Summary Seqs command not working

Hi! I’m currently working through the Mothur MiSeq SOP, but I’ve encountered an issue with the summary.seqs() command. It seems that a counts table file was not generated by the previous make.contigs() command.

I’m using Mothur version 1.40.4 and accessing it through my university’s HPC. I saw another user on this forum who had a similar problem, and they mentioned that updating their Mothur version resolved the issue. However, after running the command conda update -c bioconda mothur, I still have Mothur version 1.40.4.

Could anyone provide guidance on how to resolve this issue? Thanks.

Hi there,

That’s a very old version of mothur. I’d strongly encourage you to upgrade to the most recent version - 1.48.0. Either reach out to your HPC Administrators or see about setting the mothur version to 1.48.0 in your conda environment. Make sure you’re activating the environment before you run mothur.


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