unique.seqs error


When running unique.seqs command, I am getting the error below:

mothur > unique.seqs(fasta=uic.trim.contigs.good.fasta )

[ERROR]: You already have a sequence named M02127_258_000000000-B4RL2_1_1101_16099_2069 in your fasta file, sequence names must be unique, please correct. This error is repeated for all of the sequences that I will not add to this post. This seems odd that this command would require unique sequences.

The details for the mothur version used are:
Linux version
Using ReadLine
Running 64Bit Version
mothur v.1.39.5

Thanks for your assistance,


What are the commands that you are running upstream of this command?


The previous commands were:

make.contigs(file=uic.files, processors=8)


screen.seqs(fasta=current, group=current, summary=current, maxambig=0, maxlength=275)



Using uic.trim.contigs.good.fasta as input file for the fasta parameter.



I also have run these same set of commands on the newest version for Mac using 1 processor, in which I still get the same error, except for only a large subset of sequences, and not every sequence.


Could you have duplicate files in your uic.files file? If not, can you send your input files and log file to


I have been getting this same error recently. When I ran my data using v 1.39.5 the error occurred after make.contigs and identified 68 repeated sequence names. However, when I updated to v.1.40.5 the error didn’t occur until the unique.seqs command and identified thousands of repeated sequence names.

Thank you for the help,



Could you send your input files and logfile to