Problem to run Core_analysis.py pipline ...

[shahi...@yahoo.com]

I am trying to run

I am running Qiime work flow Core_diversity_analyses.py, but its gives error like this :

*** ERROR RAISED DURING STEP: Rarefaction plot: All metrics

Command run was:

 make_rarefaction_plots.py -i CorDiver/arare_max20//alpha_div_collated/ -m /proj/b2017129/b2017112-analysis/map-files/map_file_collapsed_final_GP1.txt -o CorDiver/arare_max20//alpha_rarefaction_plots/ 

Command returned exit status: 1

Stdout:

Stderr

/sw/apps/bioinfo/Qiime/1.9.1/milou/python/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison

  if self._edgecolors == str('face'):

Traceback (most recent call last):

  File "/sw/apps/bioinfo/Qiime/1.9.1/milou/python/bin/make_rarefaction_plots.py", line 229, in <module>

    main()

  File "/sw/apps/bioinfo/Qiime/1.9.1/milou/python/bin/make_rarefaction_plots.py", line 219, in main

    generate_average_tables=generate_average_tables)

  File "/sw/apps/bioinfo/Qiime/1.9.1/milou/python/lib/python2.7/site-packages/qiime/make_rarefaction_plots.py", line 667, in make_averages

    metric_name, output_type)

  File "/sw/apps/bioinfo/Qiime/1.9.1/milou/python/lib/python2.7/site-packages/qiime/make_rarefaction_plots.py", line 37, in save_ave_rarefaction_plots

    plt.title(metric_name + ": " + mapping_category)

  File "/sw/apps/bioinfo/Qiime/1.9.1/milou/python/lib/python2.7/site-packages/matplotlib/pyplot.py", line 1349, in title

    l =  gca().set_title(s, *args, **kwargs)

  File "/sw/apps/bioinfo/Qiime/1.9.1/milou/python/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 142, in set_title

    title.set_text(label)

  File "/sw/apps/bioinfo/Qiime/1.9.1/milou/python/lib/python2.7/site-packages/matplotlib/text.py", line 1028, in set_text

    self._text = '%s' % (s,)

UnicodeDecodeError: 'ascii' codec can't decode byte 0x97 in position 57: ordinal not in range(128)

Any body can help me to figure out this error. thanks

Shahid

[Kyle Bittinger]

Shahid,

Looks like you have a non-ascii character in your mapping file (table is here for reference: http://www.asciitable.com/).  I advise only using letters (A-Z, a-z), numbers (0-9), and underscores (_) in your column names.

If possible, please let us know if that fixed your problem.

Best,

Kyle

[shahi...@yahoo.com]

Dear Kyle,

Thanks for reply. Yes now its workign after removing some characters from my map file headers. thanks


Shahid

[Kyle Bittinger]

Yes! I get to hit the "Mark as best answer" button!