"An error occurred while updating information with the server" repeatedly while running Pilon

I am experiencing “Internal Server Error (500)” messages whenever I try to run a job with Pilon. The error appears after a few hours of the job start. The detailed error message suggest Error 500, internal server error.

What should I do to avoid/fix this error.

I’m pasting the head of the error message below.

  "userAgent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/97.0.4692.71 Safari/537.36",
  "onLine": true,
  "version": "21.09",
  "xhr": {
    "readyState": 4,
    "responseText": "",
    "responseJSON": null,
    "status": 500,
    "statusText": "Internal Server Error"
  "options": {
    "parse": true,
    "filters": {
      "update_time-ge": "2022-01-19T06:13:15.000Z",
      "visible": ""
    "remove": false,
    "details": "bbd44e69cb8906b515e37ecb30744100",
    "traditional": true,
    "data": {
      "details": "bbd44e69cb8906b515e37ecb30744100",
      "order": "hid",
      "v": "dev",
      "q": [
      "qv": [
    "emulateHTTP": false,
    "emulateJSON": false,
    "textStatus": "error",
    "errorThrown": "Internal Server Error"
  "url": "https://usegalaxy.org/api/histories/3d213f5e64af4795/contents?details=bbd44e69cb8906b515e37ecb30744100&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-01-19T06%3A13%3A15.000Z&qv=False&qv=False",
  "model": [
      "state": "running",
      "deleted": false,
      "purged": false,
      "name": "FASTA from pilon on data 19 and data 7",
      "accessible": true,
      "data_type": "",
      "file_ext": "",
      "file_size": 0,
      "meta_files": [],
      "misc_blurb": "",
      "misc_info": "",
      "tags": [],
      "history_id": "3d213f5e64af4795",
      "history_content_type": "dataset",
      "hid": 46,
      "visible": true,
      "model_class": "HistoryDatasetAssociation",
      "update_time": "2022-01-19T03:16:37.313Z",
      "id": "bbd44e69cb8906b515e37ecb30744100",
      "type_id": "dataset-bbd44e69cb8906b515e37ecb30744100",
      "create_time": "2022-01-19T03:15:50.458Z",
      "extension": "fasta",
      "type": "file",
      "url": "/api/histories/3d213f5e64af4795/contents/bbd44e69cb8906b515e37ecb30744100",
      "dataset_id": "bbd44e69cb8906b5a067e46c3375b639",
      "rerunnable": true,
      "creating_job": "bbd44e69cb8906b5dc7e571a17ea8d06",
      "urls": {
        "purge": "/datasets/bbd44e69cb8906b515e37ecb30744100/purge_async",
        "display": "/datasets/bbd44e69cb8906b515e37ecb30744100/display/?preview=True",
        "edit": "/datasets/edit?dataset_id=bbd44e69cb8906b515e37ecb30744100",
        "download": "/datasets/bbd44e69cb8906b515e37ecb30744100/display?to_ext=",
        "report_error": "/dataset/errors?id=bbd44e69cb8906b515e37ecb30744100",
        "rerun": "/tool_runner/rerun?id=bbd44e69cb8906b515e37ecb30744100",
        "show_params": "/datasets/bbd44e69cb8906b515e37ecb30744100/details",
        "visualization": "/visualization",
        "meta_download": "/dataset/get_metadata_file?hda_id=bbd44e69cb8906b515e37ecb30744100&metadata_name="
1 Like

Hi @Candidomolino

This looks like a server error that can come up when the server is restarted (and sometimes when it is really really busy) – but that should resolve with a rerun. I wouldn’t expect this particular error from problematic inputs or outputs but that’s possible too. Or maybe the tool has some corner-case configuration bug.

If a rerun hasn’t worked by now, and since you were working at usegalaxy.org, I can help quicker and with more specificity if you send a bug report from one of the red error datasets. Please leave all of the inputs/outputs undeleted in the same history, plus any prior failures intact, and paste the URL to this help topic in the comments for context.

If you are using a workflow, consider one more rerun directly from the history instead to rule out problems with it. Or I can try that – but generate a share link to the workflow and also include that in the comments – or at least include the full name/version and I can find it that way. We want to be all reviewing the same exact processes that produced the error. This error tends to be technical when persistent.

Let’s start there, thanks!

1 Like