The sub.sample step could not be completed because the number of sequences did not match

After completing make.contigs, I ran sub.sample, but the following error occurred:

mothur > sub.sample(fasta=stability.trim.contigs.fasta,count=stability.contigs.count_table,persample=T,size=10000)
[ERROR]: your fasta file contains 239780 sequences, and your count file contains 147069 unique sequences, please correct.

I am running the script on linux, but this problem does not occur on Windows

I’d suggest re-running the earlier steps to see where things got out of whack. You might also double check that your windows and linux versions of mothur are the same.