# Ghost tree filtering? **URL:** https://forum.qiime2.org/t/ghost-tree-filtering/8709 **Category:** Library Support **Tags:** its, ghost-tree **Created:** [March 9, 2019, 6:20pm UTC](https://forum.qiime2.org/t/ghost-tree-filtering/8709 "2019-03-09T18:20:24Z") **Posts on this page:** 1 **Showing post:** 11
### Author: ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst) #### Post date: [April 10, 2019, 2:22pm UTC](https://forum.qiime2.org/t/ghost-tree-filtering/8709/11 "2019-04-10T14:22:48Z")
Hey there @Jennifer_Fouquier! I started back at the beginning of this thread and worked my way through, I have some ideas. So, the [main issue](https://forum.qiime2.org/t/ghost-tree-filtering/8709) was a Feature ID mismatch. I was just reviewing the [Ghost Tree Tutorial](https://forum.qiime2.org/t/q2-ghost-tree-plugin-community-tutorial-for-creating-hybrid-gene-phylogenetic-trees/6139) and noticed a discrepancy between what you suggest there, and what @ihoxie has done here. By looking at the provenance for [`extensions_otu_map_90.qza`](https://view.qiime2.org/provenance/?src=https%3A%2F%2Fforum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com%2Foriginal%2F2X%2Fe%2Fe5b190e916529e4c2200985ce0a734a0f8a87f2b.qza), I noticed that this file was built using the `extensions_cluster` command in q2-ghost-tree, but, the input sequences were @ihoxie's `FeatureData[Sequence]` from q2-dada2! My understanding is that the `extensions_cluster` step should have used the `FeatureData[Sequence]` file `sh_refs_qiime_ver7_dynamic_01.12.2017.qza`, because that is the list of features @ihoxie is attempting to build the foundation alignment from. As well, it appears that the Feature IDs are subtly different between the extension taxonomy and the extension sequences, @ihoxie --- the IDs in the taxonomy has suffixes after the Feature ID, which changes the entire ID, so even after recomputing the `OtuMap`, you will still have issues there. TLDR: input files to this command are a bit of a jumble right now, I think if you get things in order you will be all set. --- _[View the full topic](https://forum.qiime2.org/t/ghost-tree-filtering/8709)._