Kraken run time on galaxy clusters
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?
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Daniel Hand •
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