Summary Seqs command not working

mothur bugs
1

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.

2

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.

Pat

3

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