RepeatMasker安装RepBase和Dfam 3.6不兼

./configure

Building FASTA version of RepeatMasker.lib ...ERROR:__main__:Error reading file: This file cannot be read by this version of famdb.py.
##即
/home/lx_sky6/yt/soft/RepeatMasker/famdb.py -i Libraries/RepeatMaskerLib.h5 families -f embl -a -d rosids > rosids_ad.embl
ERROR:__main__:Error reading file: This file cannot be read by this version of famdb.py.

this as a problem particular to the merging of RepBase libraries (RepBase RepeatMasker Edition) and Dfam 3.6\. The problem occurs in 3.6 due to updates in the NCBI Taxonomy that shifted some scientific names to synonyms. We do not currently store synonyms in our *h5 exports causing problems with merging in specific RepBase entries. To fix this I regenerated the Dfam 3.6 *.h5 exports and updated a file in the RepeatMasker distribution "Libraries/RMRBMeta.embl". If both of these files are updated, the merger should proceed normally and RepeatMasker can be setup. Here are the steps:

*   Obtain a new copy of the Dfam 3.6 famdb export 'Dfam-p1.h5.gz' or 'Dfam-p1_curatedonly' from [](https://www.dfam.org/releases/Dfam_3.6/families)[https://www.dfam.org/releases/Dfam_3.6/families](https://www.dfam.org/releases/Dfam_3.6/families).
*   Rename the downloaded Dfam 3.6 *.h5 file "Dfam.h5" and replace the RepeatMasker "Libraries/Dfam.h5" with it.
*   Download an updated Repbase RepeatMasker Edition Metadata file (RMRBMeta.embl) from the development branch of RepeatMasker [](https://github.com/rmhubley/RepeatMasker/blob/development/Libraries/RMRBMeta.embl)[https://github.com/rmhubley/RepeatMasker/blob/development/Libraries/RMRBMeta.embl](https://github.com/rmhubley/RepeatMasker/blob/development/Libraries/RMRBMeta.embl).
*   Replace the current RepeatMasker "Libraries/RMRBMeta.embl" file with the new one.
*   Remove the RepeatMasker files "Libraries/RMRB.embl", "Libraries/RepeatMaskerLib.h5", and "Libraries/RepeatMasker.lib*" as these will be regenerated automatically.
*   Rerun the RepeatMasker configure program.

I will update the instructions on the RepeatMasker website and prioritize getting a new RepeatMasker release and containers out soon so this won't be necessary in the future. NOTE that this shouldn't be necessary at all if you only intend to use Dfam 3.6 with RepeatMasker.

下载新的Dfam

##https://www.dfam.org/releases/Dfam_3.7/families/
wget https://www.dfam.org/releases/Dfam_3.7/families/Dfam.hmm.gz
wget https://www.dfam.org/releases/Dfam_3.7/families/Dfam.h5.gz
wget https://www.dfam.org/releases/Dfam_3.7/families/Dfam.embl.gz
gunzip *

$ ./configure
Enter Selection: 5
Building FASTA version of RepeatMasker.lib ...........................................................................
Building RMBlast frozen libraries..
The program is installed with a the following repeat libraries:
File: /home/lx_sky6/yt/soft/RepeatMasker/Libraries/RepeatMaskerLib.h5
FamDB Generator: famdb.py v0.4.2
FamDB Format Version: 0.5
FamDB Creation Date: 2023-01-08 10:42:05.645898

Database: Dfam withRBRM
Version: 3.7
Date: 2023-01-11

Dfam - A database of transposable element (TE) sequence alignments and HMMs.
RBRM - RepBase RepeatMasker Edition - version 20181026

Total consensus sequences: 64595
Total HMMs: 19730


Further documentation on the program may be found here:
  /home/lx_sky6/yt/soft/RepeatMasker/repeatmasker.help