Jeb Rosen

> (1) RepeatMasker has a -lib parameter to use a custom library. Is this library in FASTA format? Yes; the format is described further in the `repeatmasker.help` file (link: The...

@jingydz in previous versions of RepeatMasker, `queryRepeatDatabase.pl` is located in the `RepeatMasker/util/` directory. RepeatMasker 4.1.1 and later use a new library file format; `RepeatMasker/famdb.py` can be used to access this...

RepeatMasker ships with [Dfam](https://www.dfam.org/home), an open database, which does not yet include any repeats for Tetrahymena nor any other Alveolates. It looks like the last RepBase RepeatMasker edition release also...

That's definitely an unhelpful message; thank you for reporting it. This problem should be detected and warned about in the `configure` program instead.

Yes, the `-lib` option for custom FASTA/HMM libraries is exclusive with the `-species` option for the installed libraries; only one or the other will be used for masking at a...

You can download either `Dfam.h5.gz` or `Dfam_curatedonly.h5.gz` as desired, and install it as `Libraries/Dfam.h5`. However, the changes between 3.2 and 3.3 were mostly in metadata that is not used by...

The `.tbl` output attempts to count base pair only once: the region of overlap will be counted for either one or the other. This should be a relatively rare occurrence...

> Then if there is a locus where a transposable elements and a tandem repeat overlap, which element will be counted in the final statics? The current algorithm counts both...

> I get a total of 141 N's in the output assembly. Do you know what the cause of this could be? That is unusual. Do the Ns in the...

Is the error consistent if you run it again? And, can you upload the full log output from a failed run?