Hey everyone!
So I have moved my .biom table from QIIME1 over into QIIME2 no problem; but, I am having problems with moving the sequences. I have imported the seqs_rep_set_aligned_pfiltered.fasta that I got from running the de novo picking in the QIIME1 454 Overview Tutorial. I am able to make a rooted tree from the data but when I go to run the qiime diversity core-metrics I end up with the following two errors:
If I try running it with a p-sampling depth of 0 I receive the following error:
Plugin error from diversity:
The rarefied table contains no samples or features. Verify your table
is valid and that you provided a shallow enough sampling depth.
When I enter a sampling depth of my smallest number of sequences I receive the following error:
Plugin error from diversity:
All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names
What do I need to do?
If you are trying to avoid rarefying your data, then you might consider using the individual q2-diversity commands (which is a bit painful right now).
It sounds like you have features in your .biom table that are not in the tree. Which is strange because it sounds like you made the tree directly from your representative sequences. Are you certain that the table you are using has exactly the same features as your representative sequences? Could you elaborate further on how you made the tree?
Hey @ebolyen,
To make the .biom tree I followed the 454 Overview Tutorial on QIIME 1. I used a fasta, qual, and mapping file to begin my data analysis. I went through the demultiplex and de novo OTU picking steps. I imported the resulting .biom table (after changing the format to hdf5) and I imported the seqs_rep_aligned_pfiltered.fasta from the de novo picking step.
I then used the seqs file I imported over to go through the masking, building the phylogenetic tree, and rooting steps (I did not do the mafft step as my sequences were already aligned). Was I supposed to import the phylogenetic tree that was made in QIIME 1 during the de novo OTU picking steps?
What q2-diversity steps would I need to run through to prepare my data for alpha and beta diversity testing?
Thank you
Hi @Kitkat14,
The seqs_rep_aligned_pfiltered.fasta file that you imported has already gone through the masking step, so that step is redundant here. I recommend instead importing the seqs_rep_set.fasta file (unaligned representative sequences), and then following the steps for building the tree with QIIME 2. You could import that file as outlined in this section of the Importing tutorial.
Once you have the tree built, you’ll be ready to move on to doing your diversity analyses with q2-diversity. I would follow the steps beginning with this section of the Moving Pictures tutorial.