@SetaPark,
You are doing the right thing with feature-table group but you are not grouping your sample metadata file correctly. As the error indicates, each sample ID must be unique, but all you have done is relabel the sample IDs of the original samples to match the group that they are being lumped into.
You need to trim out duplicated lines from your sample metadata file so that each group is represented by a single line, and only group-wide metadata values are represented. So instead of this:
| #SampleID | ExpR10677 ID | Project Code | DNA Ex ID | Experimental Sample ID | Substrate | Material Type | Time Point h | Sample Name |
|---|---|---|---|---|---|---|---|---|
| FS Pooled | S203 | P-300801-20 | KFSL_D001 | KFSL063 | FS Pooled | Faecal Slurry | 0 | FS Pooled |
| FS Pooled | S204 | P-300801-20 | KFSL_D002 | KFSL063 | FS Pooled | Faecal Slurry | 0 | FS Pooled |
| FS Pooled | S205 | P-300801-20 | KFSL_D003 | KFSL063 | FS Pooled | Faecal Slurry | 0 | FS Pooled |
You probably want something like this:
| #SampleID | Project Code | Experimental Sample ID | Substrate | Material Type | Time Point h | Sample Name |
|---|---|---|---|---|---|---|
| FS Pooled | P-300801-20 | KFSL063 | FS Pooled | Faecal Slurry | 0 | FS Pooled |
and likewise for the remaining duplicated lines in your modified sample metadata file.