Qiime2 feature classification

Technical Support
1

I am new to qiime and currently doing features classification based on Silva but after running for more than 12 hours, it gave the message " zsh: killed qiime feature-classifier classify-sklearn --i-classifier --i-reads".
I am using Mini Mac with 8GB RAM and 256GB disk (37GB available).
I am using rep-seqs-dada2.qza as my input file.

Command used:
qiime feature-classifier classify-sklearn
--i-classifier silva-138-99-nb-classifier.qza
--i-reads rep-seqs-dada2.qza
--o-classification taxonomy.qza

2

Hello Raza,

Welcome to the forums! :qiime2:

zsh: killed

This means the program was 'killed'/canceled/stopped for some reason. Perhaps because of this:

This step takes a lot of memory and this computer only has 8 GB total. Do you have any other machines on which you could run this step?

3

Dear Colin,
Thank you very much for your comment. I have an access to Cluster of High Performing Computer. I used that for QC or denoising of one data set and the job is still in queue since 9 days, while the Mini Mac completed that in 5 days. So, I tried the features classification on Mac instead of cluster.
I have to use the slurm for Cluster, as inactivity result in Broken pipe issue and the run stops.

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4

I think this step is best to run on HPC, as you can allocate enough memory for this step.

I have been there :cry:

Have you asked the HPC support team about different queues? There may be a 'short' queue (also called 'burst' or 'fast') for jobs that will run quickly. Hopefully this will let you run in under 9 days.

1 Like
5

Dear Colin, I appreciate your response and helpful suggestions. I will reach out to the Tech support and seek their help for short queue.
I will provide an update on this thread of Qiime forum. Thanks!

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6

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