Kraken run time on galaxy clusters

Question

[Daniel Hand]

I have been running 0.2-2M 300 bp kraken jobs on the bacterial database on a private cloudman cluster with one c3.large master node (set to not do jobs) and 0-10 r3.8xlarge worker nodes (32 cores, 244 gb memory).

The problem is that the jobs are taken between 6-13+ hours with the bacterial database to complete, is this normal?

It also made me think that I do not understand how Kraken works with galaxy. Is the cluster downloading the large bacterial database from NCBI and making it for each job?

[Ram]

Please search/ask Galaxy Biostar at https://biostar.usegalaxy.org/