Error in jackknifed_beta_diversity.py

[Kiran]

Hello all,
I am trying to perform betadiversity analysis using the command jackknifed_beta_diversity.py
during which I am getting an error in make_emperor.py

jackknifed_beta_diversity.py -i otus/otu_table.biom -o jackknifed_betadiv/ -e 90 -m totalmapping.txt -t otus/rep_set.tre
Traceback (most recent call last):
  File "/usr/local/bin/jackknifed_beta_diversity.py", line 183, in <module>
    main()
  File "/usr/local/bin/jackknifed_beta_diversity.py", line 179, in main
    master_tree=master_tree)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/downstream.py", line 556, in run_jackknifed_beta_diversity
    close_logger_on_success=close_logger_on_success)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/util.py", line 122, in call_commands_serially
    raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:

*** ERROR RAISED DURING STEP: emperor plots (weighted_unifrac)
Command run was:
 make_emperor.py -i jackknifed_betadiv//weighted_unifrac//pcoa/ -o jackknifed_betadiv//weighted_unifrac//emperor_pcoa_plots/ -m totalmapping.txt
Command returned exit status: 2
Stdout:

Stderr
Error in make_emperor.py: Due to the variation explained, Emperor could not plot at least 3 axes, check the input files to ensure that the percent explained is greater than 0.01 in at least three axes.

Thankyou.

[Colin Brislawn]

Hello Kiran,

That last line of the error is the most important:

Error in make_emperor.py: Due to the variation explained, Emperor could not plot at least 3 axes, check the input files to ensure that the percent explained is greater than 0.01 in at least three axes.

Looks like there was not much variation inside your plot. How many samples are you using? What are you trying to find out by running this beta diversity script?

Colin

[Kiran]

Hi Colin,
I went through the previous queries related to this issue,I found that this issue occurs when you are using small number of samples.
Yes I am using only two samples,and this could be the reason.
Beta-diversity is used to find between-sample taxonomic diversity right??
                                 (OR)
Then,is my samples are not more diversified is this the meaning for the error?

[Colin Brislawn]

Hello Kiran,

I found that this issue occurs when you are using small number of samples.

That's correct. I'm glad you were able to find the answer. 

Beta-diversity is used to find between-sample taxonomic diversity right?? 

Yes, beta diversity measure the differences / distance between each pair of samples in your data set. If you look in the output folder, you should have a file with a name like "unifrac_dm.txt". The "dm" means "distance matrix" and this file will tell you the unifrac distance between your two samples.

PCoA plots made with Emperor are useful when you have 100s or 1000s of samples, and you want to look for clustering between groups. While PCoA is not a good fit for two samples, the unifrac_dm.txt file will have the beta diversity distance you needed.

I hope that helps,

Colin

[Kiran]

Thank you Colin,I will try this command with more samples.