::Application::MPI::_load() called at
/opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 74
    Parallel::Application::MPI::MPI_Init() called at /opt/maker/bin/maker
line 279

{line 279     stat = MPI_Init(&PL_origargc, &PL_origargv);}

make: *** No targets specified and no makefile found.  Stop.

A problem was encountered while attempting to compile and install your
Inline
C code. The command that failed was:
  make > out.make 2>&1

[root at bam ~]# more
/opt/maker/perl/build/Parallel/Application/MPI/out.make_install
Makefile:123: warning: NUL character seen; rest of line ignored
Makefile:123: *** missing separator.  Stop.

also from out.make in the same directory:
make: *** [MPI.c] mv: cannot stat `MPI.xsc': No such file or directory
make: *** [MPI.c] Error 1
 or directory
make: *** [MPI.c] Error 1

What values are not getting passed to MPI.pm?

Many thanks for any help!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150611/a9c9fd8d/attachment.html>

From carsonhh at gmail.com  Thu Jun 11 17:03:57 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jun 2015 16:03:57 -0600
Subject: [maker-devel] Maker 2.31 fails with MPI.pm
In-Reply-To: <CAOramcsgnduh00kMWa6uRn3m_rWBTvW35mo0j7Skf0TCgwZwLA@mail.gmail.com>
References: <CAOramcsgnduh00kMWa6uRn3m_rWBTvW35mo0j7Skf0TCgwZwLA@mail.gmail.com>
Message-ID: <3D6860AE-2CDE-45B3-A6D5-40E3F9B40803@gmail.com>

Hi Ann,

Build.PL just configures (the status message only shows me your configuration choices).  You still have to run './Build install?.  Your error shows that you configured maker for MPI but never ran the install step successfully.

You should get something like this ?>

$ ./Build install
Installing MAKER...
Configuring MAKER with MPI support
Installing maker/2.31.8/src/../perl/lib/Parallel/Application/MPI.pm
Installing maker/2.31.8/src/../perl/lib/auto/Parallel/Application/MPI/MPI.so
Installing maker/2.31.8/src/../perl/lib/auto/Parallel/Application/MPI/MPI.inl
cp blib/config-x86_64-linux-thread-multi-5.010001 maker/2.31.8/src/../perl/config-x86_64-linux-thread-multi-5.010001


Thanks,
Carson



> On Jun 11, 2015, at 3:44 PM, Ann Danowitz <adanowitz8 at gmail.com> wrote:
> 
> Hello Yandell maker gurus,
> 
> Installed Maker 2.31 with MPICH2 .
> No errors with Build.PL and Build install 
> ==============================================================================
> STATUS MAKER v2.31.8
> ==============================================================================
> PERL Dependencies:	VERIFIED
> External Programs:	VERIFIED
> External C Libraries:	VERIFIED
> MPI SUPPORT:		ENABLED
> MWAS Web Interface:	DISABLED
> MAKER PACKAGE:		CONFIGURATION OK
> 
> but with the following command, maker fails:
> 
> dcopetti at bam:/opt/bam_processing/Dario/MAKER_mpi[4:21pm]> mpiexec -n 20 /opt/maker/bin/maker maker_opts_wg_bam_mpi.ctl maker_bopts_wg_bam_mpi.ctl maker_exe_wg_bam_mpi.ctl
> 
>  at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 236.
> --> rank=NA, hostname=bam.genome.arizona.edu <http://bam.genome.arizona.edu/>
>     ...propagated at /usr/local/share/perl5/Inline/C.pm line 772.
> --> rank=NA, hostname=bam.genome.arizona.edu <http://bam.genome.arizona.edu/>
>  at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 256.
>     Parallel::Application::MPI::_bind("/usr/lib64/openmpi/bin/mpicc", "/usr/include", "/opt/maker/bin/../perl", "") called at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 213
>     Parallel::Application::MPI::_load() called at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 74
>     Parallel::Application::MPI::MPI_Init() called at /opt/maker/bin/maker line 279
> 
> {line 279     stat = MPI_Init(&PL_origargc, &PL_origargv);}
> 
> make: *** No targets specified and no makefile found.  Stop.
> 
> A problem was encountered while attempting to compile and install your Inline
> C code. The command that failed was:
>   make > out.make 2>&1
> 
> [root at bam ~]# more /opt/maker/perl/build/Parallel/Application/MPI/out.make_install
> Makefile:123: warning: NUL character seen; rest of line ignored
> Makefile:123: *** missing separator.  Stop.
> 
> also from out.make in the same directory:
> make: *** [MPI.c] mv: cannot stat `MPI.xsc': No such file or directory
> make: *** [MPI.c] Error 1
>  or directory
> make: *** [MPI.c] Error 1
> 
> What values are not getting passed to MPI.pm?
> 
> Many thanks for any help!
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150611/53a73948/attachment.html>

From FeatherstonJ at arc.agric.za  Mon Jun 22 04:13:48 2015
From: FeatherstonJ at arc.agric.za (Jonathan Featherston)
Date: Mon, 22 Jun 2015 09:13:48 +0000
Subject: [maker-devel] Quality filter perl script
Message-ID: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>

Dear Maker users	

Could somebody kindly forward me the quality_filter perl script? It is missing from my install and I see that somebody else has had the same issue before but I can't access the link.

Kind Regards
Jonathan 
Featherstonj at arc.agric.co.za


From dence at genetics.utah.edu  Mon Jun 22 09:19:05 2015
From: dence at genetics.utah.edu (Daniel Ence)
Date: Mon, 22 Jun 2015 14:19:05 +0000
Subject: [maker-devel] Quality filter perl script
In-Reply-To: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
References: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
Message-ID: <B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>

Hi Jonathan, Here?s the script. I think this script should be included in recent distributions of maker too.

~Daniel




Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

> On Jun 22, 2015, at 3:13 AM, Jonathan Featherston <FeatherstonJ at arc.agric.za> wrote:
>
> Dear Maker users
>
> Could somebody kindly forward me the quality_filter perl script? It is missing from my install and I see that somebody else has had the same issue before but I can't access the link.
>
> Kind Regards
> Jonathan
> Featherstonj at arc.agric.co.za
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150622/365c1f09/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: quality_filter.pl
Type: text/x-perl-script
Size: 4678 bytes
Desc: quality_filter.pl
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150622/365c1f09/attachment.bin>

From carsonhh at gmail.com  Mon Jun 22 11:17:12 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 22 Jun 2015 10:17:12 -0600
Subject: [maker-devel] Quality filter perl script
In-Reply-To: <B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>
References: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
	<B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>
Message-ID: <58ECD769-4FF0-4A0B-95BC-459E723A05C7@gmail.com>

Actually, it looks like this is a one off script Mike added to the devel repository sometime last year, but it has never been included with one of the official MAKER distributions.

?Carson


> On Jun 22, 2015, at 8:19 AM, Daniel Ence <dence at genetics.utah.edu> wrote:
> 
> Hi Jonathan, Here?s the script. I think this script should be included in recent distributions of maker too. 
> 
> ~Daniel
> 
> 
> 
> 
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> 
> > On Jun 22, 2015, at 3:13 AM, Jonathan Featherston <FeatherstonJ at arc.agric.za> wrote:
> > 
> > Dear Maker users      
> > 
> > Could somebody kindly forward me the quality_filter perl script? It is missing from my install and I see that somebody else has had the same issue before but I can't access the link.
> > 
> > Kind Regards
> > Jonathan 
> > Featherstonj at arc.agric.co.za
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> <quality_filter.pl>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150622/f66b9a0e/attachment.html>

From michael.s.campbell1 at gmail.com  Mon Jun 22 11:37:01 2015
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 22 Jun 2015 10:37:01 -0600
Subject: [maker-devel] Quality filter perl script
In-Reply-To: <58ECD769-4FF0-4A0B-95BC-459E723A05C7@gmail.com>
References: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
	<B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>
	<58ECD769-4FF0-4A0B-95BC-459E723A05C7@gmail.com>
Message-ID: <CAAi6vWX6=NDvR0QGazn7XcijHDVCEiQCFMPEYEpD=BG6+c3fxA@mail.gmail.com>

That script was developed for the current protocols in bioinformatics MAKER
protocol paper. I put it in the devel repository thinking that we were
close to the next MAKER release. I should probably just add it to the
current protocols data tarball. That way everyone can get to it easier.

Mike

On Mon, Jun 22, 2015 at 10:17 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Actually, it looks like this is a one off script Mike added to the devel
> repository sometime last year, but it has never been included with one of
> the official MAKER distributions.
>
> ?Carson
>
>
> On Jun 22, 2015, at 8:19 AM, Daniel Ence <dence at genetics.utah.edu> wrote:
>
>  Hi Jonathan, Here?s the script. I think this script should be included
> in recent distributions of maker too.
>
> ~Daniel
>
>
>
>
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
>
> > On Jun 22, 2015, at 3:13 AM, Jonathan Featherston <
> FeatherstonJ at arc.agric.za> wrote:
> >
> > Dear Maker users
> >
> > Could somebody kindly forward me the quality_filter perl script? It is
> missing from my install and I see that somebody else has had the same issue
> before but I can't access the link.
> >
> > Kind Regards
> > Jonathan
> > Featherstonj at arc.agric.co.za
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>   <quality_filter.pl>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Michael Campbell MS, RD.
Doctoral Candidate
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:585-3543
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150622/3a32860f/attachment.html>

From MEC at stowers.org  Tue Jun 23 01:46:29 2015
From: MEC at stowers.org (Cook, Malcolm)
Date: Tue, 23 Jun 2015 06:46:29 +0000
Subject: [maker-devel] Questions about re-annotating
Message-ID: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>

Hi,

I am re-running an analysis after having adding `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of work is re-done.

When I re-run maker, should I provide any additional options.  In particular, either "--again" ?

On this subject, I read in http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data

"if you are using est_gff= you don't even have to repeat mask."  - does this mean I should always run maker with option -RM_off when updating annotation?

On a related note, if I have est2genome turned on, what changes to configuration should cause exonerate to run?  I'm guessing:
  adding new est= files
  turning on alt_splice=1

Thanks!

~ malcolm_cook at stowers.org


From carsonhh at gmail.com  Tue Jun 23 11:46:58 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 23 Jun 2015 10:46:58 -0600
Subject: [maker-devel] Questions about re-annotating
In-Reply-To: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
References: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
Message-ID: <03E9D8B1-09B7-42E8-B6C9-0B45B59A4B46@gmail.com>

Hi Malcolm,

If you are not running with any new evidence (EST or protein), and you are passing in all previous evidence as GFF3, then you don?t need to run the repeat masking steps if you don?t want (because you evidence is now static and won?t be affected). You could also just rerun in the same directory as a previous MAKER run as well (MAKER will reuse archived raw analysis files where appropriate). I prefer the second option to GFF3 pass-through when available.

The --again option is really only to force MAKER to rerun something if there is an error.  It won?t rerun the individual analysis steps, rather it will just re-parse saved raw reports.  This may be done because of IO issues on clusters that can be common on network mounted file systems (i.e. when you try and read and write from 2,000 CPUs simultaneously weird things sometimes happen).

Exonerate will always run if you provide ESTs or proteins as FASTA. It will never run if you provide them as GFF3.  The est2genome option just tells MAKER to try and turn polished EST alignments directly into genes (without modification).  It does not cause exonerate to run. This is generally just used to get a set of preliminary models that are sufficient for training gene predictors.

Thanks,
Carson



> On Jun 23, 2015, at 12:46 AM, Cook, Malcolm <MEC at stowers.org> wrote:
> 
> Hi,
> 
> I am re-running an analysis after having adding `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of work is re-done.
> 
> When I re-run maker, should I provide any additional options.  In particular, either "--again" ?
> 
> On this subject, I read in http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data
> 
> "if you are using est_gff= you don't even have to repeat mask."  - does this mean I should always run maker with option -RM_off when updating annotation?
> 
> On a related note, if I have est2genome turned on, what changes to configuration should cause exonerate to run?  I'm guessing:
>  adding new est= files
>  turning on alt_splice=1
> 
> Thanks!
> 
> ~ malcolm_cook at stowers.org
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From michael.s.campbell1 at gmail.com  Tue Jun 23 11:57:25 2015
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Tue, 23 Jun 2015 10:57:25 -0600
Subject: [maker-devel] Questions about re-annotating
In-Reply-To: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
References: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
Message-ID: <CAAi6vWWY=8RD=LdmrD+MHh_NGQx75HFtscTHfdwhx-nNphsy5A@mail.gmail.com>

Hi Malcom,

What you do depends on if you just want to just add three and five prime
UTR to gene models that you are otherwise happy with or if you wan't to use
the RNA-seq data to find new genes and alternatively spliced transcripts.
If you just want to add the UTR you can pass MAKER the current models as
pred_gff= and the RNA-seq data as est_gff=. for this you don't gain much
with repeatmasking.

If on the other hand you want to get more than UTR on current models I
would edit the control file and rerun MAKER in the same directory you ran
before. MAKER will check to see what has already been done and only rerun
what is necessary. For this you do need to repeat mask.

If you want to find alternatively spliced transcripts set alt_splice=1. As
a side note, MAKER is quite conservative in annotating alternatively
spliced transcripts. There must be EST/RNA-seq evidence supporting the
alternative splice to be considered.

