# GTDB-Tk, reference data, and job queues: leave jobs queued for this competitive cluster group! **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** tool-help, gtdb\_to\_taxdump\ **Created:** [August 4, 2026, 9:16pm UTC](https://help.galaxyproject.org/t/gtdb-tk-reference-data-and-job-queues-leave-jobs-queued-for-this-competitive-cluster-group/18237 "2026-08-04T21:16:46Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![horikini](https://avatars.discourse-cdn.com/v4/letter/h/8797f3/32.png) [@horikini](https://help.galaxyproject.org/u/horikini)\ **Post date:** [August 4, 2026, 9:16pm UTC](https://help.galaxyproject.org/t/gtdb-tk-reference-data-and-job-queues-leave-jobs-queued-for-this-competitive-cluster-group/18237/1 "2026-08-04T21:16:46Z")
Hi, I have a GTDB-Tk classify\_wf job that has been stuck in “queued” state (never transitioned to “running”) for over 73 hours. Job ID: 4838ba20a6d86765aad1b932f8f80dd1 Tool: toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk\_classify\_wf/gtdbtk\_classify\_wf/2.7.2+galaxy0 Database: full\_database\_release\_226\_downloaded\_2026-02-25 Submitted: 2026-08-01 00:16 UTC Current state: queued (still, as of 2026-08-03) Username: horikini Input is a single history dataset collection of 1,263 bins (draft genomes) produced by a MetaBAT2 binning run on a 75-sample metagenome co-assembly. Checking the job via the API, external\_id, handler, and job\_runner\_name are all still null, suggesting it hasn’t been dispatched to a compute destination at all yet. No error messages or job\_messages are present. Could someone take a look at whether this is expected queue depth for this tool/destination right now, or whether something is blocking scheduling specifically for this job? Happy to share more details if useful. Thanks! ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [August 4, 2026, 10:05pm UTC](https://help.galaxyproject.org/t/gtdb-tk-reference-data-and-job-queues-leave-jobs-queued-for-this-competitive-cluster-group/18237/2 "2026-08-04T22:05:00Z")
Welcome @horikini Hopefully we can help! Yes, the tool does appear to be processing as expected [UseGalaxy.eu](http://UseGalaxy.eu) → [How to see the UseGalaxy.eu job queue statistics - #2 by jennaj](https://help.galaxyproject.org/t/how-to-see-the-usegalaxy-eu-job-queue-statistics/11837/2) ### Updated Homepage The view on the server homepage changed a bit recently, so this is how the same landmarks are now organized: ![2026_usegalaxy-eu-usage-statistics](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/8/8caf93f0935a21711832281d2fe8cfe1c79827cb.png) ### GTDB-Tk status I see about 120 queued jobs right now (seems to range between 110-140 recently), and the server is processing through about 4 of these jobs concurrently at any particular time. ![gtdb-tk-queued](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/4/4038758f58b5e8a34f2b895cf494d441277d8561.png) ![gtdb-tk-running](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/0/01e0c2e053b9d222070dd32d25727fd7c18398f3.png) ### Reference data, node resources, and combined impact on throughput The reference data is _extremely large_ (as I am sure you know!) and the 4 dedicated nodes are given significant working memory resources as compared to most if not all other tools. Leaving your job(s) queued will be important to keep them competitive for a slot in the processing! More discussion in these topics have similar advice to this. #gtdbtk_classify_wf And, if you are looking for a workflow, these are our HTP versions from the IWC! - ⚙ [MAGs taxonomy annotation | IWC](https://iwc.galaxyproject.org/workflow/mags-taxonomy-annotation-main/) - ⚙ [Intergalactic Workflow Commission](https://iwc.galaxyproject.org/?filter=Microbiome&q=mags) (All MAGs) * * * Did this help to explain what is going on and to know what to do? Follow up questions are welcome. 🙂 ---
**Author:** ![horikini](https://avatars.discourse-cdn.com/v4/letter/h/8797f3/32.png) [@horikini](https://help.galaxyproject.org/u/horikini)\ **Post date:** [August 8, 2026, 1:47am UTC](https://help.galaxyproject.org/t/gtdb-tk-reference-data-and-job-queues-leave-jobs-queued-for-this-competitive-cluster-group/18237/3 "2026-08-08T01:47:41Z")
Thanks for the explanation, that all makes sense! Update: after ~169 hours in queue, the job finally got a compute slot — but it failed immediately (exit code 2) with: usage: gtdbtk {de\_novo\_wf,classify\_wf,identify,align,infer,classify,root,decorate,infer\_ranks,ani\_rep,test,trim\_msa,remove\_labels,convert\_to\_itol,convert\_to\_species,export\_msa,check\_install} … gtdbtk: error: unrecognized arguments: --skip\_ani\_screen It looks like the tool wrapper (gtdbtk\_classify\_wf/2.7.2+galaxy0) is passing --skip\_ani\_screen as a default argument, but the installed GTDB-Tk CLI binary doesn’t recognize that flag. This seems like a version mismatch between the wrapper and the underlying GTDB-Tk installation, not something caused by our inputs/parameters. Job ID: 4838ba20a6d86765aad1b932f8f80dd1 Since this looks like a deterministic argument-parsing bug rather than a transient issue, I wanted to flag it rather than just resubmit (which I understand would just fail the same way and lose queue position for no reason). Is this a known issue, and is there a fix in progress or a workaround? Thanks again for your help! ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [August 10, 2026, 6:21pm UTC](https://help.galaxyproject.org/t/gtdb-tk-reference-data-and-job-queues-leave-jobs-queued-for-this-competitive-cluster-group/18237/4 "2026-08-10T18:21:52Z")
Hi @horikini Oh I’m so sorry, I thought this was corrected already but it appears to be still pending. - [Current implementation of GTDB-Tk Classify genomes is broken (wrong default arguments) - #2 by wm75](https://help.galaxyproject.org/t/current-implementation-of-gtdb-tk-classify-genomes-is-broken-wrong-default-arguments/18057/2) - [GTDB-Tk bug · Issue #7980 · galaxyproject/tools-iuc · GitHub](https://github.com/galaxyproject/tools-iuc/issues/7980) Let’s close this topic out and redirect over to the single active tracking topic for this! 🛠 ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [August 10, 2026, 6:21pm UTC](https://help.galaxyproject.org/t/gtdb-tk-reference-data-and-job-queues-leave-jobs-queued-for-this-competitive-cluster-group/18237/5 "2026-08-10T18:21:58Z")