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WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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DRAM distill output errors: almost all values are zeros #287

Closed Somebodyatthdoor closed 11 months ago

Somebodyatthdoor commented 1 year ago

Hi,

I am having an unusual problem when running dram distill. I end up with a summary that has zero values for practically all of my MAGs . metabolism_summary.xlsx. But when I look in the annotate.tsv file there are clearly genes that are annotated with some of the functions described as "0.0" in the metabolism summary file. So I think it is a problem with the distill command, rather than with the annotation.

I do get some errors when running dram distill (dram_distill_drep_err.txt), but I don't see why any of them would cause this problem.

I am using dram v1.4.6.

Any advice you can give would be appreciated.

Cheers, Laura

BioRRW commented 1 year ago

Apologies for the late reply but thank your for reaching out. Which databases did you use to annotate? - KEGG formatting can result in this issue.

Good luck and keep us posted

jrr-microbio commented 1 year ago

See this entry for help relating to KEGG database formatting: https://github.com/WrightonLabCSU/DRAM/issues/305

Somebodyatthdoor commented 1 year ago

Thank you both for your comments.

I have been using an oldish version of KEGG, so I'll give your suggestion a try.

Cheers, Laura