I have been trying to analyse a whole genome fastq sequence, which is a file of about 100Gb. When I run the fastq groomer it generates a single file of ~273Gb, which exceeds the quota. I have tried to send it to the cloud database at Amazon AWS, but the cloud send tool option pauses the job, due to disk quota being exceeded… Would it be possible to get a temporary increased quota so that I can overcome this hurdle? Or is there another approach? It took me a week to get the fastq-groomer file, and so I am reluctant to try again. I am not interested in the whole genome, just ~0.5Mb, so I am not expecting the BAM files to be very large once generated. Any help would be appreciated.
How-to varies by server … for the UseGalaxy.eu server there is a quota request form. Where to find it is explained in the guide. Short answer: on the server homepage. Click on the far upper left Galaxy icon to reset your view to that homepage on any server.
For an emergency, or really any reason, you could move data around between public servers and use them like another cloud storage resource – because that is exactly what they are! This isn’t live storage but still storage. How to do everything is in that guide but let us know if you have any questions. The EU server will take up to a few days to grant your request – but moving data around is entirely under your control, so you can do that right now.
I re-read through you post. You are running a step that is probably not needed. Most current sequencing already has the quality scores scaled how you will want them for use with downstream tools.
How to load and check fastq data plus general help
Troubleshooting
Try the tool form Help, linked resources, then come back here if you have new questions. Try a search since you might find that already asked and answered, plus that can add context for your issue if you do decide it needs a bit more, and can try to help more.
and new datasets that get added to that history should go to the cloud directly.
It’s a rather new feature called Bring Your Own Storage so please report bugs you encounter with it (for example, last time I tested it I had to log out and back in after configuring new storage before I was able to select it from my histories).
