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wurmlab / flo

Same species annotation lift over pipeline.
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Expecting number line ERROR #40

Closed matoller closed 2 years ago

matoller commented 2 years ago

Hello, I want to thank you for create this amazing tool and helping people with their flo issues. I am having a problem with a flo run and I am not able to solve it. I think is related with the gff file but I dont know what is the problem (I downloaded it directly from NCBI). These are the files I am using to run flo flo_files.zip

Here is the error:

liftOver -gff /home/jose/flo_haloferax/new.gff run/liftover.chn run/new/lifted.gff3 run/new/unlifted.gff3 Reading liftover chains Mapping coordinates WARNING: -gff is not recommended. Use 'ldHgGene -out=' and then 'liftOver -genePred ' Expecting number line 12 of /home/jose/flo_haloferax/new.gff rake aborted! Command failed with status (255): [liftOver -gff /home/jose/flo_haloferax/new...] /home/jose/flo/Rakefile:45:in block (2 levels) in <top (required)>' /home/jose/flo/Rakefile:40:ineach' /home/jose/flo/Rakefile:40:in block in <top (required)>' /var/lib/gems/2.7.0/gems/rake-13.0.6/exe/rake:27:in<top (required)>' Tasks: TOP => default

I tryed to preprocess the gff file using gt gff3 -tidy -sort -addids -retainids and also to delete the gene feature with gff_remove_feats.rb gene but the same error appears.

Thank you so much in advance!

matoller commented 2 years ago

Problem solved. The .gff file has some features that seem to be not campatible with flo. I removed them to simplify the file and it finally worked.

yannickwurm commented 2 years ago

Thanks for the update @matoller - apologies for our lack of response. Typically the main issues are with gffs having too much info / or weird fields in them.

Take care