Mike

On Tue, Jun 23, 2015 at 12:46 AM, Cook, Malcolm <MEC at stowers.org> wrote:

> Hi,
>
> I am re-running an analysis after having adding
> `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of
> work is re-done.
>
> When I re-run maker, should I provide any additional options.  In
> particular, either "--again" ?
>
> On this subject, I read in
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data
>
> "if you are using est_gff= you don't even have to repeat mask."  - does
> this mean I should always run maker with option -RM_off when updating
> annotation?
>
> On a related note, if I have est2genome turned on, what changes to
> configuration should cause exonerate to run?  I'm guessing:
>   adding new est= files
>   turning on alt_splice=1
>
> Thanks!
>
> ~ malcolm_cook at stowers.org
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Michael Campbell MS, RD.
Doctoral Candidate
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:585-3543
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150623/2baba09f/attachment.html>

From srividya.ramki at gmail.com  Tue Jun 23 08:52:47 2015
From: srividya.ramki at gmail.com (Srividya Ramakrishnan)
Date: Tue, 23 Jun 2015 09:52:47 -0400
Subject: [maker-devel] Maker failing a number of contigs when running
	tblastx or blastn
Message-ID: <CAJFdZXGp6QOeZX92Pr+byhQjQMjey5EKKm6EJq7tGiAFcux0Mw@mail.gmail.com>

?
 error.log.gz
<https://drive.google.com/file/d/0BxTwS_7TqV3GUVVYSTFPM3M0TDQ/edit?usp=drive_web>
?Hi ,

I am trying to run maker on a rice genome assembly. The assembly has about
1074 contigs and maker successfully runs on about 655 contigs and fails on
the rest of them. I ran a few times on the failed contigs changing the
number of tries , clean try option set to true and also increasing the
memory.  None of these options worked. Please help me figure  out the
problem with my maker run. I have attached the error file with this mail


Thanks

Srividya Ramakrishnan
Computational Science Analyst,
Cold Spring Harbor Laboratory,
1 Bungtown Rd,
Cold Spring Harbor , NY 11743??
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150623/9f27a130/attachment.html>

From carsonhh at gmail.com  Tue Jun 23 12:09:37 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 23 Jun 2015 11:09:37 -0600
Subject: [maker-devel] Maker failing a number of contigs when running
	tblastx or blastn
In-Reply-To: <CAJFdZXGp6QOeZX92Pr+byhQjQMjey5EKKm6EJq7tGiAFcux0Mw@mail.gmail.com>
References: <CAJFdZXGp6QOeZX92Pr+byhQjQMjey5EKKm6EJq7tGiAFcux0Mw@mail.gmail.com>
Message-ID: <23ED51F7-38B0-425F-A753-7ABDC8A78BF4@gmail.com>

Hi Srividya,

First make sure you are using the most recent version of MAKER (currently 2.31.8).  Some of your error log information suggests that you have an older version. After installing the newest version, delete the mpi_blastdb directory from you current run before retrying.

The errors suggest there are issues either with the sequence you are using, or perhaps with the /tmp directory becoming full on one of your nodes during the run.  The current version of MAKER may give you a little more info if it is a sequence file content error.

Thanks,
Carson



> On Jun 23, 2015, at 7:52 AM, Srividya Ramakrishnan <srividya.ramki at gmail.com> wrote:
> 
> ?
> ?error.log.gz <https://drive.google.com/file/d/0BxTwS_7TqV3GUVVYSTFPM3M0TDQ/edit?usp=drive_web>?Hi ,
> 
> I am trying to run maker on a rice genome assembly. The assembly has about 1074 contigs and maker successfully runs on about 655 contigs and fails on the rest of them. I ran a few times on the failed contigs changing the number of tries , clean try option set to true and also increasing the memory.  None of these options worked. Please help me figure  out the problem with my maker run. I have attached the error file with this mail
> 
> 
> Thanks 
> 
> Srividya Ramakrishnan
> Computational Science Analyst,
> Cold Spring Harbor Laboratory,
> 1 Bungtown Rd,
> Cold Spring Harbor , NY 11743??
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150623/405f072d/attachment.html>

From jcornel3 at asu.edu  Mon Jun 29 17:45:15 2015
From: jcornel3 at asu.edu (John Cornelius)
Date: Mon, 29 Jun 2015 15:45:15 -0700
Subject: [maker-devel] Best way to assemble RNA-seq for MAKER
Message-ID: <CAEvDUFAuvurios_8_knB3TvTyVYiwgCiWbSkjREKD_7pbusYdQ@mail.gmail.com>

Hi I have a quick question, I have RNA-seq from several different tissue
types and I was wondering, would it be better to pool them and assemble
them as one large transcriptome? Or, should I assemble each tissue
separately and then use MAKER to integrate the smaller assemblies into the
annotation? Thanks.

-- 
John Cornelius
MCB PhD Candidate
Arizona State University
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20150629/f947990d/attachment.html>

From carsonhh at gmail.com  Mon Jun  1 13:18:12 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 1 Jun 2015 13:18:12 -0600
Subject: [maker-devel] Training Augustus
In-Reply-To: <CAEvDUFDAp1kUorSrv=NCc_=VHO2NkoLXZ06deKHJisjUXFDBXw@mail.gmail.com>
References: <CAEvDUFDAp1kUorSrv=NCc_=VHO2NkoLXZ06deKHJisjUXFDBXw@mail.gmail.com>
Message-ID: <6196307E-7E67-4DA0-8639-E4C0B37A5FDD@gmail.com>

If your using the maker2zff script you can take MAKER results. And filter them.  This produces ZFF.  Then follow the training steps mentioned for SNAP (removing any obvious errors).  Then use this script to convert the ZFF used for SNAP training to an Augustus training file ?> https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl <https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl>

Another thread with more info ?> http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html <http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html>

?Carson



> On May 27, 2015, at 4:57 PM, John Cornelius <jcornel3 at asu.edu> wrote:
> 
>  Hi all, I'm trying to train augustus with a non-model organism, I've run Maker, then trained and run SNAP twice and would now like to run Augustus on the results as well. I've seen the Augustus page on training the program and it mentioned needing a list of 200+ quality gene structures for training, is there a way that I could filter the SNAP results for the highest quality genes to feed into augustus? Thanks.
> 
> -- 
> John Cornelius
> MCB PhD Candidate
> Arizona State University
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/046ecbfb/attachment-0001.html>

From panos.ioannidis at gmail.com  Mon Jun  1 13:55:30 2015
From: panos.ioannidis at gmail.com (Panos Ioannidis)
Date: Mon, 1 Jun 2015 21:55:30 +0200
Subject: [maker-devel] new tool for assembly validation
Message-ID: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>

Hello MAKER users,

Our lab has recently developed a new tool for genome/transcriptome assembly
validation called BUSCO (for Benchmarking Universal Single-Copy Orthologs) (
busco.ezlab.org). It works in a way similar to CEGMA, but with certain key
differences.

One of its important features (that actually "pushed" me to write this
post), is that it can train Augustus using the BUSCOs models it identifies
in the genome.

The manuscript is accepted in Bioinformatics and will soon be published,
but you can already download it from the website above and try it.

And please let me know if you have any questions or problems!

Panos
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/db26a5d7/attachment-0001.html>

From carsonhh at gmail.com  Mon Jun  1 14:15:54 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 1 Jun 2015 14:15:54 -0600
Subject: [maker-devel] new tool for assembly validation
In-Reply-To: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>
References: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>
Message-ID: <6BAC7138-500F-4273-B141-1657D78F44EA@gmail.com>

Thanks Panos,

I?ve heard good things about BUSCO, in fact someone from the CEGMA/SNAP group recommended we try it instead of CEGMA on a project I?m collaborating on.

Cheers,
Carson


> On Jun 1, 2015, at 1:55 PM, Panos Ioannidis <panos.ioannidis at gmail.com> wrote:
> 
> Hello MAKER users,
> 
> Our lab has recently developed a new tool for genome/transcriptome assembly validation called BUSCO (for Benchmarking Universal Single-Copy Orthologs) (busco.ezlab.org <http://busco.ezlab.org/>). It works in a way similar to CEGMA, but with certain key differences.
> 
> One of its important features (that actually "pushed" me to write this post), is that it can train Augustus using the BUSCOs models it identifies in the genome.
> 
> The manuscript is accepted in Bioinformatics and will soon be published, but you can already download it from the website above and try it.
> 
> And please let me know if you have any questions or problems!
> 
> Panos
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/9bdad9a4/attachment-0001.html>

From cjfields at illinois.edu  Mon Jun  1 14:19:39 2015
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 1 Jun 2015 20:19:39 +0000
Subject: [maker-devel] new tool for assembly validation
In-Reply-To: <6BAC7138-500F-4273-B141-1657D78F44EA@gmail.com>
References: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>
	<6BAC7138-500F-4273-B141-1657D78F44EA@gmail.com>
Message-ID: <6C93DB7D-B6B3-4B8F-A796-ECA83A8F386F@illinois.edu>

From Keith Bradnam?s blog:

http://www.acgt.me/blog/2015/5/18/goodbye-cegma-hello-busco

chris

On Jun 1, 2015, at 3:15 PM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:

Thanks Panos,

I?ve heard good things about BUSCO, in fact someone from the CEGMA/SNAP group recommended we try it instead of CEGMA on a project I?m collaborating on.

Cheers,
Carson


On Jun 1, 2015, at 1:55 PM, Panos Ioannidis <panos.ioannidis at gmail.com<mailto:panos.ioannidis at gmail.com>> wrote:

Hello MAKER users,

Our lab has recently developed a new tool for genome/transcriptome assembly validation called BUSCO (for Benchmarking Universal Single-Copy Orthologs) (busco.ezlab.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__busco.ezlab.org_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=AKkb8CF-lF01USB-JaE2pC35TfJN0Hooxv99KwJ5Pbk&s=RbVHeUwGcQW1WqgFdfRnYPPekTRaFr49a8g_G0Ibj5c&e=>). It works in a way similar to CEGMA, but with certain key differences.

One of its important features (that actually "pushed" me to write this post), is that it can train Augustus using the BUSCOs models it identifies in the genome.

The manuscript is accepted in Bioinformatics and will soon be published, but you can already download it from the website above and try it.

And please let me know if you have any questions or problems!

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

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/c3616d22/attachment-0001.html>

From EDUOnline at requentist.eu  Mon Jun  1 15:20:42 2015
From: EDUOnline at requentist.eu (EDU Online)
Date: Mon, 1 Jun 2015 14:20:42 -0700
Subject: [maker-devel] Earn.. a State Issued teaching Credential
Message-ID: <10383881310011211038319418992274255@90rniy3ps.requentist.eu>

An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/afd2238a/attachment-0001.html>

From yuejiaxing at gmail.com  Sun Jun  7 14:14:12 2015
From: yuejiaxing at gmail.com (Jia-Xing Yue)
Date: Sun, 7 Jun 2015 22:14:12 +0200
Subject: [maker-devel] ERROR: Failed while gathering ab-init output files
Message-ID: <CAETgyPQuYiE-4FT97k_7a3-bWnYAUVBoNB9UD2RHOG2sFH1jAw@mail.gmail.com>

Hello,

I was trying to run maker (version 2.31.8) for a yeast genome (a
sacharymyceise species). However, I got the following error message:
...
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
preparing masked sequence
preparing ab-inits
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/yjx/Programs/augustus-3.1/bin/augustus --species=saccharomyces
--UTR=off /tmp/maker_Vsb8Io/chrI_pilon.abinit_masked.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_masked.0.saccharomyces.augustus
#-------------------------------#
running  trnascan.
#--------- command -------------#
Widget::trnascan:
/home/yjx/local/bin/tRNAscan-SE -b -q
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0.eukaryotic.trnascan
#-------------------------------#
running  snoscan.
#--------- command -------------#
Widget::snoscan:
/home/yjx/local/bin/snoscan /home/yjx/Programs/snoscan/Sc-all-snos.fa
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0.Sc-all-snos%2Efa.snoscan
#-------------------------------#
gathering ab-init output files

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Did not specify a Query End or Query Begin
STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Root/Root.pm:449
STACK: Bio::Search::HSP::GenericHSP::_query_seq_feature
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/GenericHSP.pm:1525
STACK: Bio::Search::HSP::GenericHSP::query
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/GenericHSP.pm:956
STACK: Bio::Search::HSP::HSPI::start
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/HSPI.pm:503
STACK: PhatHit_utils::add_offset
/home/yjx/Programs/maker/bin/../lib/PhatHit_utils.pm:1462
STACK: GI::parse_abinit_file /home/yjx/Programs/maker/bin/../lib/GI.pm:1199
STACK: Process::MpiChunk::_go
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:1469
STACK: Process::MpiChunk::run
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: Process::MpiTiers::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: /home/yjx/Programs/maker/bin/maker:686
-----------------------------------------------------------
--> rank=NA, hostname=octopus.itc.unipi.it
ERROR: Failed while gathering ab-init output files
ERROR: Chunk failed at level:1, tier_type:2
FAILED CONTIG:chrI_pilon

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:chrI_pilon

examining contents of the fasta file and run log


For this run, I modified the maker_opts.ctl file to specify the genome
sequences, customed EST sequences and customed proteome sequences (all in
fasta format) for the annotation. My setting for gene prediction is as
follows:

#-----Gene Prediction
snaphmm= #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus_species=saccharomyces #Augustus gene prediction species model
fgenesh_par_file= #FGENESH parameter file
pred_gff= #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation
pass-through)
est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
trna=1 #find tRNAs with tRNAscan, 1 = yes, 0 = no
snoscan_rrna=/home/yjx/Programs/snoscan/Sc-all-snos.fa #rRNA file to have
Snoscan find snoRNAs
unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 =
yes, 0 = no


BTW: I've also test maker with the sample data provided with the maker
package (dpp_contig.fasta, dpp_est.fasta and dpp_protein.fasta) and it ran
fine.

Could you help me to figure out what is the cause of this problem? Thanks
in advance!

Best,
Jia-Xing
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150607/5a7fd72a/attachment-0001.html>

From aaronmck at uw.edu  Mon Jun  8 23:13:26 2015
From: aaronmck at uw.edu (Aaron McKenna)
Date: Mon, 8 Jun 2015 22:13:26 -0700
Subject: [maker-devel] Trouble with gmhmme3 setup
Message-ID: <CANy9vOJ6hbq7-WbMZEjcFRk+23EMWCGnd+wdQdjres2phcmYAg@mail.gmail.com>

Hi Maker-dev list,

I've just started with the Maker2 pipeline, but I seem to be stuck at the
gmhmme3 part.   The install script says this is optional:

**(OPTIONAL COMPONENTS)

1. Augustus 2.0 or higher. Download from
http://bioinf.uni-greifswald.de/augustus/
2. GeneMark-ES. Download from http://exon.biology.gatech.edu
...

but if don't list a path in my exe file I get:

ERROR: You have failed to provide a value for 'gmhmme3' in the control
files.

If I do provide a link to the latest (GeneMark.hmm eukaryotic, version
3.48) version I get the following error a little later in the run:

error in file format, /tmp/neZlIonRi_/4rlZBFukur_mod
ERROR: GeneMark Failed
--> rank=NA, hostname=parvati.grid.gs.washington.edu
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2

Has anyone seen this before?  Thanks for any info you have.

