no html file from plot_taxa_summary.py

[Rossella Calvaruso]

Hi there,
I don't have much experience with this types of analysis but I am trying to learn... :) 
My question: I am running the plot_taxa_summary.py script including -c -s -d and -l options
Unfortunately what I get as output is a .png a pdf. file for each of the chart type selected a .js and a .css file. I am missing the .html file where all the informations are. I am attaching a bar graph and a pie chart as an example of what I get.
Thanks in advance for your time!

[Greg Caporaso]

Hello,

Can you post the command that you ran, and if you don't mind, attach the input files that you provided to that command. Also, can you please run print_qiime_config.py, and paste the results into your reply. 

Thanks!

[Rossella Calvaruso]

Hi,
thank you very much for your reply!
so I run print_qiime_config.py and I got this:

System information
==================
         Platform: linux2
   Python version: 2.7.10 (default, Oct 14 2015, 16:09:02)  [GCC 5.2.1
20151010]
Python executable: /usr/bin/python

QIIME default reference information
===================================
For details on what files are used as QIIME's default references, see here:
 https://github.com/biocore/qiime-default-reference/releases/tag/0.1.3

Dependency versions
===================
          QIIME library version: 1.9.1
           QIIME script version: 1.9.1
qiime-default-reference version: 0.1.3
                  NumPy version: 1.11.0
                  SciPy version: 0.17.0
                 pandas version: 0.17.1
             matplotlib version: 1.5.1
            biom-format version: 2.1.5
                   h5py version: 2.5.0 (HDF5 version: 1.8.15)
                   qcli version: 0.1.1
                   pyqi version: 0.3.2
             scikit-bio version: 0.2.3
                 PyNAST version: 1.2.2
                Emperor version: 0.9.51
                burrito version: 0.9.1
       burrito-fillings version: 0.1.1
              sortmerna version: SortMeRNA version 2.0-dev, 29/11/2014
              sumaclust version: SUMACLUST Version 1.0.00
                  swarm version: Swarm 1.2.19 [Mar  7 2016 12:58:25]
                          gdata: Installed.

QIIME config values
===================
For definitions of these settings and to learn how to configure QIIME, see
here:
 http://qiime.org/install/qiime_config.html
 http://qiime.org/tutorials/parallel_qiime.html

                     blastmat_dir: None
      pick_otus_reference_seqs_fp:
/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
                         sc_queue: all.q
      topiaryexplorer_project_dir: None
     pynast_template_alignment_fp:
/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
                  cluster_jobs_fp: start_parallel_jobs.py
pynast_template_alignment_blastdb: None
assign_taxonomy_reference_seqs_fp:
/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
                     torque_queue: friendlyq
                    jobs_to_start: 1
                       slurm_time: None
            denoiser_min_per_core: 50
assign_taxonomy_id_to_taxonomy_fp:
/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
                         temp_dir: /tmp/
                     slurm_memory: None
                      slurm_queue: None
                      blastall_fp: blastall
                 seconds_to_sleep: 1


the command I ran to obtain the graph is this:
plot_taxa_summary.py -i
plots/taxa_summary/otu_table_L2.txt,plots/taxa_summary/otu_table_L3.txt,plots/taxa_summary/otu_table_L4.txt,plots/taxa_summary/otu_table_L5.txt,plots/taxa_summary/otu_table_L6.txt
-o plots/taxa_summary/charts_qiime_ -c bar -d 300 -s -l phylum,class,order

I would only replace "bar" with "pie" to get the pie chart. Input files are
attached!
Thank you again for your time!
Rossella

[Jai Ram Rideout]

Hi Rossella,

I was able to run your command locally and produce an HTML file (it's called bar_charts.html in the output folder). I have matplotlib version 1.4.3 installed. It's possible your version of matplotlib (1.5.1) isn't compatible with QIIME. Can you try downgrading matplotlib to version 1.4.3 and rerunning the command?

Best,

Jai

[Rossella Calvaruso]

I'll try!

Thanks again!