Hi! i’m new in this forum and i start to use Mothur v.1.33.3 for my thesis about 16s rRNA gene of seagrass’s microbial community. I have this type of error: when i run the command unique.seqs (after trim.seqs) Mothur says me
[ERROR]: You already have a sequence named JH5B4ZK02F5COJ in your fasta file, sequence names must be unique, please correct.
[ERROR]: You already have a sequence named JH5B4ZK02GFIU3 in your fasta file, sequence names must be unique, please correct.
So i try to change the name in my fasta and name files (for the name file i use the line command to open the file with gedit) but with this new file Mothur don’t run and says me that is unable to open my fasta file.
So, I explicitly ignored this problem and i try to continue with my analysis.
Mothur seem run good until the pre.cluster command:
Your name file contains 0 valid sequences, and your groupfile contains 183493, please correct.
Running command: unique.seqs(fasta=/home/irene/060215LmcomFTH.shhh.trim.unique.good.filter.unique.precluster.fasta, name=/home/irene/060215LmcomFTH.shhh.trim.unique.good.filter.unique.precluster.names)
[ERROR]: /home/irene/060215LmcomFTH.shhh.trim.unique.good.filter.unique.precluster.fasta is blank, aborting.
Using /home/irene/060215LmcomFTH.shhh.trim.unique.good.filter.unique.fasta as input file for the fasta parameter.
[ERROR]: /home/irene/060215LmcomFTH.shhh.trim.unique.good.filter.unique.precluster.names is blank, aborting.
How it’s possible? my file aren’t blank…
i saw that in this forum it was posted a problem like mine with another version’s mothur(1.32.1) but there isn’t a real conclusion.
Someone help me?
Thanks all, is my first approach to a bioinformatic program and i have some difficulty!!
Irene
Welcome to the mothur community! I would recommend upgrading to our current version. Here’s a link, https://github.com/mothur/mothur/releases/tag/v1.36.1. The errors you are getting likely all stem from the unique.seqs error. Could you post the commands you ran before you ran the unique.seqs command? Also, here are a few links you may find helpful as you get started with mothur.
http://www.mothur.org/wiki/454_SOP
http://www.mothur.org/wiki/MiSeq_SOP
http://www.mothur.org/wiki/Frequently_asked_questions
http://www.mothur.org/wiki/Silva_reference_files
http://www.mothur.org/wiki/RDP_reference_files
http://www.mothur.org/wiki/Greengenes-formatted_databases
http://www.mothur.org/wiki/Lookup_files
thanks! i try to install the new version but the installation haven’t successfully.
Howewer the command for the unique.seqs are this, like in the mothur’s wiki 454SOP:
unique.seqs(fasta=060…shhh.trim.fasta, name=060…shhh.trim.name)
and mothur give me the error that i describe before.
For the new mothur’s version i unistalled the first version so in this moment i don’t have anymore mothur in my pc.
I can risolve this problem with the new version??
Obviusly i have problem with the installation.
I come from we says: never a joy.
Thanks a lot again
Hello,
I have also got these problems, and I am using an updated version of mothur following the Miseq SOP.
make.contigs(file=stability.files, processors=4)
screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, contigsreport=stability.contigs.report, maxambig=0, minlength=240, maxlength=275, maxhomop=8, mismatches=25)
unique.seqs(fasta=stability.trim.contigs.good.fasta)
[ERROR]: You already have a sequence named M02127_93_000000000-AF4PJ_1_1101_18193_1706 in your fasta file, sequence names must be unique, please correct.
[ERROR]: You already have a sequence named M02127_93_000000000-AF4PJ_1_1101_14186_1714 in your fasta file, sequence names must be unique, please correct.
…
[ERROR]: You already have a sequence named M02127_93_000000000-AF4PJ_1_2114_17720_28797 in your fasta file, sequence names must be unique, please correct.
23599780 752011
Output File Names:
E:\Miseq_CF\1923OP\stability.trim.contigs.good.names
E:\Miseq_CF\1923OP\stability.trim.contigs.good.unique.fasta
Even though it gave output files, but there was also problem when I run the count.seqs command.
Error: your group file contains more than 1 sequence named…, sequence names must be unique. Please correct
Error: your group file contains more than 1 sequence named…, sequence names must be unique. Please correct
Error: your group file contains more than 1 sequence named…, sequence names must be unique. Please correct
At the end, error: processes reported processing …sequences, but group file indicates you have … sequences. do you have a file mismatch?
I have also tried to rerun again, or using 1 processor at that step, but it repeated these errors.
Could anyone give an suggestion 
?
Thanks
Junnie
Hi there,
From the command line where you are running mothur can you type the following and post the output?
mothur -v
Also, can you post the content of your stability.files file?
Pat
Dear Dr. Schloss,
I too am receiving the error described above. I typed “mothur -v” into my command prompt but the command is not recognized.
[ERROR]: You are missing (
Invalid.
I am running mothur through puTTy in a HPC.
Katherine
The contents of my files.file are as follows:
…/stability/Alexa-1_S76_L001_R1_001.fastq …/stability/Alexa-1_S76_L001_R2_001.fastq
…/stability/Alexa-2_S77_L001_R1_001.fastq …/stability/Alexa-2_S77_L001_R2_001.fastq
I am using the latest version of mothur as well:
$module display mothur
(“PATH”,"/usr/local/mothur/1.36.1/bin")
Hi Pat,
Thanks for your time and reply.
I have just found that I have one repeated sample ID in my stability.files by mistake. It works now after I correct that.
Katherine, maybe you also check whether it is the same problem for you?
Best,
Junnie
Thank you for your suggestion. I do not have any duplicate files within a sample, but it appears that I have sequences in different samples with the same names. I created an oligos file, and adding that option to my make.contigs command- believing that may solve my problem. Unfortunately I must not creating it properly because though the contigs are made, the fasta file is not written. Any suggestions would be greatly appreciated. This is the first sample set I have processed in mothur.
Thank you in advance for your assistance!
Katherine
Katherine
Your files file doesn’t seem to have group names. Can you add those to the file and try again?
Also, the mothur -v command should be run from the command line, not from within mothur.
Pat