MiSeq SOP errors


I’m not sure if this is a bug report or a command question. I’ve upgraded to the most recent release of mothur and saw some new commands in the SOP. So I ran through the SOP but the outputs begin diverging from the reported steps in the SOP just slightly. When I get to the beta diversity section where heatmap.bin produces a very dull figure and then dist.shared no longer functions. I can’t see that I’m doing anything other than what the SOP says to do so I am assuming it has just not been updated with the new release? Could the SOP and outputs be checked?


Just to add… the deviation begins after the chimera screen - total number of sequences differs from the report on the SOP.

I have rerun this several times to try and isolate the problem… the first actual errors are starting at the rename.files section of “Analysis” where the files specified are “unable to be opened”.

When I then run “count.groups” the only output is Mock contains 4045 but that should have been removed earlier I think.

I think there is a call to the wrong file in one step.

Thanks for bringing this to my attention. I will take a closer look at the wiki page. You may see some variability in the chimera detection. This is due to the uchime / vsearch algorithm.