The integrity of results in regards to a failed evaluation step #204
Description
Hey there, and thanks for all work you put into EDTA.
(some background)
At first, I installed EDTA directly from an existing conda environment, and used it to annotate the Turquoise killifish Genome for some joint project I'm part of. Only when it was time to submit my results I noticed I had a bug with RepeatModeler (same as 23).
Therefore, I installed EDTA by cloning the git repository and creating a fresh conda environment out of the YAML file. This time the annotation was successful, but the TEanno.sum file was empty and the last evaluation step was crushed (same as 171 and 178).
In both times the command used was something like:
conda activate EDTA
cd OutDir
nohup ~/anaconda3/envs/EDTA/bin/perl \
~/anaconda3/envs/EDTA/bin/EDTA.pl \
--genome Nothobranchius_furzeri_genome.fasta \
--cds CDS.fasta \
--curatedlib Repeats-DB-families.fa \
--sensitive 1 \
--anno 1 \
--evaluate 1 \
--threads 25 \
> EDTA.out &(BTW, the same happened with a Genome of another organism, except then I didn't provide a --curatedlib Repeats-DB-families.fa that was generated with RepeatMasker's queryRepeatDatabase.pl)
So, I would like to know if I may use the output of the last results, specifically the TEanno.gff3 file.
If the answer is yes, I'd like to know what is the best way to summarize the results in the same way as they would appear in the TEanno.sum file. I found 174 but it mostly dealt with costume summaries.
Thanks a lot!