make.shared(biom=otu_table.biom)

Integrating mothur with other programs
1

Hi mothur users,

I have a problem and i hope somebody can help me. I have an otu_table.biom file obtained with qiime and i want to use it in mothur to make an alpha-diversity analysis. So, i am trying with make.shared(biom=otu_table.biom), but only I has obtained an empty otu_table.shared file. Whats the problem with that? I am novice with this. i will appreciate any help. Thanks. Regards,

Marcos

2

Is mothur giving you an error message? If you want to send your biom file to mothur.bugs@gmail.com, I can take a look.

3

Thanks for your response!!
mothur didn’t show me any error, just produce a shared file empty. i’ve sent you the biom file to your gmail address.

4

I guess i am facing the same problem.

Do you mind in telling how to resolve this problem. i am getting an empty file with an error

[b]mothur > make.shared(biom=F16_closed_ref.biom)


Output File Names: F16_closed_ref.shared
mothur >

[ERROR]: You are missing (
Invalid.[/b]

5

What version of mothur are you using?

6

Mothur 1.25

how can i update it ? i am working on Ubuntu.

7

You’ll need to re-download the new code like you (or whoever) did before and recompile the source code.

Pat

8

Hi!
I am writing here because I am interested to create a alfa and beta diversity as well “marcosjaune”.
Unfortunately my start data are solely: .biom file, .tre file, fasting_map.txt.
Using make.shared command on my biom file I reached the rabund files.

Now I am lost. :?

In my idea, I would like reaching a table with the abundance of bacteria species for each subject analyzed. From this table I should be able to create the alfa and beta diversity.

Someone could be so kind to help me.

9

Pat’s example analysis should be helpful. http://www.mothur.org/wiki/454_SOP#Alpha_diversity and http://www.mothur.org/wiki/454_SOP#Beta_diversity_measurements

10

Maybe I am loosing myself in a glass of water… I would like to use my data in order to follow the tutorial but from biom file I don’t know how to do this… how to insert myself in the tutorial. The rabund file doesn’t help me too.
For instance, to follow the link that you sent me I have to obtain .shared file and I don’t know how to reach it from biom, so I cannot imitate the pipeline shown. I don’t know if my problem is clear. :oops:

11

No worries, we are glad to help. What are the results you are getting from the make.shared(biom=yourBiomFile)? You should be getting a list of rabund files and a shared file. If you do, then you should be able to run the following:

mothur > make.shared(biom=yourBiomFile)
mothur > collect.single(shared=current, calc=chao-invsimpson, freq=100))
mothur > rarefaction.single(shared=current, calc=sobs, freq=100)
mothur > summary.single(shared=current, calc=nseqs-coverage-sobs-invsimpson, subsample=yourSubsampleSize)

mothur > tree.shared(shared=current, calc=thetayc-jclass, subsample=yourSubsampleSize)
mothur > parsimony(tree=current, group=yourDesignFile, groups=all)
mothur > unifrac.weighted(tree=current, group=yourDesignFile, random=T)
…

12

THANK YOU very much! It is exactly the reply that I hoped! :smiley:
I m trying immediately.