- Aaron
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150608/b7ed7ca5/attachment-0001.html>

From carsonhh at gmail.com  Tue Jun  9 10:50:57 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 9 Jun 2015 10:50:57 -0600
Subject: [maker-devel] Trouble with gmhmme3 setup
In-Reply-To: <CANy9vOJ6hbq7-WbMZEjcFRk+23EMWCGnd+wdQdjres2phcmYAg@mail.gmail.com>
References: <CANy9vOJ6hbq7-WbMZEjcFRk+23EMWCGnd+wdQdjres2phcmYAg@mail.gmail.com>
Message-ID: <E7288876-FF0C-4F8B-8E2A-BB910FFC022E@gmail.com>

Use the gmhmme3 and probuild executable bundled with the GeneMark-ES / ET v.4.29 download (not the GeneMark.hmm eukaryotic download). Also make sure you have set up the gm_key according to the install instructions for the package.  You can also test out the validity of the *.mod file you are trying to run with by running gmhmme3 manually once on the command line.

Thanks,
Carson


> On Jun 8, 2015, at 11:13 PM, Aaron McKenna <aaronmck at uw.edu> wrote:
> 
> Hi Maker-dev list,
> 
> I've just started with the Maker2 pipeline, but I seem to be stuck at the gmhmme3 part.   The install script says this is optional:
> 
> **(OPTIONAL COMPONENTS)
> 
> 1. Augustus 2.0 or higher. Download from http://bioinf.uni-greifswald.de/augustus/ <http://bioinf.uni-greifswald.de/augustus/>
> 2. GeneMark-ES. Download from http://exon.biology.gatech.edu <http://exon.biology.gatech.edu/>
> ...
> 
> but if don't list a path in my exe file I get:
> 
> ERROR: You have failed to provide a value for 'gmhmme3' in the control files.
> 
> If I do provide a link to the latest (GeneMark.hmm eukaryotic, version 3.48) version I get the following error a little later in the run:
> 
> error in file format, /tmp/neZlIonRi_/4rlZBFukur_mod
> ERROR: GeneMark Failed
> --> rank=NA, hostname=parvati.grid.gs.washington.edu <http://parvati.grid.gs.washington.edu/>
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:0, tier_type:2
> 
> Has anyone seen this before?  Thanks for any info you have.
> 
> - Aaron
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150609/75502ffc/attachment-0001.html>

From adanowitz8 at gmail.com  Thu Jun 11 15:44:59 2015
From: adanowitz8 at gmail.com (Ann Danowitz)
Date: Thu, 11 Jun 2015 14:44:59 -0700
Subject: [maker-devel] Maker 2.31 fails with MPI.pm
Message-ID: <CAOramcsgnduh00kMWa6uRn3m_rWBTvW35mo0j7Skf0TCgwZwLA@mail.gmail.com>

Hello Yandell maker gurus,

Installed Maker 2.31 with MPICH2 .
No errors with Build.PL and Build install
==============================================================================
STATUS MAKER v2.31.8
==============================================================================
PERL Dependencies: VERIFIED
External Programs: VERIFIED
External C Libraries: VERIFIED
MPI SUPPORT: ENABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE: CONFIGURATION OK

but with the following command, maker fails:

dcopetti at bam:/opt/bam_processing/Dario/MAKER_mpi[4:21pm]> mpiexec -n 20
/opt/maker/bin/maker maker_opts_wg_bam_mpi.ctl maker_bopts_wg_bam_mpi.ctl
maker_exe_wg_bam_mpi.ctl

 at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 236.
--> rank=NA, hostname=bam.genome.arizona.edu
    ...propagated at /usr/local/share/perl5/Inline/C.pm line 772.
--> rank=NA, hostname=bam.genome.arizona.edu
 at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 256.
    Parallel::Application::MPI::_bind("/usr/lib64/openmpi/bin/mpicc",
"/usr/include", "/opt/maker/bin/../perl", "") called at
/opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 213
    Parallel::Application::MPI::_load() called at
/opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 74
    Parallel::Application::MPI::MPI_Init() called at /opt/maker/bin/maker
line 279

{line 279     stat = MPI_Init(&PL_origargc, &PL_origargv);}

make: *** No targets specified and no makefile found.  Stop.

A problem was encountered while attempting to compile and install your
Inline
C code. The command that failed was:
  make > out.make 2>&1

[root at bam ~]# more
/opt/maker/perl/build/Parallel/Application/MPI/out.make_install
Makefile:123: warning: NUL character seen; rest of line ignored
Makefile:123: *** missing separator.  Stop.

also from out.make in the same directory:
make: *** [MPI.c] mv: cannot stat `MPI.xsc': No such file or directory
make: *** [MPI.c] Error 1
 or directory
make: *** [MPI.c] Error 1

What values are not getting passed to MPI.pm?

Many thanks for any help!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150611/a9c9fd8d/attachment-0001.html>

From carsonhh at gmail.com  Thu Jun 11 16:03:57 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jun 2015 16:03:57 -0600
Subject: [maker-devel] Maker 2.31 fails with MPI.pm
In-Reply-To: <CAOramcsgnduh00kMWa6uRn3m_rWBTvW35mo0j7Skf0TCgwZwLA@mail.gmail.com>
References: <CAOramcsgnduh00kMWa6uRn3m_rWBTvW35mo0j7Skf0TCgwZwLA@mail.gmail.com>
Message-ID: <3D6860AE-2CDE-45B3-A6D5-40E3F9B40803@gmail.com>

Hi Ann,

Build.PL just configures (the status message only shows me your configuration choices).  You still have to run './Build install?.  Your error shows that you configured maker for MPI but never ran the install step successfully.

You should get something like this ?>

$ ./Build install
Installing MAKER...
Configuring MAKER with MPI support
Installing maker/2.31.8/src/../perl/lib/Parallel/Application/MPI.pm
Installing maker/2.31.8/src/../perl/lib/auto/Parallel/Application/MPI/MPI.so
Installing maker/2.31.8/src/../perl/lib/auto/Parallel/Application/MPI/MPI.inl
cp blib/config-x86_64-linux-thread-multi-5.010001 maker/2.31.8/src/../perl/config-x86_64-linux-thread-multi-5.010001


Thanks,
Carson



> On Jun 11, 2015, at 3:44 PM, Ann Danowitz <adanowitz8 at gmail.com> wrote:
> 
> Hello Yandell maker gurus,
> 
> Installed Maker 2.31 with MPICH2 .
> No errors with Build.PL and Build install 
> ==============================================================================
> STATUS MAKER v2.31.8
> ==============================================================================
> PERL Dependencies:	VERIFIED
> External Programs:	VERIFIED
> External C Libraries:	VERIFIED
> MPI SUPPORT:		ENABLED
> MWAS Web Interface:	DISABLED
> MAKER PACKAGE:		CONFIGURATION OK
> 
> but with the following command, maker fails:
> 
> dcopetti at bam:/opt/bam_processing/Dario/MAKER_mpi[4:21pm]> mpiexec -n 20 /opt/maker/bin/maker maker_opts_wg_bam_mpi.ctl maker_bopts_wg_bam_mpi.ctl maker_exe_wg_bam_mpi.ctl
> 
>  at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 236.
> --> rank=NA, hostname=bam.genome.arizona.edu <http://bam.genome.arizona.edu/>
>     ...propagated at /usr/local/share/perl5/Inline/C.pm line 772.
> --> rank=NA, hostname=bam.genome.arizona.edu <http://bam.genome.arizona.edu/>
>  at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 256.
>     Parallel::Application::MPI::_bind("/usr/lib64/openmpi/bin/mpicc", "/usr/include", "/opt/maker/bin/../perl", "") called at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 213
>     Parallel::Application::MPI::_load() called at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 74
>     Parallel::Application::MPI::MPI_Init() called at /opt/maker/bin/maker line 279
> 
> {line 279     stat = MPI_Init(&PL_origargc, &PL_origargv);}
> 
> make: *** No targets specified and no makefile found.  Stop.
> 
> A problem was encountered while attempting to compile and install your Inline
> C code. The command that failed was:
>   make > out.make 2>&1
> 
> [root at bam ~]# more /opt/maker/perl/build/Parallel/Application/MPI/out.make_install
> Makefile:123: warning: NUL character seen; rest of line ignored
> Makefile:123: *** missing separator.  Stop.
> 
> also from out.make in the same directory:
> make: *** [MPI.c] mv: cannot stat `MPI.xsc': No such file or directory
> make: *** [MPI.c] Error 1
>  or directory
> make: *** [MPI.c] Error 1
> 
> What values are not getting passed to MPI.pm?
> 
> Many thanks for any help!
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150611/53a73948/attachment-0001.html>

From FeatherstonJ at arc.agric.za  Mon Jun 22 03:13:48 2015
From: FeatherstonJ at arc.agric.za (Jonathan Featherston)
Date: Mon, 22 Jun 2015 09:13:48 +0000
Subject: [maker-devel] Quality filter perl script
Message-ID: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>

Dear Maker users	

Could somebody kindly forward me the quality_filter perl script? It is missing from my install and I see that somebody else has had the same issue before but I can't access the link.

Kind Regards
Jonathan 
Featherstonj at arc.agric.co.za


From dence at genetics.utah.edu  Mon Jun 22 08:19:05 2015
From: dence at genetics.utah.edu (Daniel Ence)
Date: Mon, 22 Jun 2015 14:19:05 +0000
Subject: [maker-devel] Quality filter perl script
In-Reply-To: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
References: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
Message-ID: <B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>

Hi Jonathan, Here?s the script. I think this script should be included in recent distributions of maker too.

~Daniel




Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

> On Jun 22, 2015, at 3:13 AM, Jonathan Featherston <FeatherstonJ at arc.agric.za> wrote:
>
> Dear Maker users
>
> Could somebody kindly forward me the quality_filter perl script? It is missing from my install and I see that somebody else has had the same issue before but I can't access the link.
>
> Kind Regards
> Jonathan
> Featherstonj at arc.agric.co.za
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150622/365c1f09/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: quality_filter.pl
Type: text/x-perl-script
Size: 4678 bytes
Desc: quality_filter.pl
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150622/365c1f09/attachment-0001.bin>

From carsonhh at gmail.com  Mon Jun 22 10:17:12 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 22 Jun 2015 10:17:12 -0600
Subject: [maker-devel] Quality filter perl script
In-Reply-To: <B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>
References: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
	<B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>
Message-ID: <58ECD769-4FF0-4A0B-95BC-459E723A05C7@gmail.com>

Actually, it looks like this is a one off script Mike added to the devel repository sometime last year, but it has never been included with one of the official MAKER distributions.

?Carson


> On Jun 22, 2015, at 8:19 AM, Daniel Ence <dence at genetics.utah.edu> wrote:
> 
> Hi Jonathan, Here?s the script. I think this script should be included in recent distributions of maker too. 
> 
> ~Daniel
> 
> 
> 
> 
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> 
> > On Jun 22, 2015, at 3:13 AM, Jonathan Featherston <FeatherstonJ at arc.agric.za> wrote:
> > 
> > Dear Maker users      
> > 
> > Could somebody kindly forward me the quality_filter perl script? It is missing from my install and I see that somebody else has had the same issue before but I can't access the link.
> > 
> > Kind Regards
> > Jonathan 
> > Featherstonj at arc.agric.co.za
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> <quality_filter.pl>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150622/f66b9a0e/attachment-0001.html>

From michael.s.campbell1 at gmail.com  Mon Jun 22 10:37:01 2015
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 22 Jun 2015 10:37:01 -0600
Subject: [maker-devel] Quality filter perl script
In-Reply-To: <58ECD769-4FF0-4A0B-95BC-459E723A05C7@gmail.com>
References: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
	<B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>
	<58ECD769-4FF0-4A0B-95BC-459E723A05C7@gmail.com>
Message-ID: <CAAi6vWX6=NDvR0QGazn7XcijHDVCEiQCFMPEYEpD=BG6+c3fxA@mail.gmail.com>

That script was developed for the current protocols in bioinformatics MAKER
protocol paper. I put it in the devel repository thinking that we were
close to the next MAKER release. I should probably just add it to the
current protocols data tarball. That way everyone can get to it easier.

Mike

On Mon, Jun 22, 2015 at 10:17 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Actually, it looks like this is a one off script Mike added to the devel
> repository sometime last year, but it has never been included with one of
> the official MAKER distributions.
>
> ?Carson
>
>
> On Jun 22, 2015, at 8:19 AM, Daniel Ence <dence at genetics.utah.edu> wrote:
>
>  Hi Jonathan, Here?s the script. I think this script should be included
> in recent distributions of maker too.
>
> ~Daniel
>
>
>
>
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
>
> > On Jun 22, 2015, at 3:13 AM, Jonathan Featherston <
> FeatherstonJ at arc.agric.za> wrote:
> >
> > Dear Maker users
> >
> > Could somebody kindly forward me the quality_filter perl script? It is
> missing from my install and I see that somebody else has had the same issue
> before but I can't access the link.
> >
> > Kind Regards
> > Jonathan
> > Featherstonj at arc.agric.co.za
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>   <quality_filter.pl>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Michael Campbell MS, RD.
Doctoral Candidate
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:585-3543
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150622/3a32860f/attachment-0001.html>

From MEC at stowers.org  Tue Jun 23 00:46:29 2015
From: MEC at stowers.org (Cook, Malcolm)
Date: Tue, 23 Jun 2015 06:46:29 +0000
Subject: [maker-devel] Questions about re-annotating
Message-ID: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>

Hi,

I am re-running an analysis after having adding `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of work is re-done.

When I re-run maker, should I provide any additional options.  In particular, either "--again" ?

On this subject, I read in http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data

"if you are using est_gff= you don't even have to repeat mask."  - does this mean I should always run maker with option -RM_off when updating annotation?

On a related note, if I have est2genome turned on, what changes to configuration should cause exonerate to run?  I'm guessing:
  adding new est= files
  turning on alt_splice=1

Thanks!

~ malcolm_cook at stowers.org


From carsonhh at gmail.com  Tue Jun 23 10:46:58 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 23 Jun 2015 10:46:58 -0600
Subject: [maker-devel] Questions about re-annotating
In-Reply-To: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
References: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
Message-ID: <03E9D8B1-09B7-42E8-B6C9-0B45B59A4B46@gmail.com>

Hi Malcolm,

If you are not running with any new evidence (EST or protein), and you are passing in all previous evidence as GFF3, then you don?t need to run the repeat masking steps if you don?t want (because you evidence is now static and won?t be affected). You could also just rerun in the same directory as a previous MAKER run as well (MAKER will reuse archived raw analysis files where appropriate). I prefer the second option to GFF3 pass-through when available.

The --again option is really only to force MAKER to rerun something if there is an error.  It won?t rerun the individual analysis steps, rather it will just re-parse saved raw reports.  This may be done because of IO issues on clusters that can be common on network mounted file systems (i.e. when you try and read and write from 2,000 CPUs simultaneously weird things sometimes happen).

