EDTA stopped after finding no SINEs

[beibeiliu1008]

Hi Dr. Ou,

I am trying to run Extensive de-novo TE Annotator (EDTA) v2.2.2, on tomato.
here is the code: perl ../EDTA/EDTA.pl --genome ./TS15_final.fasta --cds ./SL5.cds.fa --overwrite 1 --sensitive 1 --anno 1 --threads 30

I got error like this:

File "/home/beiliu/.conda/envs/EDTA/bin/AnnoSINE_v2", line 6, in
from AnnoSINE.AnnoSINE_v2 import main
ModuleNotFoundError: No module named 'AnnoSINE'
cp: cannot stat 'TS15_final.fasta.mod.SINE.raw.fa': No such file or directory
Error: SINE results not found!

ERROR: Raw SINE results not found in TS15_final.fasta.mod.EDTA.raw/TS15_final.fasta.mod.SINE.raw.fa
If you believe the program is working properly, this may be caused by the lack of SINEs in your genome

I am using the latest version EDTA (v.2.2.2), any suggestions to work around this issue?

Thanks

[shehongbing]

Hi,
I’ve sorted this out now; I hope this helps. I noticed that the ‘pytz’ module was missing from TIR-Learner. Once I installed pytz, the pipeline ran without any issues.

[yaoxkkkkk]

Hi, I met same error too using latest v2.3.0.

[linyuiz]

Hi, I met same error too using latest v2.3.0.您好，我使用最新的 v2.3.0 版本也遇到了同样的错误。
You can try this.
https://github.com/linyuiz/EDTA_update/releases/tag/v2.3.0-2

[yaoxkkkkk]

@linyuiz Thank you for your work. It looks like that you re-construct all the pipeline using nextflow, is it support panEDTA feature now? Because I have ~80 genomes to annotate.

[linyuiz]

@linyuiz Thank you for your work. It looks like that you re-construct all the pipeline using nextflow, is it support panEDTA feature now? Because I have ~80 genomes to annotate.

For panEDTA, you can run EDTA-nextflow for each genome, then rename the sequence IDs in the edta.lib.fa output files for each genome, merge them, and use

perl $path/bin/cleanup_nested.pl -in $outfile.panEDTA.TElib.fa.raw -cov 0.95 -minlen 80 -miniden 80 -t $threads

Just run RepeatMasker again, it's very simple.

[Ju1232]

Hello, I am a staff member in Dr. Ou's lab. I recently posted a response on Issue #565, and I believe your SINE issue may be related to Cause A because you encountered the following message:

"cp: cannot stat 'Pgroen.Genome02.fa.mod.SINE.raw.fa': No such file or directory"

Please check the explanation there, and I hope it helps resolve your problem.
Thank you!