Issue Using Qiime2R to Create Phyloseq Objects

[Ellenphant (Ellen)]

I have been trying to use the qiime2R package and just can’t get it to work.

I have set my working directory correctly and am able to import my qza files into the workspace for R studio. However, when trying to use the qza_to_phyloseq command (after setting the tmp to an empty folder) I keep getting the following error:

Error in file(con, “r”) : cannot open the connection

I can’t figure out what I am doing wrong and this is so frustrating! Has anyone else had this issue?

[Nicholas_Bokulich]

Hi @Ellenphant,
See this current topic for troubleshooting this error:

qiime2R visualization error message

Hi all, I am using qiime2R to make some plots for my 16s data in R, and I am following the tutorial found in this forum: But when I am creating phyloseq object from QIIME2 artifacts, an error came up: Error in file(con, "r") : cannot open the connection All these artifacts were imported into R successfully (in my opinon). Here is the commands I used to create the phyloseq: pilot_physeq=qza_to_phyloseq("pilot_table_group.qza", "pilot_rooted-tree.qza", "pilot_taxonomy.qza", "metadata2_gor…

Good luck!