Dear Galaxy support,
I was wondering if you might be able to assist me. I have been trying to process some raw Fastqs with several of the RNA-seq tools on the Galaxy main server (usegalaxy.org) for a batch of 22 sample files. I first concatenated the raw fastqs corresponding to the same samples from different lanes, and used the merged file as my input for read trimming, mapping, and counting (using Trimmomatic, HiSat2 and Featurecounts). The merging of the files worked with minimal difficulty (a few of the data sets had errors the first time, but when I reran the jobs, the merged fastQs all looked fine). I then made a collection of all of the FastQs, and queued the read trimming, HiSat2 and Featurecounts. The read trimming went well for all 22 files in the collection, and for 18/22 files in the collection, the HiSat2 job and featurecounts jobs ran. This was last Thursday, 5/28/2020. The other 4 trimmed fastqsanger files have been sitting in the gray “queued status” (pre-mapping) since last Thursday. The files are formatted identically to the other 18 jobs, which ran just fine. Per your guidelines about not cancelling a restarting jobs, I have not cancelled the jobs. I know HiSat2 is a relatively computationally intensive tool, but is it typical to have a wait time of more than four days without any progress? I don’t want to cancel the jobs and lose my spot in the queue, but if anyone could chime in as to why this might be taking so long, I would very kindly appreciate it.
The other thing that happened with a couple of the 18 jobs that did run, is the trimmed fastQ files did not map properly in HiSat2. The trimmed fastQ itself looked fine- identical format to the successful 16/18 jobs, but the output of the read mapping in HiSat2 for 2/18 jobs that did run came out as “0 mapped reads,” which is very strange. I have attempted to rerun these jobs, but they have also been sitting in the queue since last Thursday.
I am not nearly at my storage limit either, so I do not think that is the issue here… I checked the Galaxy server status on https://status.galaxyproject.org/, and it looks like there has not been any reported downtime in the last 4 days, so I really do not understand this. Please let me know if there is something you would recommend I do to move these jobs forward.
Thank you for your consideration,