Exonerate will always run if you provide ESTs or proteins as FASTA. It will never run if you provide them as GFF3.  The est2genome option just tells MAKER to try and turn polished EST alignments directly into genes (without modification).  It does not cause exonerate to run. This is generally just used to get a set of preliminary models that are sufficient for training gene predictors.

Thanks,
Carson



> On Jun 23, 2015, at 12:46 AM, Cook, Malcolm <MEC at stowers.org> wrote:
> 
> Hi,
> 
> I am re-running an analysis after having adding `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of work is re-done.
> 
> When I re-run maker, should I provide any additional options.  In particular, either "--again" ?
> 
> On this subject, I read in http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data
> 
> "if you are using est_gff= you don't even have to repeat mask."  - does this mean I should always run maker with option -RM_off when updating annotation?
> 
> On a related note, if I have est2genome turned on, what changes to configuration should cause exonerate to run?  I'm guessing:
>  adding new est= files
>  turning on alt_splice=1
> 
> Thanks!
> 
> ~ malcolm_cook at stowers.org
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From michael.s.campbell1 at gmail.com  Tue Jun 23 10:57:25 2015
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Tue, 23 Jun 2015 10:57:25 -0600
Subject: [maker-devel] Questions about re-annotating
In-Reply-To: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
References: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
Message-ID: <CAAi6vWWY=8RD=LdmrD+MHh_NGQx75HFtscTHfdwhx-nNphsy5A@mail.gmail.com>

Hi Malcom,

What you do depends on if you just want to just add three and five prime
UTR to gene models that you are otherwise happy with or if you wan't to use
the RNA-seq data to find new genes and alternatively spliced transcripts.
If you just want to add the UTR you can pass MAKER the current models as
pred_gff= and the RNA-seq data as est_gff=. for this you don't gain much
with repeatmasking.

If on the other hand you want to get more than UTR on current models I
would edit the control file and rerun MAKER in the same directory you ran
before. MAKER will check to see what has already been done and only rerun
what is necessary. For this you do need to repeat mask.

If you want to find alternatively spliced transcripts set alt_splice=1. As
a side note, MAKER is quite conservative in annotating alternatively
spliced transcripts. There must be EST/RNA-seq evidence supporting the
alternative splice to be considered.

Mike

On Tue, Jun 23, 2015 at 12:46 AM, Cook, Malcolm <MEC at stowers.org> wrote:

> Hi,
>
> I am re-running an analysis after having adding
> `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of
> work is re-done.
>
> When I re-run maker, should I provide any additional options.  In
> particular, either "--again" ?
>
> On this subject, I read in
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data
>
> "if you are using est_gff= you don't even have to repeat mask."  - does
> this mean I should always run maker with option -RM_off when updating
> annotation?
>
> On a related note, if I have est2genome turned on, what changes to
> configuration should cause exonerate to run?  I'm guessing:
>   adding new est= files
>   turning on alt_splice=1
>
> Thanks!
>
> ~ malcolm_cook at stowers.org
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Michael Campbell MS, RD.
Doctoral Candidate
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:585-3543
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150623/2baba09f/attachment-0001.html>

From srividya.ramki at gmail.com  Tue Jun 23 07:52:47 2015
From: srividya.ramki at gmail.com (Srividya Ramakrishnan)
Date: Tue, 23 Jun 2015 09:52:47 -0400
Subject: [maker-devel] Maker failing a number of contigs when running
	tblastx or blastn
Message-ID: <CAJFdZXGp6QOeZX92Pr+byhQjQMjey5EKKm6EJq7tGiAFcux0Mw@mail.gmail.com>

?
 error.log.gz
<https://drive.google.com/file/d/0BxTwS_7TqV3GUVVYSTFPM3M0TDQ/edit?usp=drive_web>
?Hi ,

I am trying to run maker on a rice genome assembly. The assembly has about
1074 contigs and maker successfully runs on about 655 contigs and fails on
the rest of them. I ran a few times on the failed contigs changing the
number of tries , clean try option set to true and also increasing the
memory.  None of these options worked. Please help me figure  out the
problem with my maker run. I have attached the error file with this mail


Thanks

Srividya Ramakrishnan
Computational Science Analyst,
Cold Spring Harbor Laboratory,
1 Bungtown Rd,
Cold Spring Harbor , NY 11743??
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150623/9f27a130/attachment-0001.html>

From carsonhh at gmail.com  Tue Jun 23 11:09:37 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 23 Jun 2015 11:09:37 -0600
Subject: [maker-devel] Maker failing a number of contigs when running
	tblastx or blastn
In-Reply-To: <CAJFdZXGp6QOeZX92Pr+byhQjQMjey5EKKm6EJq7tGiAFcux0Mw@mail.gmail.com>
References: <CAJFdZXGp6QOeZX92Pr+byhQjQMjey5EKKm6EJq7tGiAFcux0Mw@mail.gmail.com>
Message-ID: <23ED51F7-38B0-425F-A753-7ABDC8A78BF4@gmail.com>

Hi Srividya,

First make sure you are using the most recent version of MAKER (currently 2.31.8).  Some of your error log information suggests that you have an older version. After installing the newest version, delete the mpi_blastdb directory from you current run before retrying.

The errors suggest there are issues either with the sequence you are using, or perhaps with the /tmp directory becoming full on one of your nodes during the run.  The current version of MAKER may give you a little more info if it is a sequence file content error.

Thanks,
Carson



> On Jun 23, 2015, at 7:52 AM, Srividya Ramakrishnan <srividya.ramki at gmail.com> wrote:
> 
> ?
> ?error.log.gz <https://drive.google.com/file/d/0BxTwS_7TqV3GUVVYSTFPM3M0TDQ/edit?usp=drive_web>?Hi ,
> 
> I am trying to run maker on a rice genome assembly. The assembly has about 1074 contigs and maker successfully runs on about 655 contigs and fails on the rest of them. I ran a few times on the failed contigs changing the number of tries , clean try option set to true and also increasing the memory.  None of these options worked. Please help me figure  out the problem with my maker run. I have attached the error file with this mail
> 
> 
> Thanks 
> 
> Srividya Ramakrishnan
> Computational Science Analyst,
> Cold Spring Harbor Laboratory,
> 1 Bungtown Rd,
> Cold Spring Harbor , NY 11743??
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150623/405f072d/attachment-0001.html>

From jcornel3 at asu.edu  Mon Jun 29 16:45:15 2015
From: jcornel3 at asu.edu (John Cornelius)
Date: Mon, 29 Jun 2015 15:45:15 -0700
Subject: [maker-devel] Best way to assemble RNA-seq for MAKER
Message-ID: <CAEvDUFAuvurios_8_knB3TvTyVYiwgCiWbSkjREKD_7pbusYdQ@mail.gmail.com>

Hi I have a quick question, I have RNA-seq from several different tissue
types and I was wondering, would it be better to pool them and assemble
them as one large transcriptome? Or, should I assemble each tissue
separately and then use MAKER to integrate the smaller assemblies into the
annotation? Thanks.

-- 
John Cornelius
MCB PhD Candidate
Arizona State University
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150629/f947990d/attachment-0001.html>

From carsonhh at gmail.com  Mon Jun  1 13:18:12 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 1 Jun 2015 13:18:12 -0600
Subject: [maker-devel] Training Augustus
In-Reply-To: <CAEvDUFDAp1kUorSrv=NCc_=VHO2NkoLXZ06deKHJisjUXFDBXw@mail.gmail.com>
References: <CAEvDUFDAp1kUorSrv=NCc_=VHO2NkoLXZ06deKHJisjUXFDBXw@mail.gmail.com>
Message-ID: <6196307E-7E67-4DA0-8639-E4C0B37A5FDD@gmail.com>

If your using the maker2zff script you can take MAKER results. And filter them.  This produces ZFF.  Then follow the training steps mentioned for SNAP (removing any obvious errors).  Then use this script to convert the ZFF used for SNAP training to an Augustus training file ?> https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl <https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl>

Another thread with more info ?> http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html <http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html>

?Carson



> On May 27, 2015, at 4:57 PM, John Cornelius <jcornel3 at asu.edu> wrote:
> 
>  Hi all, I'm trying to train augustus with a non-model organism, I've run Maker, then trained and run SNAP twice and would now like to run Augustus on the results as well. I've seen the Augustus page on training the program and it mentioned needing a list of 200+ quality gene structures for training, is there a way that I could filter the SNAP results for the highest quality genes to feed into augustus? Thanks.
> 
> -- 
> John Cornelius
> MCB PhD Candidate
> Arizona State University
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/046ecbfb/attachment-0002.html>

From panos.ioannidis at gmail.com  Mon Jun  1 13:55:30 2015
From: panos.ioannidis at gmail.com (Panos Ioannidis)
Date: Mon, 1 Jun 2015 21:55:30 +0200
Subject: [maker-devel] new tool for assembly validation
Message-ID: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>

Hello MAKER users,

Our lab has recently developed a new tool for genome/transcriptome assembly
validation called BUSCO (for Benchmarking Universal Single-Copy Orthologs) (
busco.ezlab.org). It works in a way similar to CEGMA, but with certain key
differences.

One of its important features (that actually "pushed" me to write this
post), is that it can train Augustus using the BUSCOs models it identifies
in the genome.

The manuscript is accepted in Bioinformatics and will soon be published,
but you can already download it from the website above and try it.

And please let me know if you have any questions or problems!

Panos
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/db26a5d7/attachment-0002.html>

From carsonhh at gmail.com  Mon Jun  1 14:15:54 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 1 Jun 2015 14:15:54 -0600
Subject: [maker-devel] new tool for assembly validation
In-Reply-To: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>
References: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>
Message-ID: <6BAC7138-500F-4273-B141-1657D78F44EA@gmail.com>

Thanks Panos,

I?ve heard good things about BUSCO, in fact someone from the CEGMA/SNAP group recommended we try it instead of CEGMA on a project I?m collaborating on.

Cheers,
Carson


> On Jun 1, 2015, at 1:55 PM, Panos Ioannidis <panos.ioannidis at gmail.com> wrote:
> 
> Hello MAKER users,
> 
> Our lab has recently developed a new tool for genome/transcriptome assembly validation called BUSCO (for Benchmarking Universal Single-Copy Orthologs) (busco.ezlab.org <http://busco.ezlab.org/>). It works in a way similar to CEGMA, but with certain key differences.
> 
> One of its important features (that actually "pushed" me to write this post), is that it can train Augustus using the BUSCOs models it identifies in the genome.
> 
> The manuscript is accepted in Bioinformatics and will soon be published, but you can already download it from the website above and try it.
> 
> And please let me know if you have any questions or problems!
> 
> Panos
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/9bdad9a4/attachment-0002.html>

From cjfields at illinois.edu  Mon Jun  1 14:19:39 2015
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 1 Jun 2015 20:19:39 +0000
Subject: [maker-devel] new tool for assembly validation
In-Reply-To: <6BAC7138-500F-4273-B141-1657D78F44EA@gmail.com>
References: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>
	<6BAC7138-500F-4273-B141-1657D78F44EA@gmail.com>
Message-ID: <6C93DB7D-B6B3-4B8F-A796-ECA83A8F386F@illinois.edu>

From Keith Bradnam?s blog:

http://www.acgt.me/blog/2015/5/18/goodbye-cegma-hello-busco

chris

On Jun 1, 2015, at 3:15 PM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:

Thanks Panos,

I?ve heard good things about BUSCO, in fact someone from the CEGMA/SNAP group recommended we try it instead of CEGMA on a project I?m collaborating on.

Cheers,
Carson


On Jun 1, 2015, at 1:55 PM, Panos Ioannidis <panos.ioannidis at gmail.com<mailto:panos.ioannidis at gmail.com>> wrote:

Hello MAKER users,

Our lab has recently developed a new tool for genome/transcriptome assembly validation called BUSCO (for Benchmarking Universal Single-Copy Orthologs) (busco.ezlab.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__busco.ezlab.org_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=AKkb8CF-lF01USB-JaE2pC35TfJN0Hooxv99KwJ5Pbk&s=RbVHeUwGcQW1WqgFdfRnYPPekTRaFr49a8g_G0Ibj5c&e=>). It works in a way similar to CEGMA, but with certain key differences.

One of its important features (that actually "pushed" me to write this post), is that it can train Augustus using the BUSCOs models it identifies in the genome.

The manuscript is accepted in Bioinformatics and will soon be published, but you can already download it from the website above and try it.

And please let me know if you have any questions or problems!

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

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/c3616d22/attachment-0002.html>

From EDUOnline at requentist.eu  Mon Jun  1 15:20:42 2015
From: EDUOnline at requentist.eu (EDU Online)
Date: Mon, 1 Jun 2015 14:20:42 -0700
Subject: [maker-devel] Earn.. a State Issued teaching Credential
Message-ID: <10383881310011211038319418992274255@90rniy3ps.requentist.eu>

An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/afd2238a/attachment-0002.html>

From yuejiaxing at gmail.com  Sun Jun  7 14:14:12 2015
From: yuejiaxing at gmail.com (Jia-Xing Yue)
Date: Sun, 7 Jun 2015 22:14:12 +0200
Subject: [maker-devel] ERROR: Failed while gathering ab-init output files
Message-ID: <CAETgyPQuYiE-4FT97k_7a3-bWnYAUVBoNB9UD2RHOG2sFH1jAw@mail.gmail.com>

Hello,

I was trying to run maker (version 2.31.8) for a yeast genome (a
sacharymyceise species). However, I got the following error message:
...
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
preparing masked sequence
preparing ab-inits
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/yjx/Programs/augustus-3.1/bin/augustus --species=saccharomyces
--UTR=off /tmp/maker_Vsb8Io/chrI_pilon.abinit_masked.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_masked.0.saccharomyces.augustus
#-------------------------------#
running  trnascan.
#--------- command -------------#
Widget::trnascan:
/home/yjx/local/bin/tRNAscan-SE -b -q
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0.eukaryotic.trnascan
#-------------------------------#
running  snoscan.
#--------- command -------------#
Widget::snoscan:
/home/yjx/local/bin/snoscan /home/yjx/Programs/snoscan/Sc-all-snos.fa
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0.Sc-all-snos%2Efa.snoscan
#-------------------------------#
gathering ab-init output files

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Did not specify a Query End or Query Begin
STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Root/Root.pm:449
STACK: Bio::Search::HSP::GenericHSP::_query_seq_feature
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/GenericHSP.pm:1525
STACK: Bio::Search::HSP::GenericHSP::query
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/GenericHSP.pm:956
STACK: Bio::Search::HSP::HSPI::start
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/HSPI.pm:503
STACK: PhatHit_utils::add_offset
/home/yjx/Programs/maker/bin/../lib/PhatHit_utils.pm:1462
STACK: GI::parse_abinit_file /home/yjx/Programs/maker/bin/../lib/GI.pm:1199
STACK: Process::MpiChunk::_go
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:1469
STACK: Process::MpiChunk::run
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: Process::MpiTiers::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: /home/yjx/Programs/maker/bin/maker:686
-----------------------------------------------------------
--> rank=NA, hostname=octopus.itc.unipi.it
ERROR: Failed while gathering ab-init output files
ERROR: Chunk failed at level:1, tier_type:2
FAILED CONTIG:chrI_pilon

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:chrI_pilon

examining contents of the fasta file and run log


For this run, I modified the maker_opts.ctl file to specify the genome
sequences, customed EST sequences and customed proteome sequences (all in
fasta format) for the annotation. My setting for gene prediction is as
follows:

#-----Gene Prediction
snaphmm= #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus_species=saccharomyces #Augustus gene prediction species model
fgenesh_par_file= #FGENESH parameter file
pred_gff= #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation
pass-through)
est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
trna=1 #find tRNAs with tRNAscan, 1 = yes, 0 = no
snoscan_rrna=/home/yjx/Programs/snoscan/Sc-all-snos.fa #rRNA file to have
Snoscan find snoRNAs
unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 =
yes, 0 = no


BTW: I've also test maker with the sample data provided with the maker
package (dpp_contig.fasta, dpp_est.fasta and dpp_protein.fasta) and it ran
fine.

