Thanks, I found your account.
Some tools still need uncompressed fastq inputs even when compressed are given as the input. These tools create the uncompressed version of the data as part of processing – and that is what happened in your case, putting you over quota.
The compressed data is over 50GB per paired-end input, so over 100GB combined. This is too much data to send to Trinity on the public server.
Downsample your data and continue to use the public server. If you want to do this, permanently delete the larger combined files to recover working space. You might need to pre-process the data in batches before combining them. We can help with space short term – see below.
Consider working at your own Galaxy server where more resources can be allocated. Cloudman is a popular choice for scientists. Please see: https://galaxyproject.org/choices/, https://galaxyproject.org/use/, and https://galaxyproject.github.io/.
This is for academic work, correct? We can help with a bit more quota for the short term. Note this won’t help Trinity to assemble the full 100GB+ data, just give you more space to store/prep the data in your account. Send us an email (using your academic registered account email address) to the private mailing list for Galaxy Main: email@example.com and explain your project briefly. Include a link to this post for reference. FAQ: https://galaxyproject.org/support/account-quotas/#i-purged-but-still-need-more-space