Hi, I tried to import fastq.gz files from URL to our galaxy instance (v17). Some files seems to be downloaded completely (4 to 5 Gb), other don't (< the expected size). All of them appear in green box in the history. If I try and continue working with the looks-like complete file, doing a FASTQ Groomer for example I got an error message : "gzip: /data/galaxy/galaxy-server/database/files/000/dataset_381.dat: unexpected end of file". The files definitely didn't upload correctly despite the green box and I have no error message in the log file. Is there some settings I should modify in the Galaxy configuration files? Could someone help me ? Thanks!
If the file is not served from the remote server completely, this can occur. Galaxy has no way of knowing if loaded data is complete or not. Any data uploaded should be double-checked for completeness no matter what the source/upload method.
Thanks, Jen, Galaxy team