No output from training with feature-classifier

Hello, I'm a beginner with the system. I've been trying to train a classifier from the SILVA 138.1 NR99 for the 18S V4-V5 region following the rescript plugin guide (Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt). I've been able to run through the whole process until the final step where no outputs are generated for the classifier, I receive no errors as well and --verbose shows a warning related to version incompatibility. Please see the attached image for the error. Thanks!

Hi @RielAlfonso ,

The command is still running (until you see the command prompt again). It could take some time (e.g., a few hours) to train the classifier.

The message you see is a warning, not an error — something to read while you wait!

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Hi @Nicholas_Bokulich,

Thank you for the response. I did see a previous post that suggested a similar solution. My jupyter notebook however changes its status from busy to idle, which led me to think it was done running. Should I ignore the notebook status and just let it run on?

Hello, I noticed that running on the command line instead of the notebook resulted in this "Killed" message. What I understood from my googling is that this is likely a memory issue. I did notice my device has been running low on memory. I will follow-up when I clear up some space and retry, but this looks like the solution so far.


Very strange — I was going to ask if the job was being killed, but I would expect this to also be reported in Jupyter notebook in that case.

You can check the forum history for quite a few topics on troubleshooting memory issues — SILVA in particular can take quite some memory (usually at least 12 GB RAM).

Good luck!

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