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DerKevinRiehl / transposon_annotation_reasonaTE

Transposon annotation tool "resonaTE" (part of TransposonUltimate)
GNU General Public License v3.0
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RepeatModeler version Error #27

Closed Riccardo1274 closed 8 months ago

Riccardo1274 commented 8 months ago

Good morning Kevin, while running "reasonaTE -mode annotate -projectFolder workspace -projectName project -tool repeatmodel", I got the following error: Building database sequence_index: Adding sequence.fasta to database Number of sequences (bp) added to database: 617 ( 1105955550 bp ) ERROR: The -pa parameter has been deprecated. Please use the newer "-threads #" parameter which precisely controls the maximum number of simultaneous threads this program will use. Note that the -pa parameter previously controlled the number of simultaneous batches each run with rmblast using 4 threads, therefore -pa 4 could potentially have used up to 16 threads. Keep this in mind when comparing runtime differences between versions. I tried modifying your python scripts to replace the "-pa" parameter with "-threads" in "Dupmask", but I still got the same message. I fixed it by removing repeatmodel and downloading (with conda) version 1.0.11, now it seems to work fine. As your tool is really useful and well done, it would be nice to use the latest versions. If you could tell me where I need to modify your python scripts, I would be very grateful. Thanks in advance.

Kind regards, Riccardo Rossi

DerKevinRiehl commented 8 months ago

Dear Riccardo, thank you very much for your interest in our work.

A challenge with enabling latest versions is version incompatibility issues with other tools. It would require not only to change the python code (as you did replacing -pa and -threads) but also the conda environment YML that I composed to work in this context. It might be possible to use updated software versions, however there is a high chance that this conflicts with another tool.

If you want to try, you can find all software packages and versions in the YML files. https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE/tree/main/environment_yml

Hope this can help a little, Best regards, Kevin

Riccardo1274 commented 8 months ago

Thank you for your reply and suggestion. I'll keep using the previous version of RepeatModeler as it worked. Thanks again for developing this pipeline!