Hi, I launched a job on Friday for alignment on SPADES on usegalaxy.org I used FASTQ to check the quality of my uploaded sequences and Trimmomatic to trim my data beforehand. I used the “paired” output from Trimmomatic to launch SPADES. I launched 24 alignments at the same time (all from a same p…

[image] run Unicycler always got " unicycler: command not found" -- RESOLVED at UseGalaxy.org 20230210 usegalaxy.org support run Unicycler always got “/jetstream2/scratch/main/jobs/47842391/command.sh: line 110: unicycler: command not found” I am wondering if there are so…

Hi @vanina.guernier Yes, there were some server issues and SPAdes was one impacted tool. Not all runs, just some. The error message you posted can be produced by a server/cluster issue or an input issue. Given what you state and the timing, this seems to be likely server related. Rerun the failed …

Thank you !! Galaxy is down for scheduled maintenance at the moment so I will try to rerun the failed jobs when everything is back to normal and will keep you posted. Thanks again Vanina

Yes, please try again after the scheduled maintenance is completed. For others curious about downtime for server upgrades (now or later), this is where to find out about usegalaxy.* server and related core component status: https://galaxyproject.statuspage.io/

Hi! So I tried to re-run the 10 failed jobs. I now had 6 successful jobs and 4 that still failed. Because it seems a bit inconsistent, I reported a bug as you suggested, flagging this galaxy help link. Thanks for helping Vanina

@vanina.guernier Thanks! reviewing now

Hi I wanted to let you know that I just tried to run some of the same data with Unicycler as I had both short and long reads for 9 samples. All of them failed in a few minutes. Again it’s showing the same error: tool error An error occurred with this dataset: Remote job server indicated a pro…

No need to open another topic here, let’s keep it all together for context. If the Unicycler runs are in the same history, I’ll load it up again to capture the new runs and review it with the others. If it is in a different history, please send in another bug report – that makes it easy to make sur…

If I am not mistaken, I have only one history. But just to be sure, I reported one of the bug and linked to this chat again. Of note, as I ran into trouble before when using trimmed sequences (with Trimmomatic) in Unicycler, I tested a few different options for a same sample: trimmed Illumina re…

Thanks, I saw your report plus can reproduce the “fails immediately” issue with test data across a set of specific tools. There is a problem with one of our dedicated clusters. Unicycler, Spades, plus a few other tools are impacted. Our administrator is working on it. We’ll post back an update tomo…

Thanks! It’s kind of reassuring to know that it’s a server issue rather than a problem with my data. I’m guessing that if I want to use http://usegalaxy.eu I will need to upload all my raw data again on the european server? (the different servers are not “linked” right?) Vanina

SPADES - Remote job server indicated a problem running or monitoring this job.

usegalaxy.org support

jennaj February 10, 2023, 8:18pm 16