[maker-devel] problem with the example

[Carson Holt]

To access files for individual sequences use the datastore index:
/scratchsan/caceronn/Results/MAKER/data/hsap_contig.maker.output/hsap_contig_master_datastore_index.log


look in that file to find the location of individual contig results. For merged results you have to use the gff3_merge script together with the datastore index.

Here is a nice tutorial with step by step instructions and a video to easilly follow along —> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014 <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014>

—Carson



> On Feb 16, 2016, at 2:17 PM, Alejandro Cerón Noriega <alejocn5 at gmail.com> wrote:
> 
> hello i am Alejandro
> 
> I have tried to follow the tutorial MAKER
> 
> 1-I Copy the files in the data directories to a temporary directory    where i  run an example file.
> 2-I Type maker -CTL to generate generic MAKER control files (foto_1)
> 3-I  edit the control files to include the path of    the genome file  ( hsap_contig.fasta from the example) (foto_2)
> then I  give the paht maker maker_exe.ctl maker_opts.ctl maker_bopts.ctl (foto 3)
> 
> that generate a expected folder 
> hsap_contig.maker.output
> 
> but when i whatn to look for the gff file i dont find it, inside the /data/hsap_contig.maker.output/hsap_contig_datastore, i dont find  the all subdirectories
> 
> seq_name.gff - a gff file that can be loaded into GMOD, GBROWSE,
>       or Apollo
>     * seq_name.maker.transcripts.fasta - a fasta file of the MAKER
>       annotated transcript sequences
>     * seq_name.maker.proteins.fasta - a fasta file of the MAKER
>       annotated protein sequences
>     * seq_name.maker.XXX.transcript.fasta - a fasta file of ab-initio
>       predicted transcript sequences from program XXX
>     * seq_name.maker.XXX.proteins.fasta - a fasta file of ab-inito
>       predicted protein sequences from program XXX
>     * seq_name.maker.non_overlapping_ab_initio.transcripts.fasta - a
>       fasta file of filtered ab-inito transcript sequences that don't
>       overlap maker annotations
>     * seq_name.maker.non_overlapping_ab_initio.proteins.fasta - a
>       fasta file of filtered ab-inito protein sequences that don't
>       overlap maker annotations
>     * theVoid.seq_name/ - a directory containing all of the raw
>       output files produced by MAKER, including BLAST reports, SNAP
>       output, exonnerate output and the masked genomeic sequence.
> 
> i only find a directorie named 80 (foto 4)
> 
> i dont know if a make somthing wrong, 
> 
> also try to change the path of the EST (foto_5)
> 
> 
> thanks for your attention
> 
> 
> -- 
> Alejandro Cerón Noriega, B.Sc 
> MSc. Candidate Bioinformatics
> K ♣♣♣
> 
> <foto_1.png><foto_2.png><Foto_3.png><foto_4.png><foto_5.png>_______________________________________________
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