[maker-devel] Fwd: Issue with make, no prediction after gff3_merge

[Barry Moore]

Hi David,

First of all apologies for the delay in addressing your e-mail, our mailing list software (provided by an external ISP) has stopped supporting the MailMan software that is running the maker-devel list and the software has been unresponsive to our attempts to add new users or moderate messages.  We will handle this message directly through e-mail for now.  We have requested a new maker mailing list through our University IT department and that is request pending approval. The new mailing list should get our experience should get our user support back to normal very soon.

Can you share a few lines of the GFF files that you passed to est_gff?

Thanks

Barry

Begin forwarded message:

From: "LOPEZ, David" <david.lopez at biogemma.com<mailto:david.lopez at biogemma.com>>
Subject: Issue with make, no prediction after gff3_merge
Date: May 3, 2016 at 1:27:03 AM PDT
To: "maker-devel-owner at yandell-lab.org<mailto:maker-devel-owner at yandell-lab.org>" <maker-devel-owner at yandell-lab.org<mailto:maker-devel-owner at yandell-lab.org>>

Dear all,
I am still waiting for my registration at maker-devell list hence I send my question as a mail but I will transfer it to the discussion group when possible.

I am a commercial licenced user of Maker and I currently currently face some issues running Maker3.00.0 on a PBS cluster with an openMPI 1.10.2 implementation (Which runs great most of the time, but that is not the issue discussed here).

After successfully testing the datatset provided in the package (dpp and pyu) I moved to my own assembly (140 000 scaffolds ~ 14GB, eukaryotic, premasked)
I have already made some rnaseq mappings (gff) as well as CDNA and Proteome from reference genome.
To me it appears that only fasta evidences are used but not the gff when I look at the predictions in IGV.
In the gff from gff3_merge, I have blastx protein2genome and maker predictions as well as est_gff:stringtie but no est_gff:somethingelse from my CDNA and EST fed to maker.
Another issue, potentially linked to this problem is that I wasn’t able to use tags in my gff evidences: maker fails to run telling that:
mygff3evidencefile.gff:mylabel was not found which means it doesn’t interpret right the semicolum.

I have attached my maker opts files. Thanks by advance for your help

Best regards,

David.


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