Hi,
I have a problem to generate the phylogenetic tree. I use QIIME2 with taxonomy label (Silva).
I used this command:
qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table.qza
--m-metadata-file sample-metadata.tsv
--p-sampling-depth (inserire il numero di minimum frequency)
--output-dir core-metrics-results
so the system created the file tree.nwk, but when I attach the file in microbiomeanalyst software , the system suggests to me that tree tip labels do not match feature names in the OTU/taxonomy tables.
Can you post you the full error you got while running core-metrics-phylogenetic? I'm looking for something that would explain the mismatching tree tip labels.
I was going to make sure you were using \
at then end of lines to let the terminal know that \
all these lines were part of the same command, and I can see you are doing that!
I wonder if you are using an older version of qiime (2021.2) with commands from a newer version. Check the docs for the diversity core-metrics-phylogenetic and select the version of Qiime2 that you have installed.
To solve the 'already exists, will not overwrite' errors, you have to remove the output directory the command made on previous runs, using the linux ReMove command rm -r core-metrics-results
Hi,
I red the instructions for 2021.2 version but I have not the files that required to run the analysis (such as --i-table ARTIFACT FeatureTable, --i-phylogeny ARTIFACT Phylogeny[Rooted].
Have you discovered the tutorials that cover each step of the process? I would start with the Moving Pictures tutorial to see how to create rooted-tree.qza and table.qza from your data.
I am sorry if I was no clear but I have just generate all file since to core metrics. So the problem fortunately is resolved because I generate yesterday evening the core metrics folder.
Now , which is the next step to generate the phylogenetic tree (.tre, .nwk) to load in Microbiomeanalyst program?