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Old 07-24-2013, 07:39 AM   #1
Location: Milwaukee

Join Date: Dec 2011
Posts: 72
Default TopHat does not recognize or use the designated output directory


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?
gwilymh is offline   Reply With Quote
Old 07-24-2013, 07:46 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,961

Only thing you need to specify is
-o /path_to/name_for_output_directory
Not sure why you have the extra "\" in your examples.
GenoMax is offline   Reply With Quote
Old 07-24-2013, 11:16 AM   #3
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Location: California

Join Date: May 2013
Posts: 1


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)

Last edited by user42; 07-24-2013 at 11:18 AM. Reason: context
user42 is offline   Reply With Quote

output, tophat 2

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