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cmkobel / CompareM2

🦠📇 Microbial genomes-to-report pipeline
https://CompareM2.readthedocs.io
GNU General Public License v3.0
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Eggnog fails if version installed is above or equal to 2.1.7 #108

Closed michoug closed 2 months ago

michoug commented 2 months ago

Hi The eggnog rule fails if eggnog mapper is above or equal to 2.1.7 because it creates a gff file ending with .emapper.genepred.gff instead of .emapper.gff as is the case now

https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.12#v217

Changes in GFF decoration to (hopefully) fix issue #367 , in which positions were relative to the ORF (1-end) instead of relative to the contig which contains the ORF. Now, 2 GFF files will be created when using gene prediction and gff decoration: one ".genepred.gff" from either Prodigal or blastx-like hits, one ".decorated.gff" with the annotations added as attributes.

May I suggest to specify the versions of the tools in the env files to avoid such issues. Cheers Greg

cmkobel commented 2 months ago

Hi Greg

Thanks for pointing this out.

I'm now pinning v2.1.12, and setting the expected output to expect .emapper.genepred.gff

Best

cmkobel commented 2 months ago

Fix is out https://github.com/bioconda/bioconda-recipes/pull/49572