QIIME Visualization App output file in Illumina BaseSpace

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Takefumi Kikusui

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Sep 4, 2018, 7:27:32 PM9/4/18
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I am new to Metagenomics analysis and I am trying to use the BaseSpace QIIME Applications. 

I have run my samples through BaseSpace QIIME Preprocessing App, and I believe it worked fine (i.e. there were no reported errors). However, when I try to run the sample through the BaseSpace QIIME Visualization App, I have three problems.

1) The visualization apps are often "Aborted".  I have looked through the "log files". In the output.log file I found the following:

---------------------------------------------------------------------------
ERROR:root:STDOUT: 
ERROR:root:STDERR: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.0520885772616 and the largest is 1.05842765718.
  RuntimeWarning
Traceback (most recent call last):
  File "/usr/local/bin/core_diversity_analyses.py", line 202, in <module>
    main()
  File "/usr/local/bin/core_diversity_analyses.py", line 199, in main
    status_update_callback=status_update_callback)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/core_diversity_analyses.py", line 327, in run_core_diversity_analyses
    retain_intermediate_files=False)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/downstream.py", line 342, in run_alpha_rarefaction
    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: Rarefaction plot: All metrics
Command run was:
 make_rarefaction_plots.py -i /data/output/appresults/89749661/corediv-out/arare_max24522//alpha_div_collated/ -m /data/output/appresults/89749661/mapping-file.txt -o /data/output/appresults/89749661/corediv-out/arare_max24522//alpha_rarefaction_plots/ 
Command returned exit status: 1
Stdout:

Stderr
Traceback (most recent call last):
  File "/usr/local/bin/make_rarefaction_plots.py", line 229, in <module>
    main()
  File "/usr/local/bin/make_rarefaction_plots.py", line 219, in main
    generate_average_tables=generate_average_tables)
  File "/usr/local/lib/python2.7/dist-packages/qiime/make_rarefaction_plots.py", line 667, in make_averages
    metric_name, output_type)
  File "/usr/local/lib/python2.7/dist-packages/qiime/make_rarefaction_plots.py", line 73, in save_ave_rarefaction_plots
    plt.savefig(imgpath, format=imagetype, dpi=res)
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/pyplot.py", line 577, in savefig
    res = fig.savefig(*args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/figure.py", line 1476, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backend_bases.py", line 2211, in print_figure
    **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_agg.py", line 526, in print_png
    filename_or_obj = open(filename_or_obj, 'wb')
IOError: [Errno 2] No such file or directory: '/data/output/appresults/89749661/corediv-out/arare_max24522//alpha_rarefaction_plots/average_plots/PD_whole_treeDog/Human.png'
----------------------------------------------------------------------------------

Is there any way to solve this abortion?


2) I have run other samples in QIIME visualization app, and sometimes the run was completed. I downloaded all the results via Basespace Downloader. However, some results cannot visualized. Taxa summary can be visualized but PCoA plot cannot. How can I solve this error?


3) Finally, even the PCoA graphs are not visualized, I can download the Distance Matrix and Principle coordinate matrix. Regarding Principle coodinate matrix, is the low B the first axis of PC, and is the low C the second? It seems 30 axises in the table. Is the data presented in Distance Matrix calculated based on the PCoA axis 1 and axis 2?  When I calculate the distance based on the Principle coordinate matrix, the distance matrix data are not corresponding. Is there any sites I can refere how to understand the matrix data means?


Sorry for  a log email, but I really need your help.

Takefumi




 
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