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Dfam-consortium / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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Genome is not getting masked after running RepaetMasker (Not getting any error after run) #185

Closed vinitamehlawat closed 1 year ago

vinitamehlawat commented 1 year ago

Hi

I am using repeatMasker to mask my de novo genome, and assembly is at scaffold level. When I ran the repeatmasker with following command : RepeatMasker -xsmall /path/genome.fa . I got only 2 files in outpur dir with name Genome.fa and another Genome.fa_batch-1.masked . I didn't got any other output. I also checked my masked genome but i got only 1st scffold in masked file which is also without masking.

(This how I load RepeatMasker on hpc server: Module load perl/5.36.0 RepeatMasker/4.0.7 gcc-11.2.1/SKYLAKEX/ncbi-rmblastn/2.11.0)

Could you please suggest me to slove this issue.

Thank you Vinita

rmhubley commented 1 year ago

Its really strange that it created an output file with a capitol "G" and what looks like an intermediate output file that should have been in the temporary directory. Is this a human assembly? If not, you would need to at least specify the species (-species) or provide a custom species-specific TE library (-lib mylibrary.fa) to correctly annotate repeats in this assembly. The default (without either -lib or -species) is to use the human library.

It also seems you are using a modern version of rmblast and a very old version of RepeatMasker (4.0.7). I would suggest upgrading to RepeatMasker 4.1.3-p2 and try again.

vinitamehlawat commented 1 year ago

Thank you @rmhubley

After updating RepeatMasker I got outputs