I managed to fix my problem.

I modified the CCAT wrapper to output the CCAT log file to Galaxy,
then got this at the end:

reading tag files......
0 tags in L1, 0 tags in L2.
tag file error!

So there was an error when running the CCAT binary, but the CCAT
wrapper thinks it succeeded and tries to move the output files.
I looked at the CCAT source and it turns out it is returning 0 on
error, which seems bizarre.

The cause of the real error was my chromosome names were "1", "2",
"Y", etc. instead of "chr1", "chr2", "chrY", etc.


On Fri, Oct 12, 2012 at 3:59 PM, Kyle Chessman <knch...@gmail.com> wrote:
> When running CCAT I get:
> Error running CCAT.
> Traceback (most recent call last):
>   File "/opt/Galaxy/tools/peak_calling/ccat_wrapper.py", line 44, in <module>
>     if __name__ == "__main__": main()
>   File "/opt/Galaxy/tools/peak_calling/ccat_wrapper.py", line 41, in main
>     return stop_err( tmp_dir, e )
>   File "/opt/Galaxy/tools/peak_calling/ccat_wrapper.py", line 15, in stop_err
>     raise exception
> IOError: [Errno 2] No such file or directory: '/tmp/tmpc3sfYR/CCAT in
> Galaxy.significant.peak'
> I'm using the latest galaxy-dist and have the CCAT binary in
> /usr/local/bin. Nothing gets put into the temp directory while CCAT is
> running.
> Any ideas?
> Thanks,
> Kyle
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