Error using Intersect the intervals of two datasets (Galaxy Version 1.0.0) tool

usegalaxy.org support
,
1

How to fix this? I was following the Introduction to Genomics and Galaxy tutorial and got stuck on the Check for overlaps part because of the error below. Here’s a copy of my history: https://usegalaxy.org/api/short_term_storage/56bd3aea-19b2-4dad-b836-e178793b4a91

Uncaught exception in exposed API method:

The server could not complete this request. Please verify your parameter settings, retry submission and contact the Galaxy Team if this error persists. A transcript of the submitted data is shown below.

{
    "history_id": "bbd44e69cb8906b54ec7aa02d404b2a0",
    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0",
    "tool_version": "1.0.0",
    "inputs": {
        "returntype": "",
        "input1": {
            "batch": false,
            "product": false,
            "values": [
                {
                    "id": "f9cad7b01a472135930250c5157a6140",
                    "src": "hda",
                    "map_over_type": null
                }
            ]
        },
        "input2": {
            "batch": false,
            "product": false,
            "values": [
                {
                    "id": "f9cad7b01a4721353e98016c8557fd9c",
                    "src": "hda",
                    "map_over_type": null
                }
            ]
        },
        "min": "1",
        "__tags": []
    }
}
2

Hi,

seems the tool is currently broken on usegalaxy.org. You can use the (slightly more complicated) tool bedtools Intersect intervals instead, with the following non-default options:

”What should be written to the output file?”: Write the original entry in A for each overlap (-wa)

”Write the original A entry _once_ if _any_ overlaps found in B.”: Yes

If you are configuring things correctly, then, for the first run of the tool, you should get 3472 regions in the output dataset.

Sorry for the inconvenience,

Wolfgang

1 Like
3

Hi @micolods and @wm75 – we were able to make the correction. Please try again now if you still want to and thanks for letting us know about the problem! :hammer_and_wrench: