Hi, I am having issues with the Kraken2–>Bracken step of my workflow and wondering if anyone could provide some assistance? I found a similar topic in the forum circa 2020, but no one answered his request so I’m hoping to have better luck. The system claims the kraken2 report is empty, but kraken2 …

Luckily this was just a configuration issue and easy to fix: on Galaxy Europe we had simply forgotten to give tools running in containers access to remote storage. Out of the tools in your workflow only kraken2 runs inside a singularity container and that’s why this was the step at which the issue …

Kraken Report Issue

usegalaxy.eu support

wm75 April 4, 2025, 10:03am 5

Trying to debug this atm, but can you also share your EU-server workflow please?

1 Like

Bracken not functioning

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Kraken Report Issue

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