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agat_sp_statistics.pl --gff Mus_musculus.GRCm38.87.gff3
Reading file Mus_musculus.GRCm38.87.gff3
2145907 warning messages: gff3 reader warning: primary_tag error
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- Primary tag values (3rd column) not expected => v_gene_segment c_gene_segment mt_gene supercontig biological_region j_gene_segment vd_gene_segment -
- Those primary tag are not yet taken into account by the parser! -
- If you wish to use it/them, pleast update the parameter feature json files accordingly (features_level1, features_level2 or features_level3). -
- To resume: -
- - it must be a level1 feature if it has no parent. -
- - it must be a level2 feature if it has a parent and this parent is from level1. -
- - it must be a level3 feature if it has a parent and this parent has also a parent. -
- -
- Currently the tool just ignore them, So if they where Level1,level2, a gene or RNA feature will be created accordingly. -
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- Primary tag values (3rd column) not expected => aberrant_processed_transcript pseudogenic_transcript c_gene_segment processed_pseudogene snorna_gene n -
- In theory these values are not compatible with gff3 format because they are not part of the Sequence Ontology. -
- If you want to follow rigourously the gff3 format, please visit this website: -
- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md -
- They provide tools to check the gff3 format. -
- Even if you have this warning, you should be able to use the gff3 output in most of gff3 tools. -
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1317 warning messages: Use of uninitialized value in string eq at /domus/h1/royfranc/miniconda3/envs/agat/lib/site_perl/5.26.2/AGAT/OmniscientI.pm line 1274.
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The text was updated successfully, but these errors were encountered: