Query regarding assessing error rate in mothur

Commands in mothur
1

Hi, I am at the phase of Processing improved sequences in mothur and I am not getting -
"stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta"
this output after running following input command -


Input command - 

mothur > chimera.vsearch(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t) 

Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.count_table
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.chimeras
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.accnos

 Please look into this. How can I proceed further with classify.seqs where 
"stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta" outuput file need as an input ?
2

I think you must have an older version of mothur. If you get the latest release of mothur you should be good to go

3

Thanks for your response. I want to say you that I am using version 1.48.0 of mothur in Linux I think it is the latest version. Now, how can I fix it? I am also getting zero chimera please tell me why so? Thanks.

4

Dear Abhi,
first check your stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta file status. followed by count file. Most probably vsearch version v2.17.1 must be running with mothur v 1.48.0, if not kindly download your mothur again, if u are using HPC then please unzip in the terminal. It will work. If not then i think you may contact Pschloss or me. I will help you for sure as much I can.
Good luck

5

Can you post the first ~10 lines of the mothur logfile that looks something like this?

Mac version

Using ReadLine,Boost,HDF5,GSL
mothur v.1.48.0
Last updated: 5/20/22
by
Patrick D. Schloss

Department of Microbiology & Immunology
6

Thank you Dr_Alok sir, for your response to my query. I performed uninstalled and reinstall mothur software but the problem still exists. I am using Ubuntu 22 directly run mothur I am not using any third-party software like Conda or HPC.

7

Thank you pschloss sir for your response regarding my query. Here following are the first ten lines of my mothur log file.

(base) omics@omics-world:~/Downloads/16S_Data/working$ mothur
Linux version

Using ReadLine,Boost,GSL
mothur v.1.48.0
Last updated: 5/20/22
by
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan

When using, please cite:

8

Mothur does not produce a new fasta file if there are no chimeras to remove. You can proceed with classify.seqs using fasta=current or fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta.

1 Like
9

Thank you @westcott for your descriptive response. I followed your suggestion and classify.seqs command worked. Look I got the following outputs. Please tell me is it normal? Because I cannot see any output files with vsearch like this.

trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pds.wang.taxonomy

My outputs -
stability.trim.contigs.good.unique.good.filter.unique.precluster.rdp.wang.taxonomy
stability.trim.contigs.good.unique.good.filter.unique.precluster.rdp.wang.tax.summary
stability.trim.contigs.good.unique.good.filter.unique.precluster.rdp.wang.flip.accnos

10

Yes, those are the correct files. Since chimera.vsearch did not create a new fasta file, the filename will not include the vsearch tag.

1 Like
11

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.