Hello everyone. I am using the Qiime2 software on the edge bioinformatic interface. When I try to run my analysis I get an error relating to my metadata mapping file that says: "Metadata mapping file: file PCR-Blank-6_S96_L001_R1_001.fastq.gz,PCR-Blank-6_S96_L001_R2_001.fastq.gz does not exist". I have attached a photo of my mapping file, is it set up correctly? I have triple checked for typos and there does not appear to be any errors or spaces.
I would start by matching SampleID, real sample names and absolute paths to the files. For example, you have "PCR-Blank_6" in the SampleID and "PCR-Blank-6" in the path. Check the names of your fastq files.
Thank you for your reply! I double checked my files and they match the file path ("PCR-Blank-6"). I changed the SampleID to match and still receive the same error message.
Thank you for providing additional screenshots.
In your folder "MyUploads", all the files have "fastq" format, while in the metadata file "fastq.gz". I assume that gzipping fastq files to fastq.gz will solve the issue.
I am not very familiar with EDGE Bioinformatics, which you are running, but looking into their tutorial they require a mapping file, in which each sample is present once:
While in your screenshot you have each sample duplicated (2 rows per sample). I think that you are mixing the mapping file they are requiring and one that is required for Qiime2 to import files.
I suggest to reformat your mapping file according to their documentation, or switch to native Qiime2 installation.