Could you help me to figure out what is the cause of this problem? Thanks
in advance!

Best,
Jia-Xing
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150607/5a7fd72a/attachment-0002.html>

From aaronmck at uw.edu  Mon Jun  8 23:13:26 2015
From: aaronmck at uw.edu (Aaron McKenna)
Date: Mon, 8 Jun 2015 22:13:26 -0700
Subject: [maker-devel] Trouble with gmhmme3 setup
Message-ID: <CANy9vOJ6hbq7-WbMZEjcFRk+23EMWCGnd+wdQdjres2phcmYAg@mail.gmail.com>

Hi Maker-dev list,

I've just started with the Maker2 pipeline, but I seem to be stuck at the
gmhmme3 part.   The install script says this is optional:

**(OPTIONAL COMPONENTS)

1. Augustus 2.0 or higher. Download from
http://bioinf.uni-greifswald.de/augustus/
2. GeneMark-ES. Download from http://exon.biology.gatech.edu
...

but if don't list a path in my exe file I get:

ERROR: You have failed to provide a value for 'gmhmme3' in the control
files.

If I do provide a link to the latest (GeneMark.hmm eukaryotic, version
3.48) version I get the following error a little later in the run:

error in file format, /tmp/neZlIonRi_/4rlZBFukur_mod
ERROR: GeneMark Failed
--> rank=NA, hostname=parvati.grid.gs.washington.edu
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2

Has anyone seen this before?  Thanks for any info you have.

- Aaron
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150608/b7ed7ca5/attachment-0002.html>

From carsonhh at gmail.com  Tue Jun  9 10:50:57 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 9 Jun 2015 10:50:57 -0600
Subject: [maker-devel] Trouble with gmhmme3 setup
In-Reply-To: <CANy9vOJ6hbq7-WbMZEjcFRk+23EMWCGnd+wdQdjres2phcmYAg@mail.gmail.com>
References: <CANy9vOJ6hbq7-WbMZEjcFRk+23EMWCGnd+wdQdjres2phcmYAg@mail.gmail.com>
Message-ID: <E7288876-FF0C-4F8B-8E2A-BB910FFC022E@gmail.com>

Use the gmhmme3 and probuild executable bundled with the GeneMark-ES / ET v.4.29 download (not the GeneMark.hmm eukaryotic download). Also make sure you have set up the gm_key according to the install instructions for the package.  You can also test out the validity of the *.mod file you are trying to run with by running gmhmme3 manually once on the command line.

Thanks,
Carson


> On Jun 8, 2015, at 11:13 PM, Aaron McKenna <aaronmck at uw.edu> wrote:
> 
> Hi Maker-dev list,
> 
> I've just started with the Maker2 pipeline, but I seem to be stuck at the gmhmme3 part.   The install script says this is optional:
> 
> **(OPTIONAL COMPONENTS)
> 
> 1. Augustus 2.0 or higher. Download from http://bioinf.uni-greifswald.de/augustus/ <http://bioinf.uni-greifswald.de/augustus/>
> 2. GeneMark-ES. Download from http://exon.biology.gatech.edu <http://exon.biology.gatech.edu/>
> ...
> 
> but if don't list a path in my exe file I get:
> 
> ERROR: You have failed to provide a value for 'gmhmme3' in the control files.
> 
> If I do provide a link to the latest (GeneMark.hmm eukaryotic, version 3.48) version I get the following error a little later in the run:
> 
> error in file format, /tmp/neZlIonRi_/4rlZBFukur_mod
> ERROR: GeneMark Failed
> --> rank=NA, hostname=parvati.grid.gs.washington.edu <http://parvati.grid.gs.washington.edu/>
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:0, tier_type:2
> 
> Has anyone seen this before?  Thanks for any info you have.
> 
> - Aaron
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150609/75502ffc/attachment-0002.html>

From adanowitz8 at gmail.com  Thu Jun 11 15:44:59 2015
From: adanowitz8 at gmail.com (Ann Danowitz)
Date: Thu, 11 Jun 2015 14:44:59 -0700
Subject: [maker-devel] Maker 2.31 fails with MPI.pm
Message-ID: <CAOramcsgnduh00kMWa6uRn3m_rWBTvW35mo0j7Skf0TCgwZwLA@mail.gmail.com>

Hello Yandell maker gurus,

Installed Maker 2.31 with MPICH2 .
No errors with Build.PL and Build install
==============================================================================
STATUS MAKER v2.31.8
==============================================================================
PERL Dependencies: VERIFIED
External Programs: VERIFIED
External C Libraries: VERIFIED
MPI SUPPORT: ENABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE: CONFIGURATION OK

but with the following command, maker fails:

dcopetti at bam:/opt/bam_processing/Dario/MAKER_mpi[4:21pm]> mpiexec -n 20
/opt/maker/bin/maker maker_opts_wg_bam_mpi.ctl maker_bopts_wg_bam_mpi.ctl
maker_exe_wg_bam_mpi.ctl

 at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 236.
--> rank=NA, hostname=bam.genome.arizona.edu
    ...propagated at /usr/local/share/perl5/Inline/C.pm line 772.
--> rank=NA, hostname=bam.genome.arizona.edu
 at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 256.
    Parallel::Application::MPI::_bind("/usr/lib64/openmpi/bin/mpicc",
"/usr/include", "/opt/maker/bin/../perl", "") called at
/opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 213
    Parallel::Application::MPI::_load() called at
/opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 74
    Parallel::Application::MPI::MPI_Init() called at /opt/maker/bin/maker
line 279

{line 279     stat = MPI_Init(&PL_origargc, &PL_origargv);}

make: *** No targets specified and no makefile found.  Stop.

A problem was encountered while attempting to compile and install your
Inline
C code. The command that failed was:
  make > out.make 2>&1

[root at bam ~]# more
/opt/maker/perl/build/Parallel/Application/MPI/out.make_install
Makefile:123: warning: NUL character seen; rest of line ignored
Makefile:123: *** missing separator.  Stop.

also from out.make in the same directory:
make: *** [MPI.c] mv: cannot stat `MPI.xsc': No such file or directory
make: *** [MPI.c] Error 1
 or directory
make: *** [MPI.c] Error 1

What values are not getting passed to MPI.pm?

Many thanks for any help!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150611/a9c9fd8d/attachment-0002.html>

From carsonhh at gmail.com  Thu Jun 11 16:03:57 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jun 2015 16:03:57 -0600
Subject: [maker-devel] Maker 2.31 fails with MPI.pm
In-Reply-To: <CAOramcsgnduh00kMWa6uRn3m_rWBTvW35mo0j7Skf0TCgwZwLA@mail.gmail.com>
References: <CAOramcsgnduh00kMWa6uRn3m_rWBTvW35mo0j7Skf0TCgwZwLA@mail.gmail.com>
Message-ID: <3D6860AE-2CDE-45B3-A6D5-40E3F9B40803@gmail.com>

Hi Ann,

Build.PL just configures (the status message only shows me your configuration choices).  You still have to run './Build install?.  Your error shows that you configured maker for MPI but never ran the install step successfully.

You should get something like this ?>

$ ./Build install
Installing MAKER...
Configuring MAKER with MPI support
Installing maker/2.31.8/src/../perl/lib/Parallel/Application/MPI.pm
Installing maker/2.31.8/src/../perl/lib/auto/Parallel/Application/MPI/MPI.so
Installing maker/2.31.8/src/../perl/lib/auto/Parallel/Application/MPI/MPI.inl
cp blib/config-x86_64-linux-thread-multi-5.010001 maker/2.31.8/src/../perl/config-x86_64-linux-thread-multi-5.010001


Thanks,
Carson



> On Jun 11, 2015, at 3:44 PM, Ann Danowitz <adanowitz8 at gmail.com> wrote:
> 
> Hello Yandell maker gurus,
> 
> Installed Maker 2.31 with MPICH2 .
> No errors with Build.PL and Build install 
> ==============================================================================
> STATUS MAKER v2.31.8
> ==============================================================================
> PERL Dependencies:	VERIFIED
> External Programs:	VERIFIED
> External C Libraries:	VERIFIED
> MPI SUPPORT:		ENABLED
> MWAS Web Interface:	DISABLED
> MAKER PACKAGE:		CONFIGURATION OK
> 
> but with the following command, maker fails:
> 
> dcopetti at bam:/opt/bam_processing/Dario/MAKER_mpi[4:21pm]> mpiexec -n 20 /opt/maker/bin/maker maker_opts_wg_bam_mpi.ctl maker_bopts_wg_bam_mpi.ctl maker_exe_wg_bam_mpi.ctl
> 
>  at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 236.
> --> rank=NA, hostname=bam.genome.arizona.edu <http://bam.genome.arizona.edu/>
>     ...propagated at /usr/local/share/perl5/Inline/C.pm line 772.
> --> rank=NA, hostname=bam.genome.arizona.edu <http://bam.genome.arizona.edu/>
>  at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 256.
>     Parallel::Application::MPI::_bind("/usr/lib64/openmpi/bin/mpicc", "/usr/include", "/opt/maker/bin/../perl", "") called at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 213
>     Parallel::Application::MPI::_load() called at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 74
>     Parallel::Application::MPI::MPI_Init() called at /opt/maker/bin/maker line 279
> 
> {line 279     stat = MPI_Init(&PL_origargc, &PL_origargv);}
> 
> make: *** No targets specified and no makefile found.  Stop.
> 
> A problem was encountered while attempting to compile and install your Inline
> C code. The command that failed was:
>   make > out.make 2>&1
> 
> [root at bam ~]# more /opt/maker/perl/build/Parallel/Application/MPI/out.make_install
> Makefile:123: warning: NUL character seen; rest of line ignored
> Makefile:123: *** missing separator.  Stop.
> 
> also from out.make in the same directory:
> make: *** [MPI.c] mv: cannot stat `MPI.xsc': No such file or directory
> make: *** [MPI.c] Error 1
>  or directory
> make: *** [MPI.c] Error 1
> 
> What values are not getting passed to MPI.pm?
> 
> Many thanks for any help!
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150611/53a73948/attachment-0002.html>

From FeatherstonJ at arc.agric.za  Mon Jun 22 03:13:48 2015
From: FeatherstonJ at arc.agric.za (Jonathan Featherston)
Date: Mon, 22 Jun 2015 09:13:48 +0000
Subject: [maker-devel] Quality filter perl script
Message-ID: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>

Dear Maker users	

Could somebody kindly forward me the quality_filter perl script? It is missing from my install and I see that somebody else has had the same issue before but I can't access the link.

Kind Regards
Jonathan 
Featherstonj at arc.agric.co.za


From dence at genetics.utah.edu  Mon Jun 22 08:19:05 2015
From: dence at genetics.utah.edu (Daniel Ence)
Date: Mon, 22 Jun 2015 14:19:05 +0000
Subject: [maker-devel] Quality filter perl script
In-Reply-To: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
References: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
Message-ID: <B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>

Hi Jonathan, Here?s the script. I think this script should be included in recent distributions of maker too.

~Daniel




Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

> On Jun 22, 2015, at 3:13 AM, Jonathan Featherston <FeatherstonJ at arc.agric.za> wrote:
>
> Dear Maker users
>
> Could somebody kindly forward me the quality_filter perl script? It is missing from my install and I see that somebody else has had the same issue before but I can't access the link.
>
> Kind Regards
> Jonathan
> Featherstonj at arc.agric.co.za
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150622/365c1f09/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: quality_filter.pl
Type: text/x-perl-script
Size: 4678 bytes
Desc: quality_filter.pl
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150622/365c1f09/attachment-0002.bin>

From carsonhh at gmail.com  Mon Jun 22 10:17:12 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 22 Jun 2015 10:17:12 -0600
Subject: [maker-devel] Quality filter perl script
In-Reply-To: <B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>
References: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
	<B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>
Message-ID: <58ECD769-4FF0-4A0B-95BC-459E723A05C7@gmail.com>

Actually, it looks like this is a one off script Mike added to the devel repository sometime last year, but it has never been included with one of the official MAKER distributions.

?Carson


> On Jun 22, 2015, at 8:19 AM, Daniel Ence <dence at genetics.utah.edu> wrote:
> 
> Hi Jonathan, Here?s the script. I think this script should be included in recent distributions of maker too. 
> 
> ~Daniel
> 
> 
> 
> 
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> 
> > On Jun 22, 2015, at 3:13 AM, Jonathan Featherston <FeatherstonJ at arc.agric.za> wrote:
> > 
> > Dear Maker users      
> > 
> > Could somebody kindly forward me the quality_filter perl script? It is missing from my install and I see that somebody else has had the same issue before but I can't access the link.
> > 
> > Kind Regards
> > Jonathan 
> > Featherstonj at arc.agric.co.za
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> <quality_filter.pl>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150622/f66b9a0e/attachment-0002.html>

From michael.s.campbell1 at gmail.com  Mon Jun 22 10:37:01 2015
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 22 Jun 2015 10:37:01 -0600
Subject: [maker-devel] Quality filter perl script
In-Reply-To: <58ECD769-4FF0-4A0B-95BC-459E723A05C7@gmail.com>
References: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
	<B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>
	<58ECD769-4FF0-4A0B-95BC-459E723A05C7@gmail.com>
Message-ID: <CAAi6vWX6=NDvR0QGazn7XcijHDVCEiQCFMPEYEpD=BG6+c3fxA@mail.gmail.com>

That script was developed for the current protocols in bioinformatics MAKER
protocol paper. I put it in the devel repository thinking that we were
close to the next MAKER release. I should probably just add it to the
current protocols data tarball. That way everyone can get to it easier.

