Robert Hubley

These are separate issues: 1. The generation of "general libraries" by RepeatMasker is a standard step. This library contains artifact sequences used by the contamination checks. It is generated by...

It's because you again used an option to disable simple repeat detection ("-noLowSimple").

A few things to note from your output. The first is that it appears you are using a conda installation of RepeatMasker. We do not currently support Conda with RepeatMasker...

I am going to close this, please let us know if you are still having problems.

The next release of RepeatMasker ( preparing the release now ), will not require downloading Dfam in order to perform custom library searches ( "-lib" ).

RepeatMasker 4.1.7 was just release and fixes this issue. You should be able to run custom library searches (-lib) out of the box without having to download/store Dfam.

I do not have access to the current versions of abblast. If you have a moment, could you run: ``` /ab-blast-20200317-linux-x64/blastp ``` In the past, without any options it would...

This is really a question about scoring matrices/gap parameters more than about rmblastn. RepeatMasker uses scoring matrices in which a substitution from N to any other base is slightly penalized...

That's really bizarre. When I run your same exact command line (with a 1MB mouse sequence) I never see more than 35KB memory use for each RepeatMasker thread. I get...

RepeatMasker is definitely not tuned for short read datasets. It's intended for assembled data with thresholds set for identifying significant alignments (typically > 30bp ). In any case, I am...