[maker-devel] Maker GFF output with features of 0 length

[Carson Holt]

Ok.  I took a look and I'm relatively sure the issue you are seeing is caused by GFF3 passthrough combined with correct_est_fusion=1.  This is something that only happens when both are used simultaneously and should be corrected in the current version of MAKER.

Thanks,
Carson


From: Marc Höppner <mphoeppner at gmail.com<mailto:mphoeppner at gmail.com>>
Date: Wednesday, August 6, 2014 at 12:14 AM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Cc: <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Maker GFF output with features of 0 length

Hi,

I suspect that Augustus plays a role, since the affected features are seeded by augustus (based on the name anyway).

What I found was that this seems to only happen when using pre-aligned (i.e. GFF3-formatted) cdna2genome and protein2genome evidence (created by Maker in a previous run). And this seems to be quit reproducible - and doesn’t only affect CDS features.

I have put the Maker output for a test scaffold here:

https://dl.dropboxusercontent.com/u/1918141/maker_output.tar.bz2

The problematic lines:
scaffold_563    maker   five_prime_UTR  38501   38501   .       -       .       ID=augustus_masked-scaffold_563-processed-gene-0.14-mRNA-1:five_prime_utr;Parent=augustus_masked-scaffold_563-processed-gene-0.14-mRNA-1
scaffold_563    maker   exon    69967   69967   .       -       .       ID=augustus_masked-scaffold_563-processed-gene-0.18-mRNA-1:exon:148;Parent=augustus_masked-scaffold_563-processed-gene-0.18-mRNA-1
scaffold_563    maker   CDS     69967   69967   .       -       1       ID=augustus_masked-scaffold_563-processed-gene-0.18-mRNA-1:cds;Parent=augustus_masked-scaffold_563-processed-gene-0.18-mRNA-1


Strange stuff…

Regards,

Marc

On 05 Aug 2014, at 22:49, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:

One more thing.  From the example you gave, is is important to note that the terminal CDS (first or last) can be a single base pair in length (start and end will be the same value). Augustus sometimes does this for example.  Do you have non-CDS feature types where this happens, or any internal CDS's where this happens?

--Carson


From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Tuesday, August 5, 2014 at 2:21 PM
To: Marc Höppner <mphoeppner at gmail.com<mailto:mphoeppner at gmail.com>>, <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Maker GFF output with features of 0 length

Were you using GFF3 pass-through or correct_est_fusion options? When you rerun do the same features still have lengths of zero (I.e. is it random or is it reproducable)?

--Carson


From: Marc Höppner <mphoeppner at gmail.com<mailto:mphoeppner at gmail.com>>
Date: Wednesday, July 30, 2014 at 4:44 AM
To: <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: [maker-devel] Maker GFF output with features of 0 length

Hi,

I’ve - more by accident - found that many of the gene builds I have generated with Maker (2.31.3) contain features with identical start and stop positions.

For example:

scaffold_2927   maker   CDS     13013   13013   .       +       1       ID=maker-scaffold_2927-augustus-gene-0.8-mRNA-1:cds;Parent=maker-scaffold_2927-augustus-gene-0.8-mRNA-1


This occurs seemingly randomly for all sorts of feature types and I have only seen this when running Maker on full assemblies. Before I start turning every stone, any ideas about possible explanations for this phenomenon? Is this likely some MPI-related communication issue, or NFS problems with synching data? Maker runs fine on our system, but that doesn’t mean that there aren’t any cryptic issues that only on these occasions read their head… Regarding the frequency, out of 450.000 GFF lines, 270 were affected in the case that I looked into the most. So it is pretty rare, but still...

I am currently using Maker with openmpi-1.7.4 and the file system is mounter of NFS4 and IPoIB. I now switched to Maker 2.31.6, but have no strong reason to suspect that this will make a difference.

Regards,

Marc


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