Hello, I launched a bowtie2 job on fastq files. The system told me that they were in queue but their status is not "waiting to run" but "!" which means "This is a new dataset and not all of its data are available yet". I have no idea of which data it's waiting for. Here is what I did: 1) upload several fragmented R1 and R2 fastq files from Illumina, and concatenate them as one R1 and one R2 2) changed their format to fastqsanger 3) launched bowtie2 on these 2 with mouse mm10 as ref genome 4) wait....... Are those job really on queue (I don't mind waiting) or something is missing for them to run? Thanks for your help jp
The jobs are being prepared for server deployment to the cluster. Our team discussed breaking this out to be clearer in the user interface, but nothing has been decided yet. This stage is generally quick but has been a bit slower lately due to ongoing cluster/server changes. We expect it to normalise soon.
Under regular circumstances, jobs can be in a grey state (combined) for up to 24 hrs if the server is very busy. And leaving jobs alone to run is the quickest way to have them execute. However, there have been some known hiccups with job deployment and we are now recommending - just for now - to delete and restart jobs that have been queued for longer than 10 hours.
You don't want to do this usually - as restarting delays processing time as explained in the wiki below.
Our apologies for the confusion during this upgrade phase at http://usegalaxy.org.
Thanks, Jen, Galaxy team