Jeb Rosen

> **EDIT:** Seems I forgot to include `-no_is` in my command line. So if I understand correctly not including that will make `RepeatMasker` look for bacterial IS elements from a...

Unlike `RepeatModeler`, `RepeatMasker` writes the temporary `RM_*` files to the current directory. If that directory is not writable, it also tries the `-dir` option, and the directory where the input...

Your `-g` parameter looks wrong, since it doesn't accept commas: the genome will be interpreted as being 2 base pairs long, instead of 2 Gbp. This might change the generated...

Some of these look like they should be fixed in `createRepeatLandscape.pl`: `DNA/Crypton-A`, `LINE/I-Jockey`, and `DNA/hAT-hAT19`. I am working on testing a fix. `LTR/ERV2` and `LTR/ERV3` are not `RepeatMasker` subtypes -...

I made a short test file with a 46-character header and it was fine. In fact, exactly 50 characters is fine and 51 fails. Can you share a link to...

Ah, I think I see what's happening now. Long sequences -- longer than I tested for my previous comment -- are split into multiple files and the text `frag-` is...

That is a bit surprising, but might be explained by changes in the libraries of known repeats. What have you been using for the `-lib` or `-species` flag, and was...

I think in that case this is a duplicate of #88 - the equivalent `famdb.py` command for `queryTaxonomyDatabase.pl` needs `--include-class-in-name`. Please reopen this issue if you see significant differences after...

> RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127 This might be relevant: the classifications from RepeatModeler (specifically the `RepeatClassifier` program) are informed in part by the configured RepeatMasker library, including RepBase RepeatMasker...

Sorry, I am quickly getting lost in all the possible changes between the different versions. Could you help verify and correct this summary so that all the changes are listed...