I got another problem. I have performed taxonomy analysis for my 45 fungal sample. I got unidentified for all the sample. Previously, I performed only for some sample, I got taxonomic assignment. This time I ran the taxonomy analysis for all sample at same time. There was no taxonomic assignment at all. But, my OTU table seems good. I don't know where the mistake happened.
On the contrary, it looks like the majority of the reads were classified at species level... the only problem is that the species label in your reference database is "s__unidentified". This is not something that the taxonomy classifier is doing... this is an issue with how taxa are labeled in your reference database.
This topic has a number of links that might be useful to help you understand the difference between unclassified reads and ambiguous labels in a reference database, and maybe some guidance for troubleshooting this issue:
Thank you so much for your help and suggestions sir.
Sorry for the late reply. As you said, I guess there was some issues in classifer step. After I posted my query, I download ITS sequence from NCBI and I created customized database using rescript and got taxonomic assignment for my 48 ITS sample.
