I have been unable to make any progress in running an RNAseq analysis using HISAT2 on a collection of samples. When I posted the job on Friday, it appeared to complete but only 2 of the 3 samples in the collection generated BAM file output. The third was blank. To rerun and keep it as a collection (which I would like to do for the downstream analysis), Galaxy requires reposting alignment of all 3 samples rather than rerunning the individual missing one. When I posted this job it took about 12 hours for the first of the 3 datasets to transition from grey to yellow but this first dataset undergoing analysis wasn't complete even after about 24 hours and the other 2 remained grey (not run). The HISAT run should only require less than half an hour of compute resources so I am not sure why these jobs never post or complete. This Galaxy upgrade has been an entirely frustrating experience. Time to downgrade? Perhaps I can run each file individually and put the BAM output in a collection instead?