I tried to solve that problem by myself by searching web and the forum, but I am stuck.
So, I am very sorry, but I have to ask you again:
qiime2-2020.8, miniconda, Mac, 25GB free RAM
After training the greengene classifier without any issues (thank you for the gorgeous tutorial!) I tried to do the same with silva, using
Silva 138 SSURef NR99 full-length sequences and Silva 138 SSURef NR99 full-length taxonomy.
First I extracted the reference reads - and it worked nicely:
qiime feature-classifier extract-reads \ --i-sequences silva/silva-138-99-seqs.qza \ --p-f-primer GTGCCAGCMGCCGCGGTAA \ --p-r-primer CCGYCAATTYMTTTRAGTTT \ --o-reads silva/silva_99_ref.qza
Then I tried to train the classifiers:
qiime feature-classifier fit-classifier-naive-bayes \ --i-reference-reads silva_99_ref.qza \ --i-reference-taxonomy silva-138-99-tax.qza \ --o-classifier silva_99_class.qza --qiet
The first try was around 2hrs, the second one around 4hrs and the last one over night around 12hrs. Result of all runs was nothing. I mean, literally nothing happened, not even an error message popped up. I couldn’t stop it running either, not with q, nor command D or command C or kill -9. I had to shut down my laptop to get out.
I sent the code to my PI and he tried to run it for me, but it didn’t work either. In my opinion qiime couldn’t find the files, so we will try again on Monday.
In case it is of any help, I can provide the verbose output.
I am very sorry, that I have to bother you with questions again.
Every kind of help is greatly appreciated!