Error in using FastQC in Galaxy EU

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Welcome @Pedro_Fernandes_de_S

Data files can be compressed (commonly ending with a gz) or uncompressed (plain text). The compression state, along with the base file type, is encoded on the datatype format attribute in Galaxy. Tools use this when reading in the data.

When FastQC reads in data files that have an incorrect datatype assignment, an error like yours can be reported. Meaning, what was input is not what is expected.

One good way to load up data into Galaxy is to use all default settings with the Upload tool. This allows Galaxy to “guess” about the datatype.

What to try

  1. Load the data again, allowing Galaxy to autodetect the datatype format → Getting Data into Galaxy

  2. Or, click into the pencil icon → Edit Dataset Attributes → Datatypes tab for your dataset, and use the Autodetect button.

    • Note that this might not work well for all data!
    • If you keep getting errors, you’ll need to load the again from the source instead.
    • Example: if the file was corrupted during initial data loading or possibly somewhere upstream from Galaxy, reloading may help or you might need to correct the file before loading it up to Galaxy. Tools in Galaxy work just like they do anywhere else, and need valid data to process an analysis.

More help for getting data into Galaxy, running FastQC and trimming tools like Fastp, and optionally tools like MultiQC to summarize results. → Quality Control Start Here! multQC issue and guidance? (be sure to see the workflow!)

Please let us know if this actually helps and you are welcome to share back your history for more feedback about your exact situation! → How to get faster help with your question :slight_smile:

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