This is a test version of Biostars. For the public version, visit https://www.biostars.org.
RepeatMasker on Sun Grid Engine (SGE)

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

chip-seq genome
• 1,816 views • link
updated by Ram Ram • written by Menachem Sklarz • Menachem Sklarz

1 answer

Problem identified!!

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

• 0 views • link
updated by Ram Ram • written by Menachem Sklarz • Menachem Sklarz

Log in to answer this question.

More posts like this