Customizing RepeatMasker libraries: Absent

[jsg8145]

Hello,
thank you for tools, and I had some errors when I tried to customize my own repeat masker libraries.
Now, I use this tools from singularity:
singularity pull dfam-tetools-latest.sif docker://dfam/tetools:latest

Then, I used this command to use singularity container.
singularity run dfam-tetools-latest.sif

Next, I copied the opt/ReaPeatMasker/Libraries to /home/$USER and download dfam38_full.8.h5.gz in the folder after exit.
cp -r Libraries /home/$USER
exit
cd /home/$USER/Libraries/famdb
wget https://www.dfam.org/releases/Dfam_3.8/families/FamDB/dfam38_full.8.h5.gz && gunzip dfam38_full.8.h5.gz
chown -R $USER ./Libraries

And I mounted my home directory to /work inside the container:
cd /home/$USER
singularity run -B $(pwd):/work dfam-tetools-latest.sif

Finally, I tried to regenerate my own libraries:
cd /opt/RepeatMasker
./tetoolsDfamUpdate.pl
but I had a log like this. It seems the tools cannot find Partition 8.

perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = "en_US.utf-8",
LANG = "C"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").

Checking for libraries...

• Found a FamDB root partition

Building RMBlast frozen libraries..
The program is installed with a the following repeat libraries:

FamDB Directory : /opt/RepeatMasker/Libraries/famdb
FamDB Generator : famdb.py v1.0
FamDB Format Version: 1.0
FamDB Creation Date : 2023-11-15 11:30:15.311827

Database: Dfam
Version : 3.8
Date : 2023-11-14

Dfam - A database of transposable element (TE) sequence alignments and HMMs.

1 Partitions Present
Total consensus sequences present: 295552
Total HMMs present : 295552

Partition Details

Partition 0 [dfam38_full.0.h5]: root - Mammalia, Amoebozoa, Bacteria , Choanoflagellata, Rhodophyta, Haptista, Metamonada, Fungi, Sar, Placozoa, Ctenophora , Filasterea, Spiralia, Discoba, Cnidaria, Porifera, Viruses
Consensi: 295552, HMMs: 295552

Partition 1 [ Absent ]: Obtectomera

Partition 2 [ Absent ]: Euteleosteomorpha

Partition 3 [ Absent ]: Sarcopterygii - Sauropsida, Coelacanthimorpha, Amphibia, Dipnomorpha

Partition 4 [ Absent ]: Diptera

Partition 5 [ Absent ]: Viridiplantae

Partition 6 [ Absent ]: Deuterostomia - Chondrichthyes, Hemichordata, Cladistia, Holostei, Tunicata, Cephalochordata, Cyclostomata , Osteoglossocephala, Otomorpha, Elopocephalai, Echinodermata, Chondrostei

Partition 7 [ Absent ]: Hymenoptera

Partition 8 [ Absent ]: Ecdysozoa - Nematoda, Gelechioidea, Yponomeutoidea, Incurvarioidea, Chelicerata, Collembola, Polyneoptera, Tineoidea, Apoditrysia, Monocondylia, Strepsiptera, Palaeoptera, Neuropterida, Crustacea, Coleoptera, Siphonaptera, Trichoptera, Paraneoptera, Myriapoda, Scalidophora

Further documentation on the program may be found here:
/opt/RepeatMasker/repeatmasker.help

Is there anything wrong with the progress of the task? How can I fix it?

[asgray]

Hi, instead of
singularity run -B $(pwd):/work dfam-tetools-latest.sif,
try running
singularity run -B /home/$USER/Libraries:/opt/RepeatMasker/Libraries dfam-tetools-latest.sif

If the steps to copy the library data out of the container worked, and you've added any additional files to the host system library directory, you just need to bind it in where RepeatMasker knows to look for it and run the update script. The /work directory in the container is just used for copying the data out, and any time you want the container to use your local library, just bind it in as above.
Also bear in mind that you may need to delete rmlib.config for tetoolsDfamUpdate.pl to work.

Let me know if that works!

[jsg8145]

Hi,
Now it works! Thank you for your advice.
I think not deleting the rmlib.config file might also have been the cause.