TopHat does not recognize or use the designated output directory

[gwilymh]

Hi,

I am trying to set up a data analysis pipeline in TopHat. For some reason, I cannot seem to get the program to use my designated output directory. I have tried the following commands:
--output-dir "/path" \
--output-dir /path \
-o "/path" \
-o /path \

However, all the files keep being written to ./tophat_out

Has anyone encountered a similar problem?

[GenoMax]

Only thing you need to specify is

-o /path_to/name_for_output_directory

Not sure why you have the extra "\" in your examples.

[user42]

Hi,

I've seen tophat have issues writing output to secondary (non-root) drives if you have selinux configured and enforcing. Drove me nuts because there was no obvious root cause. If you're outputting to a mounted device, try disabling selinux (disable/reboot).

(Note: selinux is active and enforcing by default on most redhat/centos family distros)