[maker-devel] Maker installation-RepeatMasker (or running RepeatMasker outside maker)

[Linnie Linnie]

Dear Maker team,

I am analyzing a number of genomes in a cluster. I had previously installed
RepeatMasker and RepeatModeler independently without problem in order to
obtain the repeat libraries that are required by maker. This installation
runs perfectly.
However, when I install maker, it does not recognize that a successful
installation of RepeatMasker is already available. How can tell maker where
RepeatMasker is already located?

I have alternatively tried to install RepeatMasker from within maker and
then try to run maker. But it gives me the following error:

Unrecognized character \x7F; marked by <-- HERE after <-- HERE near column
1 at /data1/home/maker/exe/RepeatMasker/TRF.pm line 1.

Compilation failed in require at
/data1/home/maker/exe/RepeatMasker/RepeatMasker line 339.

BEGIN failed--compilation aborted at
/data1/home/maker/exe/RepeatMasker/RepeatMasker line 339.

ERROR: RepeatMasker failed

--> rank=NA, hostname=loma

ERROR: Failed while doing repeat masking

ERROR: Chunk failed at level:0, tier_type:1

FAILED CONTIG:NQYS01000001.1


ERROR: Chunk failed at level:2, tier_type:0

FAILED CONTIG:NQYS01000001.1


examining contents of the fasta file and run log

As a last option, I think I could run RepeatMasker with the installation I
already have and then pass its .gff file to maker. In this case, which
parameters should I pass in the maker_opts.ctl file?


Thank you so much for all your help (and Happy New Year to everyone!)
L.
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