Error spam (list index out of range, could not query sidecar)

[nienkevanunen]

For a while now I've had the issue shown in the screenshots. My jobs seem to run fine, but I am being spammed with these errors at the same time. Also, before my jobs run the time is shown as "INVALID". I've tried reinstalling my whole conda environment but that doesn't seem to fix it, and I don't understand a whole lot about the slurm integration with Snakemake that I installed from here using cookiecutter. I used it for at least 10 months or so without issue, and I haven't changed anything. It could be related to something the IT changed on the cluster, but going to them for help about this I know from experience is going to end up nowhere. So hopefully someone could point me in the right direction, or maybe knows what the IT might've changed so I could perhaps e-mail them something more concrete.

I've tried Snakemake 7.24.0 and 7.24.2.

(ignore the PartitionTimeLimit ones, they've just stuck in limbo there for a long time ...)

[mbhall88]

Might be related to #96

[mbhall88]

@nienkevanunen I just started having the same issue and I can confirm the patch fix in #96 worked for me

[nienkevanunen]

I applied the patch, and also getting the Could not parse ' '(try x of 10), like someone else in the comments of the issue, but I suppose its better than the previous spam. 😅

I definitely seem to be having a lot of issues with jobs failing for seemingly no reason, and files not being created even tho the script runs fine... but on a rerun it sometimes works fine so just gotta get lucky. Wasn't an issue until recently, like 2 days ago, but so it was happening already before I applied this patch... Not sure if related or if the cluster I'm using is just not really working properly right now.

[percyfal]

Hopefully fixed via #115. Feel free to reopen should the issue reemerge.