Count and FASTA mismatch

I have read about this problem but mine seems to be unique from others I have seen because the files are mismatched by exactly half.

Here are my steps:
mothur > make.contigs(file=stability.files, processors=8)

Output File Names:





contain the sequence data and group identity for each sequence

Total of all groups is 3173672

mothur > summary.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table)

ERROR: Your count file contains 1586836 unique sequences, but your fasta file contains 3173672. File mismatch detected, quitting command.

When I look at my stability.files everything seems to be matched correctly. I reran this twice and got the same result. Any insight for me?

Hmmm, I’m not sure what’s going wrong here. What version of mothur are you using? Can you try running the following?


Let me know what the output looks like


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