Mike

On Mon, Jun 22, 2015 at 10:17 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Actually, it looks like this is a one off script Mike added to the devel
> repository sometime last year, but it has never been included with one of
> the official MAKER distributions.
>
> ?Carson
>
>
> On Jun 22, 2015, at 8:19 AM, Daniel Ence <dence at genetics.utah.edu> wrote:
>
>  Hi Jonathan, Here?s the script. I think this script should be included
> in recent distributions of maker too.
>
> ~Daniel
>
>
>
>
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
>
> > On Jun 22, 2015, at 3:13 AM, Jonathan Featherston <
> FeatherstonJ at arc.agric.za> wrote:
> >
> > Dear Maker users
> >
> > Could somebody kindly forward me the quality_filter perl script? It is
> missing from my install and I see that somebody else has had the same issue
> before but I can't access the link.
> >
> > Kind Regards
> > Jonathan
> > Featherstonj at arc.agric.co.za
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>   <quality_filter.pl>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Michael Campbell MS, RD.
Doctoral Candidate
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:585-3543
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150622/3a32860f/attachment-0002.html>

From MEC at stowers.org  Tue Jun 23 00:46:29 2015
From: MEC at stowers.org (Cook, Malcolm)
Date: Tue, 23 Jun 2015 06:46:29 +0000
Subject: [maker-devel] Questions about re-annotating
Message-ID: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>

Hi,

I am re-running an analysis after having adding `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of work is re-done.

When I re-run maker, should I provide any additional options.  In particular, either "--again" ?

On this subject, I read in http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data

"if you are using est_gff= you don't even have to repeat mask."  - does this mean I should always run maker with option -RM_off when updating annotation?

On a related note, if I have est2genome turned on, what changes to configuration should cause exonerate to run?  I'm guessing:
  adding new est= files
  turning on alt_splice=1

Thanks!

~ malcolm_cook at stowers.org


From carsonhh at gmail.com  Tue Jun 23 10:46:58 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 23 Jun 2015 10:46:58 -0600
Subject: [maker-devel] Questions about re-annotating
In-Reply-To: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
References: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
Message-ID: <03E9D8B1-09B7-42E8-B6C9-0B45B59A4B46@gmail.com>

Hi Malcolm,

If you are not running with any new evidence (EST or protein), and you are passing in all previous evidence as GFF3, then you don?t need to run the repeat masking steps if you don?t want (because you evidence is now static and won?t be affected). You could also just rerun in the same directory as a previous MAKER run as well (MAKER will reuse archived raw analysis files where appropriate). I prefer the second option to GFF3 pass-through when available.

The --again option is really only to force MAKER to rerun something if there is an error.  It won?t rerun the individual analysis steps, rather it will just re-parse saved raw reports.  This may be done because of IO issues on clusters that can be common on network mounted file systems (i.e. when you try and read and write from 2,000 CPUs simultaneously weird things sometimes happen).

Exonerate will always run if you provide ESTs or proteins as FASTA. It will never run if you provide them as GFF3.  The est2genome option just tells MAKER to try and turn polished EST alignments directly into genes (without modification).  It does not cause exonerate to run. This is generally just used to get a set of preliminary models that are sufficient for training gene predictors.

Thanks,
Carson



> On Jun 23, 2015, at 12:46 AM, Cook, Malcolm <MEC at stowers.org> wrote:
> 
> Hi,
> 
> I am re-running an analysis after having adding `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of work is re-done.
> 
> When I re-run maker, should I provide any additional options.  In particular, either "--again" ?
> 
> On this subject, I read in http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data
> 
> "if you are using est_gff= you don't even have to repeat mask."  - does this mean I should always run maker with option -RM_off when updating annotation?
> 
> On a related note, if I have est2genome turned on, what changes to configuration should cause exonerate to run?  I'm guessing:
>  adding new est= files
>  turning on alt_splice=1
> 
> Thanks!
> 
> ~ malcolm_cook at stowers.org
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From michael.s.campbell1 at gmail.com  Tue Jun 23 10:57:25 2015
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Tue, 23 Jun 2015 10:57:25 -0600
Subject: [maker-devel] Questions about re-annotating
In-Reply-To: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
References: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
Message-ID: <CAAi6vWWY=8RD=LdmrD+MHh_NGQx75HFtscTHfdwhx-nNphsy5A@mail.gmail.com>

Hi Malcom,

What you do depends on if you just want to just add three and five prime
UTR to gene models that you are otherwise happy with or if you wan't to use
the RNA-seq data to find new genes and alternatively spliced transcripts.
If you just want to add the UTR you can pass MAKER the current models as
pred_gff= and the RNA-seq data as est_gff=. for this you don't gain much
with repeatmasking.

If on the other hand you want to get more than UTR on current models I
would edit the control file and rerun MAKER in the same directory you ran
before. MAKER will check to see what has already been done and only rerun
what is necessary. For this you do need to repeat mask.

If you want to find alternatively spliced transcripts set alt_splice=1. As
a side note, MAKER is quite conservative in annotating alternatively
spliced transcripts. There must be EST/RNA-seq evidence supporting the
alternative splice to be considered.

Mike

On Tue, Jun 23, 2015 at 12:46 AM, Cook, Malcolm <MEC at stowers.org> wrote:

> Hi,
>
> I am re-running an analysis after having adding
> `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of
> work is re-done.
>
> When I re-run maker, should I provide any additional options.  In
> particular, either "--again" ?
>
> On this subject, I read in
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data
>
> "if you are using est_gff= you don't even have to repeat mask."  - does
> this mean I should always run maker with option -RM_off when updating
> annotation?
>
> On a related note, if I have est2genome turned on, what changes to
> configuration should cause exonerate to run?  I'm guessing:
>   adding new est= files
>   turning on alt_splice=1
>
> Thanks!
>
> ~ malcolm_cook at stowers.org
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Michael Campbell MS, RD.
Doctoral Candidate
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:585-3543
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150623/2baba09f/attachment-0002.html>

From srividya.ramki at gmail.com  Tue Jun 23 07:52:47 2015
From: srividya.ramki at gmail.com (Srividya Ramakrishnan)
Date: Tue, 23 Jun 2015 09:52:47 -0400
Subject: [maker-devel] Maker failing a number of contigs when running
	tblastx or blastn
Message-ID: <CAJFdZXGp6QOeZX92Pr+byhQjQMjey5EKKm6EJq7tGiAFcux0Mw@mail.gmail.com>

?
 error.log.gz
<https://drive.google.com/file/d/0BxTwS_7TqV3GUVVYSTFPM3M0TDQ/edit?usp=drive_web>
?Hi ,

I am trying to run maker on a rice genome assembly. The assembly has about
1074 contigs and maker successfully runs on about 655 contigs and fails on
the rest of them. I ran a few times on the failed contigs changing the
number of tries , clean try option set to true and also increasing the
memory.  None of these options worked. Please help me figure  out the
problem with my maker run. I have attached the error file with this mail


Thanks

Srividya Ramakrishnan
Computational Science Analyst,
Cold Spring Harbor Laboratory,
1 Bungtown Rd,
Cold Spring Harbor , NY 11743??
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150623/9f27a130/attachment-0002.html>

From carsonhh at gmail.com  Tue Jun 23 11:09:37 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 23 Jun 2015 11:09:37 -0600
Subject: [maker-devel] Maker failing a number of contigs when running
	tblastx or blastn
In-Reply-To: <CAJFdZXGp6QOeZX92Pr+byhQjQMjey5EKKm6EJq7tGiAFcux0Mw@mail.gmail.com>
References: <CAJFdZXGp6QOeZX92Pr+byhQjQMjey5EKKm6EJq7tGiAFcux0Mw@mail.gmail.com>
Message-ID: <23ED51F7-38B0-425F-A753-7ABDC8A78BF4@gmail.com>

Hi Srividya,

First make sure you are using the most recent version of MAKER (currently 2.31.8).  Some of your error log information suggests that you have an older version. After installing the newest version, delete the mpi_blastdb directory from you current run before retrying.

The errors suggest there are issues either with the sequence you are using, or perhaps with the /tmp directory becoming full on one of your nodes during the run.  The current version of MAKER may give you a little more info if it is a sequence file content error.

Thanks,
Carson



> On Jun 23, 2015, at 7:52 AM, Srividya Ramakrishnan <srividya.ramki at gmail.com> wrote:
> 
> ?
> ?error.log.gz <https://drive.google.com/file/d/0BxTwS_7TqV3GUVVYSTFPM3M0TDQ/edit?usp=drive_web>?Hi ,
> 
> I am trying to run maker on a rice genome assembly. The assembly has about 1074 contigs and maker successfully runs on about 655 contigs and fails on the rest of them. I ran a few times on the failed contigs changing the number of tries , clean try option set to true and also increasing the memory.  None of these options worked. Please help me figure  out the problem with my maker run. I have attached the error file with this mail
> 
> 
> Thanks 
> 
> Srividya Ramakrishnan
> Computational Science Analyst,
> Cold Spring Harbor Laboratory,
> 1 Bungtown Rd,
> Cold Spring Harbor , NY 11743??
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150623/405f072d/attachment-0002.html>

From jcornel3 at asu.edu  Mon Jun 29 16:45:15 2015
From: jcornel3 at asu.edu (John Cornelius)
Date: Mon, 29 Jun 2015 15:45:15 -0700
Subject: [maker-devel] Best way to assemble RNA-seq for MAKER
Message-ID: <CAEvDUFAuvurios_8_knB3TvTyVYiwgCiWbSkjREKD_7pbusYdQ@mail.gmail.com>

Hi I have a quick question, I have RNA-seq from several different tissue
types and I was wondering, would it be better to pool them and assemble
them as one large transcriptome? Or, should I assemble each tissue
separately and then use MAKER to integrate the smaller assemblies into the
annotation? Thanks.

-- 
John Cornelius
MCB PhD Candidate
Arizona State University
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150629/f947990d/attachment-0002.html>

From carsonhh at gmail.com  Mon Jun  1 13:18:12 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 1 Jun 2015 13:18:12 -0600
Subject: [maker-devel] Training Augustus
In-Reply-To: <CAEvDUFDAp1kUorSrv=NCc_=VHO2NkoLXZ06deKHJisjUXFDBXw@mail.gmail.com>
References: <CAEvDUFDAp1kUorSrv=NCc_=VHO2NkoLXZ06deKHJisjUXFDBXw@mail.gmail.com>
Message-ID: <6196307E-7E67-4DA0-8639-E4C0B37A5FDD@gmail.com>

If your using the maker2zff script you can take MAKER results. And filter them.  This produces ZFF.  Then follow the training steps mentioned for SNAP (removing any obvious errors).  Then use this script to convert the ZFF used for SNAP training to an Augustus training file ?> https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl <https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl>

Another thread with more info ?> http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html <http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html>

?Carson



> On May 27, 2015, at 4:57 PM, John Cornelius <jcornel3 at asu.edu> wrote:
> 
>  Hi all, I'm trying to train augustus with a non-model organism, I've run Maker, then trained and run SNAP twice and would now like to run Augustus on the results as well. I've seen the Augustus page on training the program and it mentioned needing a list of 200+ quality gene structures for training, is there a way that I could filter the SNAP results for the highest quality genes to feed into augustus? Thanks.
> 
> -- 
> John Cornelius
> MCB PhD Candidate
> Arizona State University
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/046ecbfb/attachment-0003.html>

From panos.ioannidis at gmail.com  Mon Jun  1 13:55:30 2015
From: panos.ioannidis at gmail.com (Panos Ioannidis)
Date: Mon, 1 Jun 2015 21:55:30 +0200
Subject: [maker-devel] new tool for assembly validation
Message-ID: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>

Hello MAKER users,

Our lab has recently developed a new tool for genome/transcriptome assembly
validation called BUSCO (for Benchmarking Universal Single-Copy Orthologs) (
busco.ezlab.org). It works in a way similar to CEGMA, but with certain key
differences.

One of its important features (that actually "pushed" me to write this
post), is that it can train Augustus using the BUSCOs models it identifies
in the genome.

The manuscript is accepted in Bioinformatics and will soon be published,
but you can already download it from the website above and try it.

And please let me know if you have any questions or problems!

Panos
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/db26a5d7/attachment-0003.html>

From carsonhh at gmail.com  Mon Jun  1 14:15:54 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 1 Jun 2015 14:15:54 -0600
Subject: [maker-devel] new tool for assembly validation
In-Reply-To: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>
References: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>
Message-ID: <6BAC7138-500F-4273-B141-1657D78F44EA@gmail.com>

Thanks Panos,

I?ve heard good things about BUSCO, in fact someone from the CEGMA/SNAP group recommended we try it instead of CEGMA on a project I?m collaborating on.

Cheers,
Carson


> On Jun 1, 2015, at 1:55 PM, Panos Ioannidis <panos.ioannidis at gmail.com> wrote:
> 
> Hello MAKER users,
> 
> Our lab has recently developed a new tool for genome/transcriptome assembly validation called BUSCO (for Benchmarking Universal Single-Copy Orthologs) (busco.ezlab.org <http://busco.ezlab.org/>). It works in a way similar to CEGMA, but with certain key differences.
> 
> One of its important features (that actually "pushed" me to write this post), is that it can train Augustus using the BUSCOs models it identifies in the genome.
> 
> The manuscript is accepted in Bioinformatics and will soon be published, but you can already download it from the website above and try it.
> 
> And please let me know if you have any questions or problems!
> 
> Panos
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/9bdad9a4/attachment-0003.html>

From cjfields at illinois.edu  Mon Jun  1 14:19:39 2015
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 1 Jun 2015 20:19:39 +0000
Subject: [maker-devel] new tool for assembly validation
In-Reply-To: <6BAC7138-500F-4273-B141-1657D78F44EA@gmail.com>
References: <CAOVgjtQmdcOM3bUEk7nyL8N7eZ-hLb5AR9rosxYzDvwusmf6wQ@mail.gmail.com>
	<6BAC7138-500F-4273-B141-1657D78F44EA@gmail.com>
Message-ID: <6C93DB7D-B6B3-4B8F-A796-ECA83A8F386F@illinois.edu>

From Keith Bradnam?s blog:

http://www.acgt.me/blog/2015/5/18/goodbye-cegma-hello-busco

chris

On Jun 1, 2015, at 3:15 PM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:

Thanks Panos,

I?ve heard good things about BUSCO, in fact someone from the CEGMA/SNAP group recommended we try it instead of CEGMA on a project I?m collaborating on.

