Countfile and fasta.align not the same amount of sequences

Halo
After running the summary.seqs command following align.seqs. I keep on receiving the following error

ERROR: Your count file contains 14258923 unique sequences, but your fasta file contains 13015360. File mismatch detected, quitting command.
Please help.

Please see commands run before error

fastq.info
trim.seqs
unique.seqs(input= #trim.seqs.fasta
merge.files (input=unique.trim.fasta
make.count (fasta= unique.trim.fasta, groups= output=count_table
unique.seqs(fasta=created during merge.files, count=created during make.count)
align.seqs(fasta=.unique.fasta, reference=Ezibiocloud_full_align.align, flip=t)
summary.seqs(fasta=unique.align, count=created during unique.seqs)-Then Error

Thank you

Hi,

Can you post the actual commands you ran? Are you sure there were no errors when you ran align.seqs?

Thanks,
Pat