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songweizhi / MarkerMAG

Linking MAGs with 16S rRNA marker genes
GNU Affero General Public License v3.0
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barrnap_16S: 'No query genome detected' #3

Closed Laura-Alex closed 2 years ago

Laura-Alex commented 2 years ago

Hello folks,

I'm pretty excited about MarkerMAG. Sadly, I can't seem to figure out the supplementary barrnap_16S module.

Standard barrnap works well on my setup. However, when I try to run barrnap 16S on MEGAHIT results as follows:

MarkerMAG barrnap_16s -p ALW -g /scratch/username/megahit/sample/ALW/final.contigs.fa -x fa -t 6 -force

Then I get the following error: No query genome detected, program exited!

I have checked whether the file final.contigs.fa is in that location and contain stuff with more , and it does indeed seem to be there. I know I can run barrnap for now and just delete what I don't need, but it would be nice to see if there's anything I can do to use the simpler version.

songweizhi commented 2 years ago

Hi Laura, The barrnap_16s module doesn't support single file input in the current version, I'll include this feature in the next release. to run barrnap_16s on a single file, you can put that file in a folder and provide that folder to barrnap_16s with -g. Cheers, Weizhi

Laura-Alex commented 2 years ago

Much appreciated, Weizhi!