Cheers,
Carson


On Jun 1, 2015, at 1:55 PM, Panos Ioannidis <panos.ioannidis at gmail.com<mailto:panos.ioannidis at gmail.com>> wrote:

Hello MAKER users,

Our lab has recently developed a new tool for genome/transcriptome assembly validation called BUSCO (for Benchmarking Universal Single-Copy Orthologs) (busco.ezlab.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__busco.ezlab.org_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=AKkb8CF-lF01USB-JaE2pC35TfJN0Hooxv99KwJ5Pbk&s=RbVHeUwGcQW1WqgFdfRnYPPekTRaFr49a8g_G0Ibj5c&e=>). It works in a way similar to CEGMA, but with certain key differences.

One of its important features (that actually "pushed" me to write this post), is that it can train Augustus using the BUSCOs models it identifies in the genome.

The manuscript is accepted in Bioinformatics and will soon be published, but you can already download it from the website above and try it.

And please let me know if you have any questions or problems!

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

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/c3616d22/attachment-0003.html>

From EDUOnline at requentist.eu  Mon Jun  1 15:20:42 2015
From: EDUOnline at requentist.eu (EDU Online)
Date: Mon, 1 Jun 2015 14:20:42 -0700
Subject: [maker-devel] Earn.. a State Issued teaching Credential
Message-ID: <10383881310011211038319418992274255@90rniy3ps.requentist.eu>

An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150601/afd2238a/attachment-0003.html>

From yuejiaxing at gmail.com  Sun Jun  7 14:14:12 2015
From: yuejiaxing at gmail.com (Jia-Xing Yue)
Date: Sun, 7 Jun 2015 22:14:12 +0200
Subject: [maker-devel] ERROR: Failed while gathering ab-init output files
Message-ID: <CAETgyPQuYiE-4FT97k_7a3-bWnYAUVBoNB9UD2RHOG2sFH1jAw@mail.gmail.com>

Hello,

I was trying to run maker (version 2.31.8) for a yeast genome (a
sacharymyceise species). However, I got the following error message:
...
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
preparing masked sequence
preparing ab-inits
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/yjx/Programs/augustus-3.1/bin/augustus --species=saccharomyces
--UTR=off /tmp/maker_Vsb8Io/chrI_pilon.abinit_masked.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_masked.0.saccharomyces.augustus
#-------------------------------#
running  trnascan.
#--------- command -------------#
Widget::trnascan:
/home/yjx/local/bin/tRNAscan-SE -b -q
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0.eukaryotic.trnascan
#-------------------------------#
running  snoscan.
#--------- command -------------#
Widget::snoscan:
/home/yjx/local/bin/snoscan /home/yjx/Programs/snoscan/Sc-all-snos.fa
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0 >
/tmp/maker_Vsb8Io/chrI_pilon.abinit_nomask.0.Sc-all-snos%2Efa.snoscan
#-------------------------------#
gathering ab-init output files

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Did not specify a Query End or Query Begin
STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Root/Root.pm:449
STACK: Bio::Search::HSP::GenericHSP::_query_seq_feature
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/GenericHSP.pm:1525
STACK: Bio::Search::HSP::GenericHSP::query
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/GenericHSP.pm:956
STACK: Bio::Search::HSP::HSPI::start
/home/yjx/local/ActivePerl-5.16/site/lib/Bio/Search/HSP/HSPI.pm:503
STACK: PhatHit_utils::add_offset
/home/yjx/Programs/maker/bin/../lib/PhatHit_utils.pm:1462
STACK: GI::parse_abinit_file /home/yjx/Programs/maker/bin/../lib/GI.pm:1199
STACK: Process::MpiChunk::_go
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:1469
STACK: Process::MpiChunk::run
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: Process::MpiTiers::run_all
/home/yjx/Programs/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: /home/yjx/Programs/maker/bin/maker:686
-----------------------------------------------------------
--> rank=NA, hostname=octopus.itc.unipi.it
ERROR: Failed while gathering ab-init output files
ERROR: Chunk failed at level:1, tier_type:2
FAILED CONTIG:chrI_pilon

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:chrI_pilon

examining contents of the fasta file and run log


For this run, I modified the maker_opts.ctl file to specify the genome
sequences, customed EST sequences and customed proteome sequences (all in
fasta format) for the annotation. My setting for gene prediction is as
follows:

#-----Gene Prediction
snaphmm= #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus_species=saccharomyces #Augustus gene prediction species model
fgenesh_par_file= #FGENESH parameter file
pred_gff= #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation
pass-through)
est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
trna=1 #find tRNAs with tRNAscan, 1 = yes, 0 = no
snoscan_rrna=/home/yjx/Programs/snoscan/Sc-all-snos.fa #rRNA file to have
Snoscan find snoRNAs
unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 =
yes, 0 = no


BTW: I've also test maker with the sample data provided with the maker
package (dpp_contig.fasta, dpp_est.fasta and dpp_protein.fasta) and it ran
fine.

Could you help me to figure out what is the cause of this problem? Thanks
in advance!

Best,
Jia-Xing
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150607/5a7fd72a/attachment-0003.html>

From aaronmck at uw.edu  Mon Jun  8 23:13:26 2015
From: aaronmck at uw.edu (Aaron McKenna)
Date: Mon, 8 Jun 2015 22:13:26 -0700
Subject: [maker-devel] Trouble with gmhmme3 setup
Message-ID: <CANy9vOJ6hbq7-WbMZEjcFRk+23EMWCGnd+wdQdjres2phcmYAg@mail.gmail.com>

Hi Maker-dev list,

I've just started with the Maker2 pipeline, but I seem to be stuck at the
gmhmme3 part.   The install script says this is optional:

**(OPTIONAL COMPONENTS)

1. Augustus 2.0 or higher. Download from
http://bioinf.uni-greifswald.de/augustus/
2. GeneMark-ES. Download from http://exon.biology.gatech.edu
...

but if don't list a path in my exe file I get:

ERROR: You have failed to provide a value for 'gmhmme3' in the control
files.

If I do provide a link to the latest (GeneMark.hmm eukaryotic, version
3.48) version I get the following error a little later in the run:

error in file format, /tmp/neZlIonRi_/4rlZBFukur_mod
ERROR: GeneMark Failed
--> rank=NA, hostname=parvati.grid.gs.washington.edu
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2

Has anyone seen this before?  Thanks for any info you have.

- Aaron
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150608/b7ed7ca5/attachment-0003.html>

From carsonhh at gmail.com  Tue Jun  9 10:50:57 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 9 Jun 2015 10:50:57 -0600
Subject: [maker-devel] Trouble with gmhmme3 setup
In-Reply-To: <CANy9vOJ6hbq7-WbMZEjcFRk+23EMWCGnd+wdQdjres2phcmYAg@mail.gmail.com>
References: <CANy9vOJ6hbq7-WbMZEjcFRk+23EMWCGnd+wdQdjres2phcmYAg@mail.gmail.com>
Message-ID: <E7288876-FF0C-4F8B-8E2A-BB910FFC022E@gmail.com>

Use the gmhmme3 and probuild executable bundled with the GeneMark-ES / ET v.4.29 download (not the GeneMark.hmm eukaryotic download). Also make sure you have set up the gm_key according to the install instructions for the package.  You can also test out the validity of the *.mod file you are trying to run with by running gmhmme3 manually once on the command line.

Thanks,
Carson


> On Jun 8, 2015, at 11:13 PM, Aaron McKenna <aaronmck at uw.edu> wrote:
> 
> Hi Maker-dev list,
> 
> I've just started with the Maker2 pipeline, but I seem to be stuck at the gmhmme3 part.   The install script says this is optional:
> 
> **(OPTIONAL COMPONENTS)
> 
> 1. Augustus 2.0 or higher. Download from http://bioinf.uni-greifswald.de/augustus/ <http://bioinf.uni-greifswald.de/augustus/>
> 2. GeneMark-ES. Download from http://exon.biology.gatech.edu <http://exon.biology.gatech.edu/>
> ...
> 
> but if don't list a path in my exe file I get:
> 
> ERROR: You have failed to provide a value for 'gmhmme3' in the control files.
> 
> If I do provide a link to the latest (GeneMark.hmm eukaryotic, version 3.48) version I get the following error a little later in the run:
> 
> error in file format, /tmp/neZlIonRi_/4rlZBFukur_mod
> ERROR: GeneMark Failed
> --> rank=NA, hostname=parvati.grid.gs.washington.edu <http://parvati.grid.gs.washington.edu/>
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:0, tier_type:2
> 
> Has anyone seen this before?  Thanks for any info you have.
> 
> - Aaron
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150609/75502ffc/attachment-0003.html>

From adanowitz8 at gmail.com  Thu Jun 11 15:44:59 2015
From: adanowitz8 at gmail.com (Ann Danowitz)
Date: Thu, 11 Jun 2015 14:44:59 -0700
Subject: [maker-devel] Maker 2.31 fails with MPI.pm
Message-ID: <CAOramcsgnduh00kMWa6uRn3m_rWBTvW35mo0j7Skf0TCgwZwLA@mail.gmail.com>

Hello Yandell maker gurus,

Installed Maker 2.31 with MPICH2 .
No errors with Build.PL and Build install
==============================================================================
STATUS MAKER v2.31.8
==============================================================================
PERL Dependencies: VERIFIED
External Programs: VERIFIED
External C Libraries: VERIFIED
MPI SUPPORT: ENABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE: CONFIGURATION OK

but with the following command, maker fails:

dcopetti at bam:/opt/bam_processing/Dario/MAKER_mpi[4:21pm]> mpiexec -n 20
/opt/maker/bin/maker maker_opts_wg_bam_mpi.ctl maker_bopts_wg_bam_mpi.ctl
maker_exe_wg_bam_mpi.ctl

 at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 236.
--> rank=NA, hostname=bam.genome.arizona.edu
    ...propagated at /usr/local/share/perl5/Inline/C.pm line 772.
--> rank=NA, hostname=bam.genome.arizona.edu
 at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 256.
    Parallel::Application::MPI::_bind("/usr/lib64/openmpi/bin/mpicc",
"/usr/include", "/opt/maker/bin/../perl", "") called at
/opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 213
    Parallel::Application::MPI::_load() called at
/opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 74
    Parallel::Application::MPI::MPI_Init() called at /opt/maker/bin/maker
line 279

{line 279     stat = MPI_Init(&PL_origargc, &PL_origargv);}

make: *** No targets specified and no makefile found.  Stop.

A problem was encountered while attempting to compile and install your
Inline
C code. The command that failed was:
  make > out.make 2>&1

[root at bam ~]# more
/opt/maker/perl/build/Parallel/Application/MPI/out.make_install
Makefile:123: warning: NUL character seen; rest of line ignored
Makefile:123: *** missing separator.  Stop.

also from out.make in the same directory:
make: *** [MPI.c] mv: cannot stat `MPI.xsc': No such file or directory
make: *** [MPI.c] Error 1
 or directory
make: *** [MPI.c] Error 1

What values are not getting passed to MPI.pm?

Many thanks for any help!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150611/a9c9fd8d/attachment-0003.html>

From carsonhh at gmail.com  Thu Jun 11 16:03:57 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jun 2015 16:03:57 -0600
Subject: [maker-devel] Maker 2.31 fails with MPI.pm
In-Reply-To: <CAOramcsgnduh00kMWa6uRn3m_rWBTvW35mo0j7Skf0TCgwZwLA@mail.gmail.com>
References: <CAOramcsgnduh00kMWa6uRn3m_rWBTvW35mo0j7Skf0TCgwZwLA@mail.gmail.com>
Message-ID: <3D6860AE-2CDE-45B3-A6D5-40E3F9B40803@gmail.com>

Hi Ann,

Build.PL just configures (the status message only shows me your configuration choices).  You still have to run './Build install?.  Your error shows that you configured maker for MPI but never ran the install step successfully.

You should get something like this ?>

$ ./Build install
Installing MAKER...
Configuring MAKER with MPI support
Installing maker/2.31.8/src/../perl/lib/Parallel/Application/MPI.pm
Installing maker/2.31.8/src/../perl/lib/auto/Parallel/Application/MPI/MPI.so
Installing maker/2.31.8/src/../perl/lib/auto/Parallel/Application/MPI/MPI.inl
cp blib/config-x86_64-linux-thread-multi-5.010001 maker/2.31.8/src/../perl/config-x86_64-linux-thread-multi-5.010001


Thanks,
Carson



> On Jun 11, 2015, at 3:44 PM, Ann Danowitz <adanowitz8 at gmail.com> wrote:
> 
> Hello Yandell maker gurus,
> 
> Installed Maker 2.31 with MPICH2 .
> No errors with Build.PL and Build install 
> ==============================================================================
> STATUS MAKER v2.31.8
> ==============================================================================
> PERL Dependencies:	VERIFIED
> External Programs:	VERIFIED
> External C Libraries:	VERIFIED
> MPI SUPPORT:		ENABLED
> MWAS Web Interface:	DISABLED
> MAKER PACKAGE:		CONFIGURATION OK
> 
> but with the following command, maker fails:
> 
> dcopetti at bam:/opt/bam_processing/Dario/MAKER_mpi[4:21pm]> mpiexec -n 20 /opt/maker/bin/maker maker_opts_wg_bam_mpi.ctl maker_bopts_wg_bam_mpi.ctl maker_exe_wg_bam_mpi.ctl
> 
>  at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 236.
> --> rank=NA, hostname=bam.genome.arizona.edu <http://bam.genome.arizona.edu/>
>     ...propagated at /usr/local/share/perl5/Inline/C.pm line 772.
> --> rank=NA, hostname=bam.genome.arizona.edu <http://bam.genome.arizona.edu/>
>  at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 256.
>     Parallel::Application::MPI::_bind("/usr/lib64/openmpi/bin/mpicc", "/usr/include", "/opt/maker/bin/../perl", "") called at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 213
>     Parallel::Application::MPI::_load() called at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 74
>     Parallel::Application::MPI::MPI_Init() called at /opt/maker/bin/maker line 279
> 
> {line 279     stat = MPI_Init(&PL_origargc, &PL_origargv);}
> 
> make: *** No targets specified and no makefile found.  Stop.
> 
> A problem was encountered while attempting to compile and install your Inline
> C code. The command that failed was:
>   make > out.make 2>&1
> 
> [root at bam ~]# more /opt/maker/perl/build/Parallel/Application/MPI/out.make_install
> Makefile:123: warning: NUL character seen; rest of line ignored
> Makefile:123: *** missing separator.  Stop.
> 
> also from out.make in the same directory:
> make: *** [MPI.c] mv: cannot stat `MPI.xsc': No such file or directory
> make: *** [MPI.c] Error 1
>  or directory
> make: *** [MPI.c] Error 1
> 
> What values are not getting passed to MPI.pm?
> 
> Many thanks for any help!
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150611/53a73948/attachment-0003.html>

From FeatherstonJ at arc.agric.za  Mon Jun 22 03:13:48 2015
From: FeatherstonJ at arc.agric.za (Jonathan Featherston)
Date: Mon, 22 Jun 2015 09:13:48 +0000
Subject: [maker-devel] Quality filter perl script
Message-ID: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>

Dear Maker users	

Could somebody kindly forward me the quality_filter perl script? It is missing from my install and I see that somebody else has had the same issue before but I can't access the link.

