I recently received the following error message "Error in filter_otus_from_otu_table.py: Filtering resulted in an empty BIOM table. This indicates that no OTUs remained after filtering". I have been unable to complete pick_open_reference_otus as I receive an error massage that my fasta file was empty during the filter_alignment.py. I backtracked and found that in the pynast_aligned_seqs folder my rep_set_aligned.fasta is empty. I inputted
filter_otus_from_otu_table.py -i otu_table_mc2_w_tax.biom -o otu_table_mc2_w_tax_no_pynast_failures.biom -e pynast_aligned_seqs/rep_set_failures.fasta
To try and create the otu_table_mc2_w_tax_no_pynast_failures.biom I needed, and this is where I received the error message that the filtering resulted in an empty BIOM table. Would anyone know how to possibly remedy this?
I'm sorry, this is just my first time using QIIME and doing any bioinformatics so I'm stuck. I can provide more information if needed. Thank you for any help you can offer.