returned non-zero exit status 1

Hi, I am following the Moving Picture tutorial and I am having an issue in the diversity analysis step. When I try to run more than 2 or 3 samples at once I get the following error on the first step

Command '['faithpd', '-i', '/tmp/qiime2/klockolabepic2/data/1adc6546-d0e9-49b8-833e-523e8d8ac21e/data/feature-table.biom', '-t', '/tmp/qiime2/klockolabepic2/data/e3831978-648f-40f7-9462-e6256d88abef/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-dqd7tfgv']' returned non-zero exit status 1.
When I've looked up the error it says it can pop up for a variety of different reasons. My question is why would the command work on 2 and 3 samples but not on more? Here's the command I am running as reference.

qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table Merged-Pet-Tables.qza
--p-sampling-depth 1661
--m-metadata-file Metadata_LANE2.tsv
--output-dir core-metrics-results

One of the reasons for such error is some sequences that are represented in feature table but missing in the rooted tree. Could you double check that tree was constructed with all sequences, present in Merged-Pet-Tables.qza?


I double checked and there are IDs that couldn't be found in the tree. How would I go about make sure all features are present in both?

Did you create your tree yourself with representative sequences from the entire dataset?
Usually when I have different subsets of data, I either merge representative sequences (if data is supposed analysed together) or create a tree for each (if subsets are treated as separated sets).

I merged all the data sets together and then created the tree myself from the merged data

Can it be that something went wrong at the merging step (you should merge both feature tables and representative sequences)? If you used merged representative sequences for tree construction all sequences should be represented there.

I think it is in the merging steps so I'll try working on that step. I do merge both the feature tables and rep-seq but I think they are merging wrong some how. Thank you for your help!

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