After a few weeks of running Maker using Dfam without selecting species, I still got empty file with @2 errors.
I am doing the last option now by using the RepeatMasked assembly to do Maker and disabled Dfam.
Sorry to hear that you are still having problems, @daikez.
In my very limited experience, I found that the @2 interpolation problem did not actually prevent Maker from giving results. @abretaud has said this as well. So although this problem with the Perl interpreter should probably be resolved, it likely isn’t the reason that your datasets are empty. Your detailed error message will likely show other errors, but unfortunately the @2 issue is listed as the main error on the metadata – leading one to think it is the reason something didn’t work. In my case, the error message revealed that the Dfam repeat database was trying to reference a species from the list that was apparently not supported (Drosophila), as you can see on my error message posted here. None of the other model organisms on the list were appropriate for my work, so I did not select a species, thereby using the entire curated Dfam consortium of repeats. Once I did that, I started getting results from Maker, and could train Augustus on the results.
(By the way, I’m now using a custom repeat library I built instead of the whole Dfam consortium, but that’s another story.)
So all I can suggest is to look closely at your entire error message, likely several lines below the initial @2 warning.
Maybe someone from Galaxy will have better suggestions.
For people who have the problem of low BUSCO recovery I described earlier, I seem to have resolved it by creating my own custom repeat library to use with Maker. I’m still in the early rounds trained with Augustus, but recovery of BUSCOs has already increased to nearly 80%. To produce a de novo repeat library, I used the EDTA workflow, which combines several packages, including RepeatModeler and LTRharvest.
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