Hi all
I am trying to do a beta diversity analysis with the beta_diversity_through_plots.py script (I have also tried with the beta_diversity.py script) and keep getting the error "No valid samples/environments found. Check whether tree tips match otus/taxa present in samples/environments"
Input:
beta_diversity_through_plots.py -i otu_table_mc2_w_tax_F_L6.biom -o bdiv_through_plots/ -t rep_phylo.tre -m RC_summary_unix_corrected.txt
*The rep_phylo.tre file is the output of the make_phylogeny.py command I ran on a .fna file of my forward read sequences. The mapping file has been validated and worked fine with other scripts.
Here is the output/error:
Traceback (most recent call last):
File "/Users/rcapouya/.conda/envs/qiime/bin/beta_diversity_through_plots.py", line 153, in <module>
main()
File "/Users/rcapouya/.conda/envs/qiime/bin/beta_diversity_through_plots.py", line 150, in main
status_update_callback=status_update_callback)
File "/Users/rcapouya/.conda/envs/qiime/lib/python2.7/site-packages/qiime/workflow/downstream.py", line 183, in run_beta_diversity_through_plots
close_logger_on_success=close_logger_on_success)
File "/Users/rcapouya/.conda/envs/qiime/lib/python2.7/site-packages/qiime/workflow/util.py", line 122, in call_commands_serially
raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:
*** ERROR RAISED DURING STEP: Beta Diversity (weighted_unifrac)
Command run was:
beta_diversity.py -i otu_table_mc2_w_tax_F_L6.biom -o bdiv_through_plots/ --metrics weighted_unifrac -t rep_phylo.tre
Command returned exit status: 1
Stdout:
Stderr
Traceback (most recent call last):
File "/Users/rcapouya/.conda/envs/qiime/bin/beta_diversity.py", line 152, in <module>
main()
File "/Users/rcapouya/.conda/envs/qiime/bin/beta_diversity.py", line 145, in main
opts.output_dir, opts.rows, full_tree=opts.full_tree)
File "/Users/rcapouya/.conda/envs/qiime/lib/python2.7/site-packages/qiime/beta_diversity.py", line 180, in single_file_beta
make_subtree=(not full_tree))
File "/Users/rcapouya/.conda/envs/qiime/lib/python2.7/site-packages/qiime/beta_metrics.py", line 44, in result
is_symmetric=is_symmetric, modes=["distance_matrix"], **kwargs)
File "/Users/rcapouya/.conda/envs/qiime/lib/python2.7/site-packages/cogent/maths/unifrac/fast_unifrac.py", line 466, in fast_unifrac
envs, count_array, unique_envs, env_to_index, node_to_index, env_names, branch_lengths, nodes, t = _fast_unifrac_setup(t, envs, make_subtree)
File "/Users/rcapouya/.conda/envs/qiime/lib/python2.7/site-packages/cogent/maths/unifrac/fast_unifrac.py", line 194, in _fast_unifrac_setup
raise ValueError, "No valid samples/environments found. Check whether tree tips match otus/taxa present in samples/environments"
ValueError: No valid samples/environments found. Check whether tree tips match otus/taxa present in samples/environments
In other similar questions, posters were using a tree from the greengenes fileset, however I used UNITE for these fungal OTUS and there is no .tre file in that set of files. I am not sure if I am using the wrong file or what. I apologize if this question has been asked before, I didn't find any solutions in previously answered questions that solved my issue.
Thank you,
Rachel