Kind Regards
Jonathan 
Featherstonj at arc.agric.co.za


From dence at genetics.utah.edu  Mon Jun 22 08:19:05 2015
From: dence at genetics.utah.edu (Daniel Ence)
Date: Mon, 22 Jun 2015 14:19:05 +0000
Subject: [maker-devel] Quality filter perl script
In-Reply-To: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
References: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
Message-ID: <B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>

Hi Jonathan, Here?s the script. I think this script should be included in recent distributions of maker too.

~Daniel




Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

> On Jun 22, 2015, at 3:13 AM, Jonathan Featherston <FeatherstonJ at arc.agric.za> wrote:
>
> Dear Maker users
>
> Could somebody kindly forward me the quality_filter perl script? It is missing from my install and I see that somebody else has had the same issue before but I can't access the link.
>
> Kind Regards
> Jonathan
> Featherstonj at arc.agric.co.za
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150622/365c1f09/attachment-0003.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: quality_filter.pl
Type: text/x-perl-script
Size: 4678 bytes
Desc: quality_filter.pl
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150622/365c1f09/attachment-0003.bin>

From carsonhh at gmail.com  Mon Jun 22 10:17:12 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 22 Jun 2015 10:17:12 -0600
Subject: [maker-devel] Quality filter perl script
In-Reply-To: <B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>
References: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
	<B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>
Message-ID: <58ECD769-4FF0-4A0B-95BC-459E723A05C7@gmail.com>

Actually, it looks like this is a one off script Mike added to the devel repository sometime last year, but it has never been included with one of the official MAKER distributions.

?Carson


> On Jun 22, 2015, at 8:19 AM, Daniel Ence <dence at genetics.utah.edu> wrote:
> 
> Hi Jonathan, Here?s the script. I think this script should be included in recent distributions of maker too. 
> 
> ~Daniel
> 
> 
> 
> 
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> 
> > On Jun 22, 2015, at 3:13 AM, Jonathan Featherston <FeatherstonJ at arc.agric.za> wrote:
> > 
> > Dear Maker users      
> > 
> > Could somebody kindly forward me the quality_filter perl script? It is missing from my install and I see that somebody else has had the same issue before but I can't access the link.
> > 
> > Kind Regards
> > Jonathan 
> > Featherstonj at arc.agric.co.za
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> <quality_filter.pl>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150622/f66b9a0e/attachment-0003.html>

From michael.s.campbell1 at gmail.com  Mon Jun 22 10:37:01 2015
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 22 Jun 2015 10:37:01 -0600
Subject: [maker-devel] Quality filter perl script
In-Reply-To: <58ECD769-4FF0-4A0B-95BC-459E723A05C7@gmail.com>
References: <372485E7-E6DB-4619-A5EA-C073D0E42D4B@arc.agric.za>
	<B58EE90F-8B57-4DFA-A2AD-6D87E39A6399@genetics.utah.edu>
	<58ECD769-4FF0-4A0B-95BC-459E723A05C7@gmail.com>
Message-ID: <CAAi6vWX6=NDvR0QGazn7XcijHDVCEiQCFMPEYEpD=BG6+c3fxA@mail.gmail.com>

That script was developed for the current protocols in bioinformatics MAKER
protocol paper. I put it in the devel repository thinking that we were
close to the next MAKER release. I should probably just add it to the
current protocols data tarball. That way everyone can get to it easier.

Mike

On Mon, Jun 22, 2015 at 10:17 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Actually, it looks like this is a one off script Mike added to the devel
> repository sometime last year, but it has never been included with one of
> the official MAKER distributions.
>
> ?Carson
>
>
> On Jun 22, 2015, at 8:19 AM, Daniel Ence <dence at genetics.utah.edu> wrote:
>
>  Hi Jonathan, Here?s the script. I think this script should be included
> in recent distributions of maker too.
>
> ~Daniel
>
>
>
>
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
>
> > On Jun 22, 2015, at 3:13 AM, Jonathan Featherston <
> FeatherstonJ at arc.agric.za> wrote:
> >
> > Dear Maker users
> >
> > Could somebody kindly forward me the quality_filter perl script? It is
> missing from my install and I see that somebody else has had the same issue
> before but I can't access the link.
> >
> > Kind Regards
> > Jonathan
> > Featherstonj at arc.agric.co.za
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>   <quality_filter.pl>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Michael Campbell MS, RD.
Doctoral Candidate
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:585-3543
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150622/3a32860f/attachment-0003.html>

From MEC at stowers.org  Tue Jun 23 00:46:29 2015
From: MEC at stowers.org (Cook, Malcolm)
Date: Tue, 23 Jun 2015 06:46:29 +0000
Subject: [maker-devel] Questions about re-annotating
Message-ID: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>

Hi,

I am re-running an analysis after having adding `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of work is re-done.

When I re-run maker, should I provide any additional options.  In particular, either "--again" ?

On this subject, I read in http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data

"if you are using est_gff= you don't even have to repeat mask."  - does this mean I should always run maker with option -RM_off when updating annotation?

On a related note, if I have est2genome turned on, what changes to configuration should cause exonerate to run?  I'm guessing:
  adding new est= files
  turning on alt_splice=1

Thanks!

~ malcolm_cook at stowers.org


From carsonhh at gmail.com  Tue Jun 23 10:46:58 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 23 Jun 2015 10:46:58 -0600
Subject: [maker-devel] Questions about re-annotating
In-Reply-To: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
References: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
Message-ID: <03E9D8B1-09B7-42E8-B6C9-0B45B59A4B46@gmail.com>

Hi Malcolm,

If you are not running with any new evidence (EST or protein), and you are passing in all previous evidence as GFF3, then you don?t need to run the repeat masking steps if you don?t want (because you evidence is now static and won?t be affected). You could also just rerun in the same directory as a previous MAKER run as well (MAKER will reuse archived raw analysis files where appropriate). I prefer the second option to GFF3 pass-through when available.

The --again option is really only to force MAKER to rerun something if there is an error.  It won?t rerun the individual analysis steps, rather it will just re-parse saved raw reports.  This may be done because of IO issues on clusters that can be common on network mounted file systems (i.e. when you try and read and write from 2,000 CPUs simultaneously weird things sometimes happen).

Exonerate will always run if you provide ESTs or proteins as FASTA. It will never run if you provide them as GFF3.  The est2genome option just tells MAKER to try and turn polished EST alignments directly into genes (without modification).  It does not cause exonerate to run. This is generally just used to get a set of preliminary models that are sufficient for training gene predictors.

Thanks,
Carson



> On Jun 23, 2015, at 12:46 AM, Cook, Malcolm <MEC at stowers.org> wrote:
> 
> Hi,
> 
> I am re-running an analysis after having adding `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of work is re-done.
> 
> When I re-run maker, should I provide any additional options.  In particular, either "--again" ?
> 
> On this subject, I read in http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data
> 
> "if you are using est_gff= you don't even have to repeat mask."  - does this mean I should always run maker with option -RM_off when updating annotation?
> 
> On a related note, if I have est2genome turned on, what changes to configuration should cause exonerate to run?  I'm guessing:
>  adding new est= files
>  turning on alt_splice=1
> 
> Thanks!
> 
> ~ malcolm_cook at stowers.org
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From michael.s.campbell1 at gmail.com  Tue Jun 23 10:57:25 2015
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Tue, 23 Jun 2015 10:57:25 -0600
Subject: [maker-devel] Questions about re-annotating
In-Reply-To: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
References: <24ba201a21cf4a7b871dfba0791c2e01@exchsrv2.sgc.loc>
Message-ID: <CAAi6vWWY=8RD=LdmrD+MHh_NGQx75HFtscTHfdwhx-nNphsy5A@mail.gmail.com>

Hi Malcom,

What you do depends on if you just want to just add three and five prime
UTR to gene models that you are otherwise happy with or if you wan't to use
the RNA-seq data to find new genes and alternatively spliced transcripts.
If you just want to add the UTR you can pass MAKER the current models as
pred_gff= and the RNA-seq data as est_gff=. for this you don't gain much
with repeatmasking.

If on the other hand you want to get more than UTR on current models I
would edit the control file and rerun MAKER in the same directory you ran
before. MAKER will check to see what has already been done and only rerun
what is necessary. For this you do need to repeat mask.

If you want to find alternatively spliced transcripts set alt_splice=1. As
a side note, MAKER is quite conservative in annotating alternatively
spliced transcripts. There must be EST/RNA-seq evidence supporting the
alternative splice to be considered.

Mike

On Tue, Jun 23, 2015 at 12:46 AM, Cook, Malcolm <MEC at stowers.org> wrote:

> Hi,
>
> I am re-running an analysis after having adding
> `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of
> work is re-done.
>
> When I re-run maker, should I provide any additional options.  In
> particular, either "--again" ?
>
> On this subject, I read in
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data
>
> "if you are using est_gff= you don't even have to repeat mask."  - does
> this mean I should always run maker with option -RM_off when updating
> annotation?
>
> On a related note, if I have est2genome turned on, what changes to
> configuration should cause exonerate to run?  I'm guessing:
>   adding new est= files
>   turning on alt_splice=1
>
> Thanks!
>
> ~ malcolm_cook at stowers.org
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Michael Campbell MS, RD.
Doctoral Candidate
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:585-3543
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150623/2baba09f/attachment-0003.html>

From srividya.ramki at gmail.com  Tue Jun 23 07:52:47 2015
From: srividya.ramki at gmail.com (Srividya Ramakrishnan)
Date: Tue, 23 Jun 2015 09:52:47 -0400
Subject: [maker-devel] Maker failing a number of contigs when running
	tblastx or blastn
Message-ID: <CAJFdZXGp6QOeZX92Pr+byhQjQMjey5EKKm6EJq7tGiAFcux0Mw@mail.gmail.com>

?
 error.log.gz
<https://drive.google.com/file/d/0BxTwS_7TqV3GUVVYSTFPM3M0TDQ/edit?usp=drive_web>
?Hi ,

I am trying to run maker on a rice genome assembly. The assembly has about
1074 contigs and maker successfully runs on about 655 contigs and fails on
the rest of them. I ran a few times on the failed contigs changing the
number of tries , clean try option set to true and also increasing the
memory.  None of these options worked. Please help me figure  out the
problem with my maker run. I have attached the error file with this mail


Thanks

Srividya Ramakrishnan
Computational Science Analyst,
Cold Spring Harbor Laboratory,
1 Bungtown Rd,
Cold Spring Harbor , NY 11743??
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150623/9f27a130/attachment-0003.html>

From carsonhh at gmail.com  Tue Jun 23 11:09:37 2015
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 23 Jun 2015 11:09:37 -0600
Subject: [maker-devel] Maker failing a number of contigs when running
	tblastx or blastn
In-Reply-To: <CAJFdZXGp6QOeZX92Pr+byhQjQMjey5EKKm6EJq7tGiAFcux0Mw@mail.gmail.com>
References: <CAJFdZXGp6QOeZX92Pr+byhQjQMjey5EKKm6EJq7tGiAFcux0Mw@mail.gmail.com>
Message-ID: <23ED51F7-38B0-425F-A753-7ABDC8A78BF4@gmail.com>

Hi Srividya,

First make sure you are using the most recent version of MAKER (currently 2.31.8).  Some of your error log information suggests that you have an older version. After installing the newest version, delete the mpi_blastdb directory from you current run before retrying.

The errors suggest there are issues either with the sequence you are using, or perhaps with the /tmp directory becoming full on one of your nodes during the run.  The current version of MAKER may give you a little more info if it is a sequence file content error.

Thanks,
Carson



> On Jun 23, 2015, at 7:52 AM, Srividya Ramakrishnan <srividya.ramki at gmail.com> wrote:
> 
> ?
> ?error.log.gz <https://drive.google.com/file/d/0BxTwS_7TqV3GUVVYSTFPM3M0TDQ/edit?usp=drive_web>?Hi ,
> 
> I am trying to run maker on a rice genome assembly. The assembly has about 1074 contigs and maker successfully runs on about 655 contigs and fails on the rest of them. I ran a few times on the failed contigs changing the number of tries , clean try option set to true and also increasing the memory.  None of these options worked. Please help me figure  out the problem with my maker run. I have attached the error file with this mail
> 
> 
> Thanks 
> 
> Srividya Ramakrishnan
> Computational Science Analyst,
> Cold Spring Harbor Laboratory,
> 1 Bungtown Rd,
> Cold Spring Harbor , NY 11743??
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150623/405f072d/attachment-0003.html>

From jcornel3 at asu.edu  Mon Jun 29 16:45:15 2015
From: jcornel3 at asu.edu (John Cornelius)
Date: Mon, 29 Jun 2015 15:45:15 -0700
Subject: [maker-devel] Best way to assemble RNA-seq for MAKER
Message-ID: <CAEvDUFAuvurios_8_knB3TvTyVYiwgCiWbSkjREKD_7pbusYdQ@mail.gmail.com>

Hi I have a quick question, I have RNA-seq from several different tissue
types and I was wondering, would it be better to pool them and assemble
them as one large transcriptome? Or, should I assemble each tissue
separately and then use MAKER to integrate the smaller assemblies into the
annotation? Thanks.

-- 
John Cornelius
MCB PhD Candidate
Arizona State University
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150629/f947990d/attachment-0003.html>