Hello All. I wish to classify my sequences using silva 132 database. I cannot run silva on local computer since silva always needs high memory. being said, i install qiime2 in our university server usimg miniconda3. ‘Source activate’ seems not working with standard slum. I also tried to specify the directory with " ~/.conda/envs/qiime2-2018.11/bin/qiime" but were also not working with slurm.
Here is the bash script:
module load miniconda3
Activate conda environment
source activate qiime2-2018.11
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads /home/users/mlnada/silva_refseqV3V4.qza --i-reference-taxonomy home/users/mlnada/silvataxonomy.qza --o-classifier silva_classifier.qza
If anyone of you has experience running qiime2 in cluster, Can you provide me a work around on this? All i need is to classify the sequences using silva in cluster, then, I can do the remaining analysis on my local computer.
Thank you very much.