"ValueError: The table does not appear to be completely represented by the phylogeny." when calculating Faith's PD

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22

@cherman2
Thank you for taking a look at this! I believe the .nwk file you used for this test is from my message on Aug 16. I noticed the "_" presented issues, and I solved that a few days ago.

I apologize for the confusion. I've attached all the most recent files to this message to avoid further confusion.

otu_mini.qza (11.4 KB)
phylo_mini.qza (6.4 KB)
phylo_tree_mini.nwk (3.5 KB)
otu_table_qiime_mini.biom (370.6 KB)

25

Hi @kirti.p,

Jumping in for @cherman2 here while she is out of the office!

Just to help me get up to speed on this, can you confirm a couple of things for me:

When you say you noticed the " _ " presented issues and you solved that, can you provide details on what your solution was? Did you replace all instances of " _ " with something like " . "? And after you did that, did you receive the exact same error message as before? If not, please provide the new error you're receiving.

Thanks! :lizard:

27

Hi @lizgehret
Thank you for stepping in! To answer your questions:

  • I replaced it with a " ". Once I did this replacement, my files all passed the pytests I included in previous messages.
  • Once I made the change, I got the error message I sent most recently (7 days ago)
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Hey @kirti.p,

After examining the most recent tables you provided, I'm still seeing ' _ ' present. Did you perhaps share an older set of tables? If not, can you double check that the replacement occurs before resending those files over? After you've done that I'll try and recreate the error on my end. Thanks!

32

Hi @lizgehret
I ended up fixing the issue! The issue was the "_"!! One quick note for the future: Removing the underscores from the .nwk file doesn't work, since QIIME no longer recognizes it as a newick file. Instead, you have to add underscores to the OTU table.

Thank you for your help!

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