Hi,

I have run some top hap output through the samtools BAM-to-SAM wrapper. It 
creates the SAM file about 50% of the time. The rest of the time it makes an 
empty file. In this case if I just rerun it often works. I was wondering if 
anyone else has seen this behavior. I am using a cloud server and think  I 
might need to change some settings. This causes my workflow to fail for many 
libraries so I also interested in any workarounds anyone has figured out.
Thanks in advance for any help.
Cheers
Mike
________________________________
--CONFIDENTIALITY NOTICE--: The information contained in this email is intended 
for the exclusive use of the addressee and may contain confidential 
information. If you are not the intended recipient, you are hereby notified 
that any form of dissemination of this communication is strictly prohibited. 
www.benaroyaresearch.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

Reply via email to