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:
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 ?
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.
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.
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.
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.
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.