umd-byob / presentations Goto Github PK

Hi,

I am running RepeatMasker and I have created the output directory where I want to save the output files generated from repeatmasker but I it keeps generating its own output folder and I have experienced previously the lost of the whole folder after the run was finished.

/home/el42208/softwares/RepeatMasker/RepeatMasker -pa 2 -s -lib /home/el42208/RepeatModeler_verrucosum/RM_26944.FriJan61254482017/combined_repeat_libs.fasta.masked -dir output_RM -e ncbi $assembly

Do you know why even tough I am adding -dir it is not saving the data into it and generating a default folder instead?

Thanks a lot for this notes

Elena

Hi,

First of all, thank you so much for writing this up, it's a great help.

But (probably because I'm incompetent when it comes to the command line) I get the above error when using your last script ([bash]$ tr -s ' ' my_input_genome_assembly.fasta.out.detailed < | sed 's/^ *//g' | tr ' ' '\t' > my_input_genome_assembly.fasta.out.detailed.tab) on the RepeatMasker .out file:

-bash: syntax error near unexpected token `|'

I've put cat at the start of the command and it seems to work ok apart from skewed first row but it's not important for what I'm trying to do with the file.

Cheers!