How to run core_diversity_py after using multiple_split_libraries.py (What mapping file to use?)

[Mgall00]

Hello,

Because of my already demultiplexed data, I split up my mapping file up and made one for each fastq file. multiple_split_libraries.py worked, and I proceeded (as in the illumina tutorial) with pick_open_reference_otus.py

However, I am not sure how to get the rarefaction curves or the plots from the tutorial, because core_diversity_analyses.py requires a (single?) mapping file. As mentioned, I have one for each fastq. I tried giving the script my master-mapping file, the one containing info for all before I split it up, but that failed. Any idea of what I could do?

Here is the error raised, by the way, but it seems pretty clear that it's just not happy with the mapping file.

qiime@qiime-190-virtual-box:~/Desktop/Shared_Folder/16S_Roskilde_2016/joined_reads/LABPrimer$ core_diversity_analyses.py -o cdout/ -i otus/otu_table_mc2_w_tax_no_pynast_failures.biom -m MappingOverview.tsv  -t otus/rep_set.tre -e 23751

/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 -0.0100882321604 and the largest is 1.02269957114.

  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 252, in run_core_diversity_analyses

    status_update_callback=status_update_callback)

  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/downstream.py", line 183, in run_beta_diversity_through_plots

    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: Make emperor plots, weighted_unifrac)

Command run was:

 make_emperor.py -i cdout//bdiv_even23751//weighted_unifrac_pc.txt -o cdout//bdiv_even23751//weighted_unifrac_emperor_pcoa_plot/ -m MappingOverview.tsv 

Command returned exit status: 2

Stdout:

Stderr

Error in make_emperor.py: None of your sample identifiers match between the mapping file and the coordinates file. Verify you are using a coordinates file and a mapping file that belong to the same dataset.