# Phyloseq to QIIME2 **URL:** https://forum.qiime2.org/t/phyloseq-to-qiime2/8703 **Category:** Other Bioinformatics Tools **Tags:** import **Created:** [March 8, 2019, 11:16pm UTC](https://forum.qiime2.org/t/phyloseq-to-qiime2/8703 "2019-03-08T23:16:50Z") **Posts on this page:** 1 **Showing post:** 9
### Author: ![ChristianEdwardson](https://forum.qiime2.org/user_avatar/forum.qiime2.org/christianedwardson/32/4215_2.png) [@ChristianEdwardson](https://forum.qiime2.org/u/ChristianEdwardson) #### Post date: [March 12, 2019, 2:32am UTC](https://forum.qiime2.org/t/phyloseq-to-qiime2/8703/9 "2019-03-12T02:32:51Z")
OK I got your RDS containing the phyloseq object and examined it. The reason it is failing is that part of my R function (phyloseq2qiime2) does a check for sequences (ATCG only) before writing a representative/reference sequence fasta file based on those sequences it finds either in the row names or column names (depending on if taxa\_are\_rows=TRUE or FALSE for your phyloseq object). In your case, your phyloseq object contained both sequences _and_ MD5 hashes in the colnames. This is probably because you ran dada2 in QIIME2 for some of your samples, where the [default parameter](https://forum.qiime2.org/t/are-feature-ids-hashed-from-reads/1625) is `--p-hashed-feature-ids`. You can add the argument `--p-no-hashed-feature-ids` to output the ASV sequences instead of hashes. Unfortunately, I don't have a fix for getting you a FASTA file right now using my script. The other files should be created correctly. If you need a FASTA file, can export a representative set of sequences from qiime2 and run `uniquesToFasta` from dada2 in R you could combine the two on the command line using `cat` and then filter for unique sequences using one of the various command line tools out there for FASTA file manipulation. Hope this helps! Christian --- _[View the full topic](https://forum.qiime2.org/t/phyloseq-to-qiime2/8703)._