Did you adjust your anchoring set of PFam domains? You can test those by specifically asking the tool to consider one or more that resulted from the upstream tool. Adjusting other parameters can help as well. We won’t be able to help with the paramaters here too much, but the guide can be found at the developer’s site:
The Galaxy implementation is still under experimentation, and only available at a single server, but it should still work “about” the same! I added some more to the original testing history above with some of more defaults plus a custom anchor file (with a text PF query against the raw files as a comparison for scope). The failures in the history are all due to parameter issues plus sparse-content issues.
My running idea list: I think the tool form could make the significance of the anchors much more important – maybe moved to the top of the form – since the output scope will always rely on this. Other ideas… detailed logs should be output by default, the HMM reference could be pre–loaded as a native index, more items could be warnings – or local to a sample within a larger collection grouping, and the MIBiG database use should probably be a on-by-default requirement (unless the HMM database input minimum changes).
If you have ideas, you are welcome to drop them into this forum topic or, more direct, you could open an issue ticket at the IUC repository for your “nice-to-have feedback” list. Working with scientists to tune tools is really important for our project!
- tools-iuc/tools/bigscape at main · galaxyproject/tools-iuc · GitHub
- Example of a prior reported item where I asked the developers for a specific change. In short, you don’t have to explain how to adjust, but what you want different with an example, then they will consider it and engineer it in, if possible. → Enhancement: allow BiG-SCAPE to process inputs without a required .gbk extension in dataset filename · Issue #6015 · galaxyproject/tools-iuc · GitHub
Those issues are not for error troubleshooting. So, if you run into what looks like an error instead, we can vet that here. Seeing the example helps!
Thanks! 