Lofreq filter hangup on Galaxy ARTIC workflow

Was attempting to use the Galaxy ARTIC workflow and the workflow is stuck at the Lofreq filter step for the last 48 hours (Gray box, “Creating jobs…”). Ive tried a previous version (2.1.4+galaxy1) and I get the same hangup at the Lofreq filter step. A few samples were not going to have enough data to assemble, but I didn’t know if that would cause such a massive hangup.

You are working on usegalaxy.eu? That’s strange because we have our regular automated analysis of COG-UK sequencing data running there and there is no issue whatsoever with that one.

Also, the “Creating jobs…” status means that the actual tool hasn’t even started to run yet (at least not on all of the data), but that Galaxy is still setting up those jobs. How big is your collection of input datasets? and which exact workflow are you trying to run (there are several flavors for Illumina and ONT data)? Can you maybe share a history?

We are processing on the usegalaxy.eu servers. We have 206 (103F/103R) reads for 103 samples total. We are using the the Illumina ARTIC Illumina workflow for variant calling and I’ve attached a genome assembly at the end of it. I haven’t had too many problems running ~50 samples at a time previously.

One wrinkle may be that we are using the QIAseq Direct SARS-CoV-2 kit, but they supply BED files for primers and amplicons here: QIAseq DIRECT SARS-CoV-2 Kits

I’ve reformatted their amplicon bed file to match the format for the one supplied by Galaxy. I would be happy to share the history and workflow, but what would be the best way to do that?