Count and FASTA mismatch

[beckc9]

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:

stability.trim.contigs.fasta

stability.scrap.contigs.fasta

stability.contigs_report

stability.contigs.count_table

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?

[pschloss]

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

summary.seqs(fasta=stability.trim.contigs.fasta)
count.groups(count=stability.contigs.count_table)

Let me know what the output looks like

Pat