Convert to biom file


I’m studying mothur followed by Misep SOP tutorial.
I’ve done the analysis before the OTU based analysis.

So, I did ‘count.groups(shared=final.opti_mcc.shared)’, and ‘sub.sample(shared=final.opti_mcc.shared, size=2403)’.

From here, I want to visualize my taxonomy data using phinch, so I’ve tried to convert mothur files to biom.

So, I used make.biom commands.

What I’ve done is below.

Mothur > make.biom(shared=final.opti_mcc.0.03.subsample.shared, constaxonomy=final.opti_mcc.0.03.cons.taxonomy, metadata

And it gave me error which is “Your constaxonomy file contains 481 otus and your shared file contain 376 otus, cannot continue”

Why they have different otu number??

I made

‘final.opti_mcc.0.03.subsample.shared’ file by sub.sample(shared=final.opti_mcc.shared, size=2403) and ‘final.opti_mcc.0.03.cons.taxonomy’ by classify.otu(list=final.opti_mcc.list, count=final.count_table, taxonomy=final.taxonomy, label=0.03)

which are said on the tutorial.

Where am I wrong? Please help.


The difference comes up in the subsample step. Can you include the cons.taxonomy file in the subsample commadn along with the shared file?


Dear Pat,

I carefully checked the subsample steps and found that I did wrong in a step.

Thanks for your help!

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