MiSeq SOP problems

[BigGabe]

Hello everyone,
I’m trying to do the MiSeq SOP as part of my bioinformatics course. I’m able to get through the first couple steps fine, but where the instructions say to use a file ending in “count_table” I had to use the stability.contigs.groups file. This led to the next issue, where we’re supposed to trim down the data sets. So, I entered this line of code:

mothur > screen.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.groups, maxambig=0, maxlength=275, maxhomop=8)

This returned an error saying there were multiple files with the same name, as well as some saying that files had a total of 0. Attached is a screenshot of the error. Can someone help me figure out how to fix this?

[pschloss]

Hi there - Are you sure you’re using mothur v.1.48.0? The older versions would output a group file and we moved to count_table files instead. With what you have, you should try running screen.seqs with the group argument rather than the count argument if you’re providing it with a groups file.

Pat

[BigGabe]

I was not. It seems that updating to the current version has in fact fixed the problem - thanks!

[ritikadev]

Is there a way to update mothur from within a conda environment?

[pschloss]

Yep. mothur is on conda

https://anaconda.org/bioconda/mothur