WARNING message

1

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,
DC7

2

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

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3

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,

DC7

4

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

1 Like
5

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

6

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

1 Like
7

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