Error while updating server

usegalaxy.org support
, ,
1

Hi, I haven’t been able to get anything to run on Galaxy all morning. I got the following error message that suggests contacting an administrator. Thanks

"An error occurred while updating information with the server. Please contact a Galaxy administrator if the problem persists.



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  "onLine": true,
  "version": "22.01",
  "xhr": {
    "readyState": 4,
    "responseText": "",
    "responseJSON": null,
    "status": 500,
    "statusText": "Internal Server Error"
  },
  "options": {
    "parse": true,
    "filters": {
      "update_time-ge": "2022-02-08T15:33:46.000Z",
      "visible": ""
    },
    "remove": false,
    "traditional": true,
    "data": {
      "order": "hid",
      "v": "dev",
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        "deleted",
        "purged"
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      "qv": [
        "2022-02-08T15:33:46.000Z",
        "False",
        "False"
      ]
    },
    "emulateHTTP": false,
    "emulateJSON": false,
    "textStatus": "error",
    "errorThrown": "Internal Server Error"
  },
  "url": "https://usegalaxy.org/api/histories/eee48555debc811e/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-08T15%3A33%3A46.000Z&qv=False&qv=False",
  "model": [
    {
      "state": "ok",
      "deleted": false,
      "purged": false,
      "name": "Barcode Splitter on data 101 and data 100: Summary",
      "accessible": true,
      "data_type": "",
      "file_ext": "",
      "file_size": 0,
      "meta_files": [],
      "misc_blurb": "",
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      "tags": [],
      "history_id": "eee48555debc811e",
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      "visible": true,
      "model_class": "HistoryDatasetAssociation",
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      "type": "file",
      "create_time": "2022-02-08T20:07:12.507Z",
      "type_id": "dataset-bbd44e69cb8906b574968129c4e2f3ec",
      "id": "bbd44e69cb8906b574968129c4e2f3ec",
      "extension": "tabular",
      "update_time": "2022-02-08T20:16:35.347Z",
      "url": "/api/histories/eee48555debc811e/contents/datasets/bbd44e69cb8906b574968129c4e2f3ec",
      "urls": {
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        "edit": "/datasets/edit?dataset_id=bbd44e69cb8906b574968129c4e2f3ec",
        "download": "/datasets/bbd44e69cb8906b574968129c4e2f3ec/display?to_ext=",
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        "show_params": "/datasets/bbd44e69cb8906b574968129c4e2f3ec/details",
        "visualization": "/visualization",
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      "collection_type": "list",
      "deleted": false,
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      "job_source_type": "Job",
      "name": "Barcode Splitter on data 101 and data 100",
      "element_count": 97,
      "hid": 102,
      "populated_state_message": null,
      "url": "/api/histories/eee48555debc811e/contents/dataset_collections/5db9dc0679243c07",
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      "contents_url": "/api/dataset_collections/5db9dc0679243c07/contents/234faa589298f537",
      "elements": []
    },
    {
      "state": "ok",
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      "purged": false,
      "name": "Non Phi reads Bowtie2 on data 8 and data 5: unaligned reads (L)",
      "accessible": true,
      "data_type": "",
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      "file_size": 0,
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      "tags": [],
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      "create_time": "2022-02-08T20:06:22.860Z",
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      "id": "bbd44e69cb8906b53e081997149ac3c6",
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      "state": "ok",
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      "name": "IL barcodes.txt",
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    "username": "bmaguire",
    "total_disk_usage": 93489887631,
    "nice_total_disk_usage": "87.1 GB",
    "quota_percent": 34,
    "is_admin": false,
    "preferences": {
      "dbkeys": "{\"test\": {\"name\": \"hopethisworks.txt\", \"fasta\": 62915310, \"len\": 62915623, \"linecount\": 62915624}}"
    },
    "tags_used": [
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    "deleted": false,
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    "quota": "250.0 GB"
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}
1 Like
2

Hi @HMcBain

Please try again. We have been updating UseGalaxy.org over the last few days to prepare for the next software release. A few jobs may run into trouble due to the timing of server restarts. The solution is to rerun.

If you end up with a different error, we can follow up from there.

3

Hi Jenna, Thanks for your reply. I’ve been trying multiple times over the last 9 hours. When I click execute nothing happens. Will let you know if I get another error message- but so far (except that one time) just nothing when I try to execute.
Thanks

1 Like
4

Hi @HMcBain

It did run into performance problems today after the original reply: slower UI response timing, occasional pop-ups, or menus not clearing.

But I ran a few more tests just now, and jobs are failing for what looks like a server-side issue. I wasn’t able to reproduce the part about jobs or workflows not submitting at all. Everything was submitted but all produced a red error result very quickly. I’ve alerted our admins about it. You may notice that things are working better before I get back to you here due to time differences, but I’ll still post an update either way.

And if you do get an error meanwhile, do send in a bug report for it. One is enough, we’ll see the other errors (if any) that are in the same history. Please include the URL link to this topic in the comments so we can associate the two. Examples of problems are useful.

Known issue: The bug report submission form does have a problem like what you stated. In short, the form doesn’t appear to have been submitted when it actually was. So it is OK to click on that submit button one (or a few times but wait a few seconds in between). We’ll notice what is going on. This specific issue was isolated as far as we know and is already on our fix-it shortlist for the upcoming Galaxy release.

More updates soon, and that you for the follow-up!

5

Hi Jenna. Still can’t get things to execute. I’ve had the odd success- maybe three or four adapter trims per day but that’s all I can get done. Thanks for all you do!

6

Hi @HMcBain

Hopefully, you’ve already solved the problem – but I can let you know that the prior performance issues are resolved at UseGalaxy.org.

If the jobs are just queued (grey in color), some wait time is expected when working at public Galaxy servers. These are shared resources: some of your jobs will run, the some of the other people’s jobs, then more of yours again, repeat. Try to not delete queued jobs – instead, allow jobs to run to completion. When jobs are deleted and rerun, the new job ends up at the back of the queue, extending the wait time. If you do that repeatedly and fast enough, it would be possible to not have many jobs complete at all.

Getting jobs queued up as soon as possible, and setting an email notification, are helpful strategies. Workflows and Dataset Collections can help to batch an analysis.

7

Hi Jenna, Thanks for your email. I haven’t been checking recently, as after a few days of trying I got set up with a local instance instead, and that has been working well. Just went back and tried executing a trim on the main Galaxy and it ran OK, so the issue seems fixed. Thanks!

1 Like
8

Great! Thanks for taking the time to check and letting us know :slight_smile: