OK, this is what is going on:
- The version of the converter available from the tool panel includes an option to trim “overhanging coordinates”, instead of failing. It is toggled on by default.
- The version of the converter available from the “auto-convert” between the datatypes does not include a trimming function by default. Why? Because that would introduce a data change that is not explicitly exposed/chosen by the user. Converters are convenience functions … and never directly change data content, on purpose.
- MACS can output coordinates that can extend past the chromosome ends. This is a known “feature” of MACS, and everyone would have to adjust for that with certain functions or downstream tools. This is definitely not just in Galaxy. Review this discussion at the MACS forum if you are curious. The tool they recommend is the same one used in Galaxy, and the trim option is available in the version from the tool panel, but not in the auto-convert method’s version (again, on purpose).
What to do:
- Extract a workflow from one of your successful histories, and make sure that it includes the direct conversion step that includes the trimming. Or, add it directly to a workflow by editing it.
- Use your workflow. It will work just like a single tool if you “favorite” it and hide the intermediate outputs, and will even show up in the tool panel.
Workflows are much easier than people assume, and will save you even more time, over time, especially since you are doing the same thing across a bunch of samples. You could even just organize and tag all of your samples at once, then run the workflow once on the whole thing. Or, keep it simple between the pairs like you are doing now. Either is fine.
Now, your files are large. If the direct conversion fails for memory reasons when using the trim option, and the database assignment is actually correct, then you can trust the error message about runtime memory. Some data will actually exceed public computational resources of course! A scaled up private server is a common solution. See the Galaxy Platform directory for options – there are both free and pay-for-use choices (apply your grant funding, etc).
Hope that helps!