RepeatMasker
RepeatMasker copied to clipboard
rmhubley
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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 `...
**Describe the issue** This command "RepeatMasker -parallel 63 -xsmall -species Primates temp/chrY.fasta" failed with the error message FastaDB::_cleanIndexAndCompact() - Error could not open file some_path/RM_49156.WedOct191733472022/chrY.fasta: Permission denied at someotherpath/.conda/envs/repeatmasking.env/bin/RepeatMasker line...
**How can I retrieve the Kimura distance for each copy?** Dear developers, I'm trying to recover the estimated kimura distance for each copy from the align file. I noticed that...
**Describe the issue** RepeatMaskerLib.embl is not built while configuring RepeatMasker-4.1.2-p1 and is requestrd by DateRepeats ``` rpm_maker:RepeatMasker/RepeatMasker-4.1.2-p1 > DateRepeats Indicate directory with the RepeatMasker repeat libraries near line 136 of...
Dear, I obtained the gff file by running repeatmasker with -gff flag. Then I converted this gff2 into gff3 with rmOutToGFF3.pl script. Next, I converted this gff3 file into GTF...
RM2Bed.py (v4.1.2) breaks on invalid literal from Mmul10.fa (https://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/bigZips/rheMac10.fa.gz) with the "human" library. I have attached the .out file from a successful RM run on chr2 of the Mmul10 genome,...
I am drawing the repeat landscape using the perl script createRepeatLandscape.pl I have masked the genome on my custom library which includes new TE superfamily names: LTR/LARD, DNA/MITE, LTR/TRIM, LINE/Outcast,...
I met the same problem when I used the custom library (about 4.3Gb). RepeatMasker version 4.1.2-p1 Search Engine: NCBI/RMBLAST [ 2.10.0+ ] NCBIBlastSearchEngine::search: Error...compressed subject database (/public1/BGI/Project/F21FTSECKF2595/PUTjinwD/02.assembly/02.hic/02.contain_hic/cc/RM_23789.FriNov120937482021/merge.TEsorter.non_similar_repeat.for_lib.fa) does not exist!...
**What do you want to know?** I'm using RepeatMasker version 4.1.2-p1. I get an error when I run the following command: /home/user/local/tool/RepeatMasker/RepeatMasker -lib /home/user/local/tool/RepeatModeler/db/species_final-families.fa /home/user/local/sample_genome.fasta -pa 45 -xsmall -poly -html...
I tried to generate landscape using the script after divergent calculation, it returns empty HTML include some of the classes not all, what if I wanted specific classes would this...
