Hi guys, I encountered some errors while trying to run taxonomy classification based on silva classifier. I had 48 16s rDNA samples, total size of my DNA is around 1.2gb.
I did some digging in the forum regarding the same issues, and try and error from those previous, like these:
4 DEC 8.18pm
$ qiime feature-classifier classify-sklearn --i-classifier silva-132-99-515-806-nb-classifier.qza --i-reads rep-seqs.qza --p-chunk-size 20000 --o-classification taxonomy.qza
4 DEC 8.30pm
$ qiime feature-classifier classify-sklearn --i-classifier silva-132-99-515-806-nb-classifier.qza --i-reads rep-seqs.qza --p-reads-per-batch 20000 --o-classification taxonomy.qza
4 DEC 8.45pm
$ qiime feature-classifier classify-sklearn --i-classifier silva-132-99-515-806-nb-classifier.qza --i-reads rep-seqs.qza --p-n-jobs 20 --p-reads-per-batch 1000 --o-classification taxonomy.qza
4 DEC 9pm
$ qiime feature-classifier classify-sklearn --i-classifier silva-132-99-515-806-nb-classifier.qza --i-reads rep-seqs.qza --p-n-jobs 1 --p-reads-per-batch 2000 --o-classification taxonomy.qza
4 DEC 9.15pm [success]
$ qiime feature-classifier classify-sklearn --i-classifier gg-13-8-99-515-806-nb-classifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
4 DEC 9.30pm
$ qiime feature-classifier classify-sklearn --i-classifier silva-132-99-515-806-nb-classifier.qza --i-reads rep-seqs.qza --p-reads-per-batch 1000 --o-classification taxonomy.qza
4 DEC 9.45pm
$ qiime feature-classifier classify-sklearn --i-classifier silva-132-99-515-806-nb-classifier.qza --i-reads rep-seqs.qza --p-reads-per-batch 1000 --p-pre-dispatch 1 --p-n-jobs 20 --o-classification taxonomy.qza
All of the command above except the one using greengenes classifier work. The same error keep killing the analysis:
Plugin error from feature-classifier:
Unable to allocate array with shape (796852224,) and data type float64
Debug info has been saved to /tmp/qiime2-q2cli-err-t6driasm.log
I am currently dual-booting my laptop, and natively install qiime2 from ubuntu. My laptop had 8gb ram and i allocated 300gb to my ubuntu os system.
SO, here is my questions:
- how reliable is greengene since it had not been updated since years ago?
- is there any possible ways to conducted the analysis by using silva classifier with my current laptop?
Thank you in advance