The purpose of this tool is to merge annotation together into a database that can be queried and graphed. The more annotation you add in, the more annotation will be grouped together in that database, and the more additional annotation that can be pulled in (from reference annotation).
Given what you state as the inputs used, your database would be maximally comprised of the transcripts, genes, predicted ORFs, and how those data are associated with each other.
What is included in the tabular report depends on the “Report options” you set. Expand that section of the tool form and note that sequences are not included by default (on purpose, as it can create a very large report that is difficult to work with).
Why other tools may be failing:
- An unfiltered full-size
Trinity assembly will be 1) very large and 2) contain very short sequences that only represent individual reads (that didn’t assemble with others).
- It would expected for jobs using an unfiltered assembly to fail due to exceeding resources (memory or runtime) at public Galaxy servers.
You might need to filter the assembly (by sequence length, or only transcripts with predicted ORFs, or however you decide to reduce the size) to create a query fasta that will not run out of resources on public Galaxy servers when using tools like BLAST and others. Sometimes it is also possible to break up a large query into smaller chunks and run tools in batches, then combine the results after.
Optionally, you can set up your own Galaxy with sufficient resources to work with large data. FAQ: https://galaxyproject.org/choices/