Cluster on intervals error

usegalaxy.eu support
1

I am trying to run Cluster the intervals of a dataset. The dataset was uploaded as a tab-delimited txt file with intervals (chr, start, end), with format set to interval. However, I keep getting an error, for instance.

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”: “11ac94870d0bb33a11a4c12ff2acb723”,
“tool_id”: “toolshed.g2.bx.psu.edu/repos/devteam/cluster/gops_cluster_1/1.0.0”,
“tool_version”: “1.0.0”,
“__tags”: [ ],
“inputs”: {
“input1”: {
“batch”: false,
“product”: false,
“values”: [
{
“id”: “26c75dcccb616ac873e01a5a9564fb0e”,
“src”: “hda”,
“map_over_type”: null
}
]
},
“distance”: “1”,
“minregions”: “2”,
“returntype”: “1”
}
}

I wonder what is wrong with the coordinates files, or there is a problem with the Cluster tool? Though I keep getting a similar error message for tool Complement intervals of a dataset, thus the problem may rather be related to the intervals dataset.

Thanks in advance

1 Like
2

Hi @jmuser

Thanks for sharing the tool errors. This might be due to a change on the server. I’ll try to test independently to replicate.

Are you working at UseGalaxy.eu or at a different public server? Would you like to share your history?

Let’s start there! :slight_smile:

3

Hi @jennaj,

Yes, I am encountering this problem at UseGalaxy.eu.

Here is the link to the history. (Please keep private.)

There are currently only two datasets with coordinates. Files/datasets without “#CHROM START END” produced the same error.

I just tested the Cluster tool with basically the same files/datasets at UseGalaxy.org — it works fine there.

Thanks a lot,
Jens

4

This is very likely a remaining issue from our recent configuration changes on Galaxy Europe.

We’ll look into it.

5

Turns out it was an older issue, but it’s now fixed for both Cluster and Complement.

Thanks for letting us know!

1 Like
6

Thanks to you, too.