Strange --preload behaviour

[Freemacl]

Hello,

I have used kraken successfully several times before with this exact command and I'm not sure how to diagnose this current issue. The command is:

kraken --preload --db ~/scratch/krakendb --paired ${READ} ${READ2} --output HEADER.kraken --threads 32

The database will slowly load into memory until it reaches about 20 Gb, where it stops, reports "Loading database... complete." The program begins to run afterwards but only uses ~15% of the available computing resources. Any idea how to troubleshoot this? Prior to this issue, I was able to finish processing a sample (50M reads) in under 15 minutes and now it wont even finish in 8 hours.

[emrahkirdok]

Dear Freemacl,

I got the same problem also. I solved it by using a ramdisk.

[your-highness]

Dear @Freemacl ,

I think the order of the commands is wrong, i.e. the file names have to be given after the arguments. Try:
kraken --preload --db ~/scratch/krakendb --paired --output HEADER.kraken --threads 32 ${READ} ${READ2}

Best