Too long waiting for collection trimming task then an error message

usegalaxy.org support
,
1

Hi, I hope you can help me.
I am following the GTN galaxy project training. when I executed the collection trimming task, the task was at waiting status for more than a hour, the I got this error message:

An error occurred while updating information with the server. Please contact a Galaxy administrator if the problem persists.
The following information can assist the developers in finding the source of the error:
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      "update_time": "2021-11-02T10:47:48.433Z",
      "populated_state_message": null,
      "visible": true,
      "url": "/api/histories/0236d76b24a78cd9/contents/dataset_collections/8b1eb4229e8addc8",
      "name": "FastQC on collection 1: RawData",
      "job_source_type": "ImplicitCollectionJobs",
      "populated_state": "ok",
      "type": "collection",
      "create_time": "2021-11-02T10:47:47.519Z",
      "tags": [],
      "hid": 15,
      "job_source_id": "ec7eb802d31434ba",
      "id": "8b1eb4229e8addc8",
      "type_id": "dataset_collection-8b1eb4229e8addc8",
      "elements": []
    },
    {
      "collection_type": "list",
      "deleted": false,
      "history_content_type": "dataset_collection",
      "model_class": "HistoryDatasetCollectionAssociation",
      "history_id": "0236d76b24a78cd9",
      "element_count": 12,
      "contents_url": "/api/dataset_collections/5c0c475454689710/contents/38f03ed32d655c55",
      "update_time": "2021-11-02T10:47:48.433Z",
      "populated_state_message": null,
      "visible": true,
      "url": "/api/histories/0236d76b24a78cd9/contents/dataset_collections/5c0c475454689710",
      "name": "FastQC on collection 1: Webpage",
      "job_source_type": "ImplicitCollectionJobs",
      "populated_state": "ok",
      "type": "collection",
      "create_time": "2021-11-02T10:47:47.519Z",
      "tags": [],
      "hid": 14,
      "job_source_id": "ec7eb802d31434ba",
      "id": "5c0c475454689710",
      "type_id": "dataset_collection-5c0c475454689710",
      "elements": []
    },
    {
      "collection_type": "list",
      "deleted": false,
      "history_content_type": "dataset_collection",
      "model_class": "HistoryDatasetCollectionAssociation",
      "history_id": "0236d76b24a78cd9",
      "element_count": 12,
      "contents_url": "/api/dataset_collections/79db1a20d5824765/contents/211ebee0a178c97e",
      "update_time": "2021-11-02T10:05:11.433Z",
      "populated_state_message": null,
      "visible": true,
      "url": "/api/histories/0236d76b24a78cd9/contents/dataset_collections/79db1a20d5824765",
      "name": "FASTQS",
      "job_source_type": "Job",
      "populated_state": "ok",
      "type": "collection",
      "create_time": "2021-11-02T10:04:13.067Z",
      "tags": [],
      "hid": 1,
      "job_source_id": "bbd44e69cb8906b5075914edf542c2a7",
      "id": "79db1a20d5824765",
      "type_id": "dataset_collection-79db1a20d5824765",
      "elements": []
    }
  ],
  "user": {
    "id": "cefe60d4448b1fb7",
    "username": "ihe-san",
    "total_disk_usage": 47344229,
    "nice_total_disk_usage": "45.2 MB",
    "quota_percent": 0,
    "is_admin": false,
    "preferences": {},
    "tags_used": [],
    "purged": false,
    "quota": "250.0 GB",
    "deleted": false
  }
}

Could you please tell me what happened and how can I avoid this problem?
Thank you in advance

1 Like
2

Hi @ihe-san

The first part would be unexpected under normal circumstances, but since the browser timed out and tossed the error, it probably just means the server had some internal connection problems submitting then returning the jobs you ran.

Try reloading the webpage and consider holding down the “shift” key while doing that to clear the browser’s cache. Then try the operation again from the start. Some on our team at usegalaxy.org noticed connection delays/drops. But don’t wait for a fix yet – try again now. The problem isn’t widespread.

If you ended up with error datasets from the initial run (red), those can be purged to recover disk space and clear up the clutter in the history. Go ahead and clear the output collection itself and all datasets in it and create them again new. Later on, once you are working with collections with more/larger data you can learn how to rerun/manipulate collection outputs when only some of the jobs failed – but for now, that wouldn’t be worth it – plus there could be problems in some of the even putatively successful (green) results nested in that output collection (if any). A complete rerun is cleaner.

If this comes up again, please confirm that you are working at usegalaxy.org and we can follow up more.

Thanks!

3

Hi jennaj
Thank you for your efficient reply, Actually, when I closed the error window I noticed that the trimming is still proocessing, so I let it continue, it took several hours to complete. When I opened the collection output, It was just one file that failed. So, after looking for solutions here and there, I used CollectionOperation to remove failed files (that I processed seperately). However, I don’t know how to re-add the successfully processed file to the collection. I tried to built collection for the failed file (to merge collections afterward) but seems not working.
THank you!

1 Like
4

Ok – next time, don’t delete the failed dataset if you intend to rerun it. Instead, expand the failed dataset and click on the rerun icon. The original tool form will present in the center panel with all of the original settings (specific for that element) plus a new option right above the submit button to replace the prior output with the new output. Check that option and submit.

The new output needs to be placed in a collection of the same exact type as the collection you are merging with for that particular collection operation to work. I’m guessing these are fastq reads – so the choice will be either a collection type “list of datasets” (single-end reads) or “list of pairs” (paired-end reads). Maybe you create a collection type “paired” (one set of paired-end reads)? If you are not sure which collection type the rest of the output is in, try adding the new output to the different collection types – one of them will work.

The first two GTN tutorials with this search cover collection operations – the second is probably more immediately helpful: Search Tutorials

Great that you got this far! :slight_smile: