KOunt run times and memory use

Welcome to the KOunt wiki!

Here are the average run times and maximum memory used by each of the rules in KOunt with the ten samples described in the KOunt manuscript:

Rule	Maximum memory used (G)	Run time
trim	2	17 minutes
megahit	24	30 hours
prodigal	1	2 hours
bwa	4	2 hours
bamdeal	0.5	1 minute
coverage	33	3 hours
kegg_db	0.75	5 minutes
kofamscan	7	19 hours
kofamscan_results	2	3 hours
kofamscan_results_no_clustering	2	1 minutes
abundance_results	0.5	1 minutes
abundance_results_noc	0.1	1 minutes
kegg_fastas	2	5 minutes
cdhit	7	15 minutes
split_keggs	0.5	1 minute
mmseq_keggs	5	5 minutes
mmseq_nohit	7	16 minutes
mmseq_cluster_count	0.5	1 minute
nohit_fastas_noclustering	0.75	1 minute
diamond_search_noclustering	18	2 hours
nohit_fastq_noclustering	62	2 hours
nohit_annotate_reads_noclustering	36	3 hours
kallisto_noclustering	14	1 hour
unmapped_reads	33	12 hours
kallisto_unmapped	15	40 minutes
abundance_matrix_annotate_with_mapping_noclust	1	1 minute