Error in filter_otus_from_otu_table.py

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Darryl M Angel

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Jan 29, 2020, 3:25:55 PM1/29/20
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Hello,


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.


-Darryl

TonyWalters

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Jan 29, 2020, 3:44:45 PM1/29/20
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Hell Darryl,

I need to give the customary message that QIIME 1 is no longer being updated, and support/features are going to be found in QIIME 2: https://qiime2.org/

Unless you've got a particular reason to use QIIME 1 for this analysis, it would probably be better to switch to QIIME 2. As for your particular issue, you would have to resolve the problem of the sequences failing to align to the core alignment. Since apparently no sequences are aligning, that means something is making your reads not match 16S.

1. Are these reads bacteria/archael 16S ribosomal small subunit reads?
2. Is it possible that there are non-16S PCR or sequencing artifacts in your reads, e.g. Illumina adapters, spacers, or barcodes? You may have to manually inspect some of the reads to determine this.

-Tony
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