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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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Evaluating the results of an already finished EDTA pipeline run #416

Closed adeoliveira86 closed 5 months ago

adeoliveira86 commented 5 months ago

Dear authors,

I am working with a highly repetitive invertebrate genome and, as expected, the last step of the EDTA pipeline (evaluate 1) is still running after almost 20 days of execution in a 24 threads machine. I would like to know, if it is possible to divide the EDTA run into two instances: one running the whole pipeline without evaluate, and later evaluating the results of the whole pipeline with the evaluate 1. I checked the "divide and conquer" suggested pipeline, but it revolves around the structural prediction of TE elements, and do not this specific step I mentioned.

Best regards and thanks a lot for the wonderful tool. André

oushujun commented 5 months ago

Hi André,

Please use the /util/evaluation.pl script for this purpose.

Thanks, Shujun