This is my first time using qiime2 and I am having questions about the import. I have my Fastq files in a directory and I am trying to execute the following command in a directory where I have the manifest file. I built the manifest file in excel and saved it as a csv file and when I do a head this is how it looks.
and so on. I save these file as pe-33manifest.csv
The command is as follows - (I am in the working directory as the manifest file)
qiime tools import \ --type 'SampleData[PairedEndSequencesWithQuality]' \ --input-path pe-33-manifest.csv \ --output-path paired-end-demux.qza \ --source-format PairedEndFastqManifestPhred33
After trying out different inputs, now I get the following error - I am working on a SGE cluster and submitting this command interactively.
OSError: [Errno 28] No space left on device
An unexpected error has occurred:
[Errno 28] No space left on device
See above for debug info.
I am working on qiime2-2018.2 version.
I am not sure what is going on or where I could have made mistake. I very much appreciate the response.
EDIT - Per Matthew’s input, I checked with my lab to see that they are Phred33 sequences and have added the the code. Thanks for the suggestion!