Description of the bug
Hello,
We are running DRAM 2.0 on the Digital Research Alliance of Canada HPC (Fir) with UniRef on high-performance scratch storage. The MMSEQS_SEARCH_UNIREF step shows no progress after 12 hours hours per genome even for a small test MAG. We plan to annotate ~3000 MAGs and at this rate UniRef alone would be impractical.
Is UniRef pre-indexed once at the database level, or is indexing happening per genome? Are there recommended MMseqs2 settings (e.g. --split-memory-limit, sensitivity, or prefilter settings) to speed up the UniRef search for large MAG datasets?
Thank you for your time and the great tool!
System information
DRAM v2.0.0-beta28
Nextflow version 25.10.2
HPC
Slurm
Apptainer
Command used and terminal output
nextflow run WrightonLabCSU/DRAM -r v2.0.0-beta28 \
--input_fasta /home/jcsm2010/scratch/2026-02-19_MetaG_FarmAD_400L/genome_qc_results/test_bins/ \
--outdir /home/jcsm2010/scratch/2026-02-19_MetaG_FarmAD_400L/DRAM_output \
--annotate \
--anno_dbs kofam,camper,canthyd,sulfur,fegenie,merops,dbcan,pfam,metals,antismash,tcdb,dram_db,vog,methyl,uniref \
--summarize \
--traits \
--visualize \
--slurm \
-profile apptainer \
-c /scratch/jcsm2010/DRAM/custom.config \
-resume
Relevant files
custom config:
process {
clusterOptions = '--account=rpp-shallam '
}
params {
tiny_gb_mem_limit = 1
small_gb_mem_limit = 8
medium_gb_mem_limit = 24
big_gb_mem_limit = 48
huge_gb_mem_limit = 400
huge_hr_time_limit = 48
}
Description of the bug
Hello,
We are running DRAM 2.0 on the Digital Research Alliance of Canada HPC (Fir) with UniRef on high-performance scratch storage. The MMSEQS_SEARCH_UNIREF step shows no progress after 12 hours hours per genome even for a small test MAG. We plan to annotate ~3000 MAGs and at this rate UniRef alone would be impractical.
Is UniRef pre-indexed once at the database level, or is indexing happening per genome? Are there recommended MMseqs2 settings (e.g. --split-memory-limit, sensitivity, or prefilter settings) to speed up the UniRef search for large MAG datasets?
Thank you for your time and the great tool!
System information
DRAM v2.0.0-beta28
Nextflow version 25.10.2
HPC
Slurm
Apptainer
Command used and terminal output
Relevant files
custom config:
process {
clusterOptions = '--account=rpp-shallam '
}
params {
tiny_gb_mem_limit = 1
small_gb_mem_limit = 8
medium_gb_mem_limit = 24
big_gb_mem_limit = 48
huge_gb_mem_limit = 400
huge_hr_time_limit = 48
}