Problems configuring RepeatClasifier on docker. about tetools HOT 8 CLOSED

Hi, can you provide the command you used to invoke RepeatClassifier? The first thing I want to confirm is that the configured library is being mounted into the container properly.

Another possible problem is that the automatic update script only extracts the curated families from the .h5 files. It's possible that it's just not including the families that would be useful to you, and if that's the case I can help work around that.

from tetools.

from tetools.

from tetools.

A read-only file system could certainly be causing issues. tetoolsDfamUpdate.pl rewrites /opt/RepeatMasker/Libraries/RepeatMasker.lib, so you could confirm if that's working by checking the timestamp with ls -al.
Can you share the error message when you use the shell -w command?

from tetools.

from tetools.

Thanks for confirming that the container is working. It looks like the issue is that tetoolsDfamUpdate.pl is only importing curated families into RepeatMasker.lib, and since there are no curated Daphnia families, it makes sense that you're not seeing any additional hits. To work around this, one solution is to use famdb.py to directly query the data you need.

First, I ran a few lineage queries to confirm what is in the FamDB files:

python3 famdb.py -i ./dfam38_full lineage -d daphnia
6668 Daphnia(8) [0]
├─6669 Daphnia pulex(8) [0]
└─35523 Daphnia pulicaria(8) [937]

python3 famdb.py -i ./dfam38_full lineage -d --curated daphnia
6668 Daphnia(8) [0]
├─6669 Daphnia pulex(8) [0]
└─35523 Daphnia pulicaria(8) [0]

This confirms that there are 937 uncurated families in file 8, though all are from Daphnia pulicaria. To extract them, you can use the families -f fasta_name command, and append them to your RepeatMasker.lib. The following command should generate the FASTA output from FamDB, prepend a new line to it, and concatenate it to RepeatMasker.lib.

python3 <host path to /RepeatMasker>/famdb.py -i <host path to /RepeatMasker>/Libraries/famdb families -d -f fasta_name daphnia | (echo && cat) >> <host path to /RepeatMasker>/Libraries/RepeatMasker.lib

More information regarding FamDB commands can be found here. If you need to add other FamDB files, just be aware that tetoolsDfamUpdate.pl will overwrite any changes you make to RepeatMasker.lib. You may choose to run tetoolsDfamUpdate.pl anyway, but if not you might need to edit rmlib.config by hand. If tetoolsDfamUpdate.pl is rerun, be sure to only export uncurated families from FamDB to avoid doubling up curated families in RepeatMasker.lib.

Hopefully that produces better results for you, but let me know either way.

from tetools.

from tetools.

from tetools.