Maker installation-RepeatMasker (or running RepeatMasker outside maker)

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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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Re: Maker installation-RepeatMasker (or running RepeatMasker outside maker)

Carson Holt-2
You can manually specify a path in maker_exe.ctl

—Carson


On Dec 29, 2019, at 3:03 PM, Linnie Linnie <[hidden email]> wrote:

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. 
_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org