Good morning, I’ll briefly tell you my problem
Since I have a large number of technical replicates, I have thought about combining them so that, in this way, I can obtain the best represented taxonomy graphs. For this I have resorted to using the qiime feature-table group command using the following script
qiime feature-table group
–p-axis sample --m-metadata-file microplasticosmerge-sample-metadata.tsv
Saved FeatureTable [Frequency] to: grouped-table.qza
The problem is that it is saved as FeatureTable [frequency] gives me error in the following commands like qiime feature-table summarize or qiime phylogeny align-to-tree-mafft-fasttree
Specifically, this happens:
qiime phylogeny align-to-tree-mafft-fasttree
–o-alignment microplasticsall microplasticsaligned-rep-seqs.qza
–o-tree microplasticsall microplasticsunrooted-tree.qza
–o-rooted-tree microplasticsall microplasticsrooted-tree.qza
Plugin error from phylogeny:
Parameter ‘sequences’ received an argument of type FeatureTable [Frequency]. An argument of subtype FeatureData [Sequence] is required.
Debug info has been saved to /tmp/qiime2-q2cli-err-i7d1twql.log
Any solution to this? The truth is that I’m quite blocked, thank you very much in advance
Hi! I don’t know what you are trying to do by this command, but you need to indicate rep-seqs.qza file here, not table.qza
sorry I confused the name of the topic and the command
the problem ocurred when I want to obtain the rep-seqs.qza
qiime feature-table tabulate-seqs
Plugin error from feature-table:
Parameter ‘data’ received an argument of type FeatureTable[Frequency]. An argument of subtype FeatureData[Sequence] is required.
And you are doing the same mistake again. You are running command for qza files with sequences (FeatureData[Sequence]) but providing qza table (FeatureTable[Frequency])
aaaa it is that I fail, thank you so much. I am so noob with qiime2. So, how can I join samples together? the idea is to unite the replicas I have with each other to facilitate their representation, both taxonomically and at the pcoa level. But right now I have no idea how to do it.
You have the correct method —
group — but you are just using the wrong file as input. This will group those samples together in the output feature table. You do not need to worry about grouping together the sequences or anything like that because the sequences are feature data, i.e., they are information about the features represented in the feature table. Since you are grouping samples (technical replicates), not features, you do not need to worry about grouping other data types (though you will need to make a new sample metadata file to represent these groups)
Okey, then what archive I have to use like a input? Sorry for the inconvenience
You have the correct command and actually it looks like you have the correct input — you already successfully grouped your feature table! It’s just that you are attempting to use that grouped feature table as input for commands that do not take a feature table as input.
So this question is answered, you just need to use the help documentation and tutorials to determine which commands accept that grouped feature table as input.
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