kmer_query memory scaling

arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

Other

328 stars 76 forks source link

kmer_query memory scaling #247

Closed Perugolate closed 9 months ago

Perugolate commented 12 months ago

any idea how rgi kmer_query memory usage scales? We are using it on output from rgi bwt. bam files are 0.4-3 GB, with 150-2200 terms.

apologies if I have missed this.

raphenya commented 10 months ago

@Perugolate, you can use something like so:

scalene --profile-all --reduced-profile \
--web --no-browser --outfile out.html \
--html /opt/miniconda3/envs/rgi603/bin/rgi kmer_query \
-i path/to/input_bam --bwt -k 61 -n 8 -o out_rgi --local --debug > run.log 2>&1 &

Ref: https://github.com/plasma-umass/scalene