I’m running IQ-TREE concordance factor analysis and the analysis completes successfully according to the log file, but the concordance output files are not being collected as separate output datasets (I’m only getting the standard outputs).I am providing a reference tree (-t), gene trees (- - gcf) and setting site concordance factors (- - scf = 100). I’ve disabled model selection and set tree search interations to zero (-n).
Is there a way to access these concordance output files, or does the Galaxy IQ-TREE tool wrapper need to be updated to collect these additional output files when concordance analysis is performed?
This is a good question and I’m not yet familiar with the exact detail you are asking about, but requesting more from the intermediate outputs seems possible! Do you have an example we can start from? Then, if something is missing in the outputs that a parameter change cannot address, we can use your example when we make the request to the developers at the their Github project.
Something small in a history by itself would be best. You can share that history back here to get things started.
When I reviewed, it looks like the tool didn’t produce any outputs at all, and the job logs are emtpy.
The first rerun to recreate the data ended with an error (query complicity). So, I started that up again and the same thing happened. This is my test history.
My first guess is that your original job also had this problem but it didn’t get reported back to the application fully.
I would suggest exploring the other parameters associated with these concordance_factor options first to test the limits of what the public server can process.
Let’s also ask the EU administrators to see if they have more ideas. Hi @wm75 – what do you think?
