mothur > align.seqs(fasta=otus_leq.fasta, reference=silva.bacteria.fasta, flip=t, processors=8)
Reading in the silva.bacteria.fasta template sequences… DONE.
It took 25 to read 14956 sequences.
Aligning sequences from otus_leq.fasta …
It took 11 secs to align 4246 sequences.
[WARNING]: 19 of your sequences generated alignments that eliminated too many bases, a list is provided in otus_leq.flip.accnos.
[NOTE]: 6 of your sequences were reversed to produce a better alignment.
It took 11 seconds to align 4246 sequences.
Output File Names:
mothur > summary.seqs(fasta=otus_leq.align, count=otus_leq.count_table)
Using 8 processors.
[ERROR]: Your name file contains 5438 unique sequences, but your fasta file contains 4246. File mismatch detected, quitting command.
mothur > remove.seqs(fasta=current, accnos=otus_leq.flip.accnos, count=current, dups=t)
Using otus_leq.count_table as input file for the count parameter.
Using otus_leq.align as input file for the fasta parameter.
[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.
Removed 19 sequences from your fasta file.
[ERROR]: NOT is not in your count table. Please correct.