-dir does not save data into it

[el42008]

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

[khughitt]

Hi Elena,

Did you try creating the (empty) directory you want to use before running RepeatMasker?

From the notes:

You can specify an output directory like -dir my_RM_output_dir, but you must create the directory first, RepeatMasker will not do it for you. If you don’t create this directory before running RepeatMasker, it will be ignored and it will create a directory similar to before...