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Code, unit tests, and tutorials for running PICRUSt2

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3,751 input sequences aligned poorly to reference sequences and removed.

hereformore opened this issue · comments

commented

Is this normal? in total i have around 9,000 input sequences. I'm not sure if 3,751 being removed/aligning poorly means I am doing something wrong or if that level of filtering is normal?

MY first time using picrust2, and wondering if I am inputing the data wrong or something?


(picrust2) picrust2_out_pipeline % place_seqs.py -s ../seqs.fna -o out.tre -p 1 \ 
              --intermediate intermediate/place_seqs
**Warning - 3751 input sequences aligned poorly to reference sequences** (--min_align option specified a minimum proportion of 0.8 aligning to reference sequences). These input sequences will not be placed and will be excluded from downstream steps.
commented

Hi there,

You can check out this related FAQ response, which might help: https://github.com/picrust/picrust2/wiki/Frequently-Asked-Questions#why-am-i-getting-the-error-stopping---all-x-input-sequences-aligned-poorly-to-reference-sequences

That does seem like a red-flag that so many sequences are thrown out, so perhaps there is an issue with the headers for those sequences.

commented

I am just closing this as there hasn't been any follow-up for a while. Please let me know if it needs to be reopened.