DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs. DRAM annotates MAGs and viral contigs using KEGG (if provided by the user), UniRef90, PFAM, dbCAN, RefSeq viral, VOGDB and the MEROPS peptidase database as well as custom user databases. DRAM is run in two stages. First an annotation step to assign database identifiers to gene, and then a distill step to curate these annotations into useful functional categories. Additionally, viral contigs are further analyzed during to identify potential AMGs. This is done via assigning an auxiliary score and flags representing the confidence that a gene is both metabolic and viral.
Activating the conda environment
Check out a node with
qrsh and run:
Using conda activate DRAM
If your conda is set up as
you can run
conda activate DRAM instead of the
source line above.
Running over SGE
To use over SGE, include the source line above in a shell script prior to your commands, e.g.
And then run
hqsub 'bash ./run_DRAM.sh' -r sge.DRAM ...
Using hqsub –conda
You can also run:
hqsub 'conda activate DRAM; DRAM.py ...' -r sge.DRAM --conda ...
Without having to write a separate shell script.
Location and version