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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 annotate_genes #233

Closed trickovicmatija closed 1 year ago

trickovicmatija commented 1 year ago

Hello,

My command is 

DRAM.py annotate_genes -i path/to/genes_in_nt_fmt.fasta -o output_dir --threads 16

to annotate genes that I have previously grouped. I want to treat all genes in one fasta file as they belong to one genome and get the functional prediction on the pathway level. I am experiencing a problem with the command:

mmseqs createindex 1073/working_dir/1073001001_full_renamed/gene.mmsdb 1073/working_dir/1073001001_full_renamed/tmp --threads 16

There is no clear error message, but when I try to run the same command manually, the message is 

"Database 1073/working_dir/1073001001_full_renamed/gene.mmsdb is a nucleotide database. Please provide the parameter --search-type 2 (translated) or 3 (nucleotide)."

When I provide the --search-type 2, it works.

Could it be a bug since "annotate_genes" is not widely used, or am I missing something?

Best and thanks, Matija

rmFlynn commented 1 year ago

Are your genes not in amino acid format? The annotate_genes command only takes faa files.

rmFlynn commented 1 year ago

Sorry for the delay!

rmFlynn commented 1 year ago

This looks to be inactive, pleas open again if you run into the problem again.