I am running Qiime2 analyses for 498 samples (after combining 2 studies which had paired-end reads). I am going to run the following command for taxonomic classification:
qiime feature-classifier classify-sklearn --i-classifier silva-132-99-nb-classifier.qza --i-reads merged-rep-seqs-295-203.qza --o-classification taxonomy-295-203.qza
Can I add something in the command to know its progress?? (I want to know how long will it take to finish the job!)
Unfortunately there is no parameter in Qiime2 commands that gives you a progress estimation. While this would be super handy, it is not really possible to estimate for most if not all commands as there are too many dependencies on your files and system. In some plugins (for example DADA2 and vsearch) Including the
--verbose parameter in your commands will show you which step of the process is currently running but it does not estimate time to completion.
Thank you for responding! It took nearly 10 hours last time to run this command!
Glad it was completed, sadly this is typical of some of these steps in a bioinformatics pipeline. You can try recruiting more powerful machines or do what some of us do and simply organize your schedule to run the heavier steps overnight/weekends.
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