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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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funannotate predict doesn't recognize soft mask assembly #996

Open MoritzKaufmann opened 5 months ago

MoritzKaufmann commented 5 months ago

Hi

I'm running funannotate using docker. I used redmask to softmask my sorted assembly. When I pass the assembly to the predict function only using the soft masked genome like this:

funannotate predict -i mygenome.fa -o output_folder -s "Aspergillus nidulans"

I get the error: Error: Genome is not repeat-masked, to ignore use --force. Or soft-mask using funannotate mask command or suitable external program.

In the assembly I can clearly see that it is soft masked (see attached snipped)

Thank you very much for your help example_error.txt

ImenAssali commented 5 months ago

I'm also getting the same exact error but after a hard mask using repeatmasker.

nextgenusfs commented 5 months ago

Strange. What version of funannotate are you running?

MoritzKaufmann commented 4 months ago

Hi Sorry for my late reply. I'm using the latest version v1.8.15

hyphaltip commented 4 months ago

strange, not seeing this error but maybe we can test with the same data as the post.

nextgenusfs commented 4 months ago

Wonder if this is related to changes in biopython? @MoritzKaufmann and @ImenAssali what version of bio python is installed in the funannotate environment?

ImenAssali commented 3 months ago

I successfully resolved the issue. Despite encountering an error message from Funannotate stating: "Error: Genome is not repeat-masked, to ignore use --force. Or soft-mask using funannotate mask command or suitable external program." The root cause was unrelated to genome masking. Instead, it stemmed from an issue with the output directory. Once I rectified this, everything functioned flawlessly.