This job was terminated because itused more memory than it wasallocated.

[1263201095]

I used the tool ‘Scanpy FilterCells’, but the result showed that it exceeded memory. However, I believe the number of cells is not that large, as shown in the image below. How could this issue occur? Thank you!

[jennaj]

Welcome @1263201095

The issue might be the size of the data (when this is reported by any tool), but it is much more likely to be some format issue or a problem with the filter query. Meaning, maybe the tool couldn’t interpret the data and died.

More details about how to interpret the error message:

@jennaj

Whenever this error is reported

This job was terminated because it used more memory than it was allocated.

The message means that there is one of these going on

1. some input or parameter problem should be adjusted before the rerun
2. or, the work is actually too large to process at the Galaxy server where it was run

The public computational resources are significant, so the first case is much more common. But these do have practical limits.

If you think your job is actually running out of processing memory resources, the solution can be to try at a different server. Please see the directory here for choices → Public Galaxy Servers.

Note: The computational processing memory utilized for job execution is unrelated to storage space (quota) for your account.

---

---

For single cell data, there can be a few formats. The tutorials for the tool can be one source of help since these cover some of the manipulations. Then we have more tutorials for the entire process – these might be really helpful for you, especially if some of the data was not generated in Galaxy.

• GTN Tutorials for Scanpy FilterCells: based on counts and numbers of genes expressed
• GTN Tutorials for Inspect AnnData: object
• All Single Cell tutorials → Single Cell / Tutorial List

One simple test to run to look at the content is Inspect AnnData. Then compare that to your query with Scanpy Filter Cells. Your object is currently missing some of the common annotation layers.

Please let us know if this helps or not!