search

Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
Other
189 stars 22 forks source link

Does RepeatModeler require a NTFS disk ? #159

Open giacuong171 opened 2 years ago

giacuong171 commented 2 years ago

Hi, I'm trying right now to test the tool with example data followed by this link: https://biohpc.cornell.edu/doc/annotation_2018_exercises1.pdf and I got stuck with the command: RepeatModeler -pa 2 -engine ncbi -database pyu >& repeatmodeler.log the errors are: """ ln: failed to create symbolic link 'tmp': Operation not permitted ln: failed to create symbolic link 'tmp2': Operation not permitted eleredef failed. Exit code 256 """ I have read that the command "ln -s" can only work with NTFS disk format. Is that correct? Does anyone encounter a similar issue?

jebrosen commented 2 years ago

Hi, and I'm sorry to see you had this issue!

The error message does suggest that the filesystem does not support symbolic links (ln -s). You can find out the particular filesystem you are using by reading the FSTYPE from this command: findmnt -T /path/to/repeatmodeler.log. If this filesystem does not support symbolic links, you might have access to other storage using a different filesystem such as local or network storage.

What you read about NTFS sounds inaccurate. Many other types of filesystems, including ext4 and btrfs and several filesystems used in computing clusters, support symbolic links! NTFS also supports symbolic links, but it has different features and limitations from Unix and Linux filesystems. Because of these differences, RepeatModeler and some programs it uses may work less well or not at all on NTFS.

I would be grateful to know what FSTYPE you have. Hopefully, this can help us determine a solution and anyone else with a similar problem in the future.