RepeatMasker on Sun Grid Engine (SGE)

Question

[Menachem Sklarz]

Hi Everyone

I'm trying to run RepeatMasker in parallel (-pa=15) in an SGE environment. Everything works well, temporary files are created, the standard output reports that the analysis is complete and there are no error messages. However, once done, the temporary files are deleted and the output files are nowhere to be found.

I tried using the -dir parameter but to no avail.

Has anyone come across this problem? Any suggestions?

Thanks

Menachem

Answer 1

[Menachem Sklarz]

Problem identified!!

The query filename contained a + character, which apparently failed in a regular expression on the filename.