How to stop RepeatModeler saving to $HOME

[Rob-murphys]

How do I stop RepeatModeler saving (temp?) files to $HOME. Can we direct this to elsewhere as my cluster has limited space on $HOME.

The directory in question:

(base) [robmur@g-12-l0002 ~]$ ll RM_996.ThuMar251125372021/
total 23232
-rw-r--r-- 1 robmur ku_00014   402661 Mar 25 12:22 consensi.fa
-rw-r--r-- 1 robmur ku_00014 15797344 Mar 25 12:22 families.stk
drwxr-xr-x 2 robmur ku_00014      265 Mar 25 11:33 round-1
drwxr-xr-x 4 robmur ku_00014     2627 Mar 25 11:36 round-2
drwxr-xr-x 4 robmur ku_00014     7771 Mar 25 11:44 round-3
drwxr-xr-x 4 robmur ku_00014    23191 Mar 25 12:22 round-4
drwxr-xr-x 7 robmur ku_00014   184614 Mar 25 14:21 round-5

[jebrosen]

By default RepeatModeler creates directories named RM_* in either the current directory or in the same directory as the database file. If neither of those choices is appropriate, you can also use the -dir option to write files to a different directory.

[Rob-murphys]

weird, $HOME is neither the current directory or the database directory yet the directory is being created there. I will try -dir and see if that works.

[Rob-murphys]

-dir is not redirecting this directory away from $HOME

Input RepeatModeler -database /home/people/robmur/ku_00014/data/termitomyces/repeatmaskerDB/termitomyces -pa 10 -LTRStruct -dir /home/people/robmur/ku_00014/data/termitomyces/repeatmaskerDB/termitomyces

The directory

(base) [robmur@g-12-l0002 ~]$ echo $HOME
/home/people/robmur
(base) [robmur@g-12-l0002 ~]$ ls
all_fasta  backup  bad_genes.lst  busco_downloads  ku_00014  people  ref  repeatmodeler.out  RM_62559.FriMar260814162021  robmur  temp
(base) [robmur@g-12-l0002 ~]$ pwd
/home/people/robmur
(base) [robmur@g-12-l0002 ~]$

[jebrosen]

Ah, I'm sorry. For RepeatModeler the -dir option only works with an already existing directory. mkdir /home/people/robmur/ku_00014/data/termitomyces/repeatmaskerDB/termitomyces should make that work.