maker 2.10 - est_reads=#unassembled nextgen mRNASeq in fasta format (not fully implemented) - ?

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maker 2.10 - est_reads=#unassembled nextgen mRNASeq in fasta format (not fully implemented) - ?

Collett, James R-2
Hello,
 
I’m just getting started with MAKER after attending the GMOD school in March (which was great!)
 
I noticed in the default maker_opts.ctl file this line below that indicates that you all are working on a way to incorporate NGS transcriptomic data in lieu of ESTs.  Is this functionality available in maker 2.10?  If not, how soon will it be functional?
 
est_reads= #unassembled nextgen mRNASeq in fasta format (not fully implemented)
 
Thanks,
 
Jim
 
__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
 
 
 
 

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Re: maker 2.10 - est_reads=#unassembled nextgen mRNASeq in fasta format (not fully implemented) - ?

Carson Hinton Holt
Re: [maker-devel] maker 2.10 - est_reads=#unassembled nextgen mRNASeq in fasta format (not fully implemented) - ? Software for mRNAseq alignment and processing is still undergoing a  lot of change, so for now, I have users process these types of data outside of MAKER using the program of their choice and then provide it to the est_gff option in the control files.  I have two scripts bundled with MAKER (tophat2gff and cufflinks2gff) that make this very easy for two of the most popular mRNAseq processing programs (TopHat and Cufflinks).

You should use those script, and if you have any problems or questions, let me know.

Thanks,
Carson




On 5/18/11 12:29 AM, "Collett, James R" <james.collett@...> wrote:

Hello,
 
I’m just getting started with MAKER after attending the GMOD school in March (which was great!)
 
 I noticed in the default maker_opts.ctl file this line below that indicates that you all are working on a way to incorporate NGS transcriptomic data in lieu of ESTs.  Is this functionality available in maker 2.10?  If not, how soon will it be functional?
 
est_reads= #unassembled nextgen mRNASeq in fasta format (not fully implemented)
 
Thanks,
 
Jim
 
__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
 

 
 


Carson Holt
Graduate Student
Yandell Lab
http:/www.yandell-lab.org/
Eccles Institute of Human Genetics
University of Utah

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Problem with section files

Felix Bemm
In reply to this post by Collett, James R-2
Hi,

I am running maker by passing a gff file (extracted with gff3_merge)
with est evidence and repeats from the first run. I allowed maker to use
est and repeat evidence from this gff file and disabled repeat masking.
as predictor snap is used with a trained hmm model from the first run.
following error occurs after a short time during the 2nd run:

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: Gen_Basel.trimmed.cleaned_c3
Length: 347464
#---------------------------------------------------------------------

DBD::SQLite::db selectall_arrayref failed: Expression tree is too large
(maximum depth 1000) at
/storage/tmp/software/maker-2.11-beta/bin/../lib/GFFDB.pm line 531.
Can't use an undefined value as an ARRAY reference at
/storage/tmp/software/maker-2.11-beta/bin/../lib/GFFDB.pm line 535.

--FAILURE--
ERROR: Failed while prepare section files!!

ERROR: Chunk failed at level:12, tier_type:2
!!
FAILED CONTIG:Gen_Basel.trimmed.cleaned_c3

ERROR: Chunk failed at level:5, tier_type:0
!!
FAILED CONTIG:Gen_Basel.trimmed.cleaned_c3

I am using version 2.11 on a multicore system.

Any help would be very nice!

Thx
Felix

--
Dipl. Biol. Felix Bemm
Department of Bioinformatics
University of Würzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
[hidden email]

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[solved] Problem with section files

Felix Bemm
Hi,

we were able to narrow down the problem. It seems as the following error
is occurring when a lot of annotations for a contig are present in the
gff file that is pass through to maker.

ERROR:

DBD::SQLite::db selectall_arrayref failed: Expression tree is too large
(maximum depth 1000) at
/storage/tmp/software/maker-2.11-beta/bin/../lib/GFFDB.pm line 531.
Can't use an undefined value as an ARRAY reference at
/storage/tmp/software/maker-2.11-beta/bin/../lib/GFFDB.pm line 535.

--FAILURE--

ERROR: Failed while prepare section files!!
ERROR: Chunk failed at level:12, tier_type:2!!
FAILED CONTIG:Gen_Basel.trimmed.cleaned_c3
ERROR: Chunk failed at level:5, tier_type:0!!
FAILED CONTIG:Gen_Basel.trimmed.cleaned_c3

SOLUTION

We recompiled the DBD::SQLite package with -DSQLITE_MAX_EXPR_DEPTH=0.
This should set the depth of the annotation tree that is loaded to a
more severe limit. After recompiling, maker is reporting no errors and
the results are looking good but it sticks quite a time to contigs that
failed earlier.

Best regards
Felix

--
Felix Bemm
Department of Bioinformatics
University of Würzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
[hidden email]

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