Skip to main content

Table 7 Runtimes and peak memory consumption for non-partitioned database construction (build) and querying for different data sets on a workstation with 512 GB RAM

From: A big data approach to metagenomics for all-food-sequencing

Data set AFS-MetaCacheCLARKKraken2Kraken2+Bracken
AFS20Build time1h 11m15h 37m1h 27m5h 32m
 Build memory64 GB428 GB69 GB147 GB
 Query time136 s93 s37 s111 s
 Query speed11.5 MR/m16.9 MR/m43.2 MR/m14.2 MR/m
 Query memory50 GB152 GB54 GB54 GB
AFS31Build time1h 47m-3h 19min11h 41min
 Build memory91 GB-107 GB296 GB
 Query time175 s-44 s58 s
 Query speed8.9 MR/m-35.9 MR/m27.0 MR/m
 Query memory78 GB-72 GB72 GB
AFS20RS90Build time1h 42m-2h 58m8h 53m
 Build memory110 GB-94 GB168 GB
 Query time180 s-43 s117 s
 Query speed8.7 MR/m-37.0 MR/m13.5 MR/m
 Query memory94 GB-79 GB79 GB
AFS31RS90Build time3h 10m-5h 55min17h 44min
 Build memory135 GB-134 GB329 GB
 Query time217 s-49 s61 s
 Query speed7.2 MR/m-32.1 MR/m25.7 MR/m
 Query memory117 GB-97 GB97 GB
  1. Query speeds are measured for the KAL_D dataset in terms of million reads per minute (MR/m). For the cases with “-” the corresponding program exceeds the main memory capacity of 512 GB. Fastest runtimes and lowest memory consumption for each dataset are indicated in bold