WARNING message

I found this following [WARNING] message after an “align.seqs” step. Can anyone please tell me should I specially deal with it? Or, should I keep as it is?

It took 193 secs to align 144966 sequences.

[WARNING]: 49 of your sequences generated alignments that eliminated too many bases, a list is provided in /home/dc7/Desktop/mothur_analysis/prjna_612042_obese_fecal/merge.paired.trim.contigs.good.unique.flip.accnos.
[NOTE]: 25 of your sequences were reversed to produce a better alignment.

It took 193 seconds to align 144966 sequences.

Thanks and regards,

those 74 sequences are most likely not your target. Just throw them away.


Ma’am, can you please tell me how can I remove them? If I just do “screen.seqs” with “start” (1968) and “end” (11550), is that enough or should I do more step before “screen.seqs”. If yes, how?

Thank You,


The screen.seqs syntax from the SOP after running align.seqs is all you need.

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Thanks a lot Dr Schloss. Will “screen.seqs” after “align.seqs” remove all of those 74 sequences?

yup seqs that start before your start or end after your end will be thrown out.

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Ok Dr. Kendra. I understand. Thanks a lot.