Hi,
I’m trying to use RepeatMasker with the GRCh38.p14 genome from NCBI. I've downloaded the Dfam-7.hmm.gz.md5 file, but I'm unsure about how to properly reconfigure RepeatMasker to use this file. Any advice would be gratly appreciated.
Taxon "homo sapiens" is in partition 7 of the current FamDB however,
this partition is absent. Please download this file from the original
source and rerun configure to proceed.
Thanks.
1 answer
There's a configure script in the RepeatMasker distribution. From the documentation: https://www.repeatmasker.org/RepeatMasker/
Run Configure Script: The program requires some initial configuration. This should also be re-run after updates to the library files.
cd /usr/local/RepeatMasker # if installed as by the manual
cd $CONDA_PREFIX/share/RepeatMasker # if installed with conda...
perl ./configure
The only difficulty here is to locate the script and to place the library in the right directory.
If RM is installed with conda, the configure location is likely: $CONDA_PREFIX/share/RepeatMasker/ and it still has to be run after conda install.
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Also: "I've downloaded the Dfam-7.hmm.gz.md5"? This is (only) the checksum for the Dfam-7.hmm.gz file. You may want to download the Dfam-7.hmm.gz file.