search

picrust / picrust2

Code, unit tests, and tutorials for running PICRUSt2
GNU General Public License v3.0
319 stars 104 forks source link

Subset of Reference 16s sequences aligned poorly to reference sequences #353

Open Abelcanc3rhack3r opened 3 weeks ago

Abelcanc3rhack3r commented 3 weeks ago

Hi,

I randomly sampled a subset of 16s RRNA sequences from the reference sequence fasta file (https://github.com/picrust/picrust2/tree/master/picrust2/default_files/prokaryotic) /pro_ref/pro_ref.fna.

Then I ran place_seqs on the random subsets.

place_seqs.py -s input_seqs -o output_tree -p 1 --intermediate intermediate_folder

I got the error : Stopping - all 4201 input sequences aligned poorly to reference sequences (--min_align option specified a minimum proportion of 0.8 aligning to reference sequences).

How can reference sequences be poorly aligned to refererence sequences?

Regards Abel Tan

R-Wright-1 commented 1 week ago

Hi Abel,

Could you send the file that contains your subset of 16S sequences please? I wouldn't expect this to happen, but can help troubleshoot if you can send the file.