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

[Carson Holt]

You can manually specify a path in maker_exe.ctl

—Carson


> On Dec 29, 2019, at 3:03 PM, Linnie Linnie <peachandolives at gmail.com> 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
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20200122/dd25ffab/attachment-0003.html>