14 months ago by
I had a similar issue with Trimmomatic earlier this week. I uploaded .gz files which Galaxy decompressed and identified as fastq files. Trimmomatic couldn't recognize the files when run from the tool bar - although oddly, workflows which had Trimmomatic as the first step in the process had absolutely no problems processing the fastq files. Weird.
Things like this happen to me rather frequently on Galaxy ever since I started using it several years ago - for whatever reason (whether it's the way my institute formats and compresses its fastq's or the way Galaxy decompresses and identifies file type) my fastq files are quite often in a format that many Galaxy tools have trouble recognizing. I'm not sure if I have the best workaround, but this is what I was taught to do by another Galaxy user: include a grooming step in my workflows. The "FASTQ GROOMER" tool seems to format my fastq files appropriately (they go in fastq, they come out fastqsanger) and after running the fastq files through it I never have this issue with tools working with my data. Just make sure you use the proper settings - the "FASTQ GROOMER" tool is more intended to switch between FASTQ score formats so make sure you tell the program what format your sequencing machine is scoring with or you might mess up your files.
Are the fastq datasets assigned the datatype
fastqsanger.gz? That is needed for the tool to recognize the inputs.
Related FAQs: https://galaxyproject.org/support/#getting-inputs-right-
Let's eliminate that sort of issue first, then troubleshoot server items if still needed. Let us know!
Jen, Galaxy team
Data sets assigned as fastqsanger.
I have no idea why I have this kind of error.
Thank you for your interest.
Do you want to share a screenshot of the dataset so we can double check? Sometimes the datatype
fastqcssangeris accidentally assigned (it is easy to mix up the two).
Also, the tutorial you are using is an older one. Better choices for learning Galaxy would be the RNA-seq and other tutorials here: https://galaxyproject.org/learn/
Here is the screenshot of my history. Files are in fastqsanger format.
Hi - I can't see the assigned datatype in the graphic, just the dataset names. The assigned datatype needs to be
I tried to find your example of the replicated history at https://usegalaxy.org but even after looked through the deleted histories, couldn't find one that matches. But it might be in there. If you want me to review, I'll need the history name and the "Create" date. You can find this info under "Saved histories" > Advanced search > status == all. Even if deleted, I may be able to see what is going on.