I have been using mothur version v.1.33.3 to process bacterial 16S rRNA sequences (generated by Miseq). I have followed the miseq sop and succeeded to go through all the steps except when I try count.seqs, mothur gives me an error. However, it still creates an output file. The error message is following:
[ERROR]: processes reported processing 1773630 sequences, but group file indicates you have 1778590 sequences. Could you have a file mismatch? It took 29 secs to create a table for 1773630 sequences.
I have tried many times with different data sets from the beginning but the same error always happens except when I processed only one sample instead of all my samples. Every time I had the same command, e.g.
Count.seqs(name=stability.trim.contigs.good.trim.names, group=stability.contigs.good.groups, processors=1)
With more than 1 processor count.seqs didn’t work at all.
I appreciate any advice. Thanks!