Benchmarks: Memory Usage - simonrharris/SKA GitHub Wiki

Memory Usage

Creating split kmer files from fasta files (ska fasta)

Species	Accession Number	# Contigs	Genome Length	Memory Used
S. aureus	HE681097	1	2,832,299	418Mb
C. jejuni	GCA_001879185.1	16	1,629,708	244Mb
E. coli	GCA_000703365.1	7	5,412,686	743Mb
L. monocytogenes	GCA_001257675.1	39	2,905,183	422Mb
S. enterica	GCA_000439415.1	2	4,808,805	704Mb

Creating split kmer files from fastq files (ska fastq)

Species	# Paired Files	Mean # Reads	Mean # Bases	Max Memory	Mean Memory
S. aureus	65	1,608,999	223,069,930	710Mb	470Mb
C. jejuni	22	3,361,254	657,706,314	1,143Mb	713Mb
E. coli	9	2,122,840	356,661,903	958Mb	833Mb
L. monocytogenes	31	1,777,006	380,854,631	686Mb	510Mb
S. enterica	23	1,859,063	278,574,418	1,116Mb	777Mb

Merging split kmer files (ska merge)

Species	# Files	Mean # kmers	# Merged kmers	Max Memory
S. aureus	65	2,761,345	7,256,936	1,197Mb
S. aureus outbreak	45	2,761,896	2,788,637	489Mb
C. jejuni	22	1,680,619	2,702,560	461Mb
E. coli	9	5,116,311	5,265,848	982Mb
L. monocytogenes	31	2,901,968	2,922,836	542Mb
S. enterica	23	4,660,457	4,966,894	872Mb

Aligning samples from merged files (ska align)

Species	# samples	# kmers	Max Memory
S. aureus	65	7,256,936	1,478Mb
S. aureus outbreak	45	2,788,637	502Mb
C. jejuni	22	2,702,560	442Mb
E. coli	9	5,265,848	768Mb
L. monocytogenes	31	2,922,836	477Mb
S. enterica	23	4,966,894	809Mb

Aligning samples from merged files against a reference (ska map)

Species	Reference	Reference Size	# samples	# kmers	Max Memory
S. aureus	HE681097	2.8Mb	65	7,256,936	713Mb
S. aureus outbreak	HE681097	2.8Mb	45	2,788,637	654Mb
C. jejuni	GCA_001879185.1	1.6Mb	22	2,702,560	331Mb
E. coli	GCA_000703365.1	5.4Mb	9	5,265,848	961Mb
L. monocytogenes	GCA_001257675.1	2.9Mb	31	2,922,836	605Mb
S. enterica	GCA_000439415.1	4.8Mb	23	4,966,894	941Mb

Pairwise distance and clustering from merged files (ska distance)

Species	# samples	# kmers	Max Memory
S. aureus	65	7,256,936	1,470Mb
S. aureus outbreak	45	2,788,637	505Mb
C. jejuni	22	2,702,560	441Mb
E. coli	9	5,265,848	761Mb
L. monocytogenes	31	2,922,836	471Mb
S. enterica	23	4,966,894	801Mb