I am new to the QIIME2 program and at the step of importing data in the form of Casava 1.8 single-end demultiplexed fastq. I am using these commands:
qiime tools import
I have tried the example data provided as well but I would always receive this error:
(1/1) Invalid value for ‘–input-path’: Path ‘cassava-18-single-end-demultiplexed’ does not exist.
Does anyone know how to troubleshoot this? Thanks.
Thanks for getting back to me. I am currently using the example data given under the importing data tab in QIIME2. So shouldn’t the path or name of directory be ‘cassava-18-single-end-demultiplexed’ as well? I’m still quite confused about this.
Thank you for providing screenshots.
As I can see, you indicated a folder with fastq files as an input, and provided a SingleEndFastqManifestPhred33V2 at the same time. So, the plugin is expecting a manifest file, which should contain paths to fastq files.
Could you try to replace SingleEndFastqManifestPhred33V2 with CasavaOneEightSingleLanePerSampleDirFmt in your command?
Hi @timanix , thanks! I managed to import my files into QIIME2. Right now I am currently at the sequence quality control step and because my data was already given to me demultiplexed, I do not have the summary of the demultiplexing results. Which allows me to determine how many sequences were obtained per sample, and also to get a summary of the distribution of sequence qualities at each position in your sequence data.
I have tried the last few commands of the demultiplexed section:
qiime demux summarize
But I received an error message that says:
There was a problem with the command:
(1/1) Invalid value for ‘–i-data’: ‘demux.qza’ is not a valid filepath
Do you know how I can go about trouble shooting this error? Thanks again.
Plugin is complaining that there is no file named ‘demux.qza’ in your working directory. You need to provide an exact name or path to the output you indicated when you imported reads in previous command.
For example, if you used command I provided above, the input should be:
Hi @timanix , thanks for this, it was extremely helpful! I managed to get the summary of the demultiplexing results. Another quick question because received this error message after the sequence quality control step using DADA2. Must I already have a metadata file to do this step?
This time plugin is complaining that you do not have a file ‘sample-metadata.tsv’ in your directory. So, if you already have a correctly formatted metadata, you can indicate it instead, or just remove this parameter since it is an optional part.