[maker-devel] FAILED contigs

[Bérénice Benayoun]

Hi maker development team,

sorry to bother you again.

I was going through the results, and it seems I have a number of contigs that are consistently failing during the annotation of my genome

(eg, in the log, I find something like "GapFilledScaffold_3308 maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/ FAILED", and no annotation gets outputted). 

No matter how many times I retry their annotation, they start then fail during. Most of the contigs in my assembly still make it through the pipeline.

Do you have any idea on why some contigs fails for annotation or any advice on what to do to force maker to produce an output on these ? Is there anything I can do to bypass this issue?

Thanks so much in advance for your insights on this issue!

Best,

Berenice

--
Bérénice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120
Stanford, CA 94305-5120
USA
Email: bena...@stanford.edu
Web: www.stanford.edu/group/brunet/

[Carson Holt]

In your MAKER STDERR (printed to screen or captured as part of run), search for the word ERROR.  That will give a more specific explanation as to why it is failing.  If you did not capture this on your first run, you may need to redirect it to a file on a retry.

Example --> maker 2> error.log

Thanks,

Carson

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[Bérénice Benayoun]