$ python prep_silva_data.py SILVA_119_LSURef_tax_silva_full_align_trunc.fasta taxonomy.outfile.txt sequence.outfile.fasta
Traceback (most recent call last):
File “prep_silva_data.py”, line 8, in
from cogent.parse.fasta import MinimalFastaParser
ImportError: No module named ‘cogent’
How can I solve this? Or is there another way to make LSU reference data at 99% for QIIME2?
I use python ver. 3.5.
This is code unrelated to QIIME 2 so I cannot really offer thorough support — the error message says you are missing cogent, so just try pip install cogent to install and that may be all you need…
The end goal is to get your files into the same format as the QIIME-compatible SILVA files here. The release notes on that file — or contacting the SILVA developers for more details — may also get you on the right track.