Hi Mike,

I am moving this over to the galaxy-...@bx.psu.edu mailing list as it concerns a local install. This is the best way to make contact with others working with the same type of Galaxy.

A few things to provide more context that will help with troubleshooting:

1 - Are you running the most current version of Galaxy?
      https://wiki.galaxyproject.org/DevNewsBriefs (Nov 4, 2013)

2 - The local has some of the initial production server changes made?
      initial install: http://getgalaxy.org
      next steps are under: https://wiki.galaxyproject.org/Admin
in particular: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer

3 - You installed SAMTools from the Tool Shed? The config is correct? And are running the latest version?

4 - When you run the same dataset(s) through on the public Main Galaxy instance at http://usegalaxy.org, is it successful or does it fail?

I wasn't sure if you meant that the same file will fail and then pass, or if some fail and some pass. If you could clarify that, it would help. It could mean the difference between a processing problem (pointing to a config or other issue) and a simple memory problem (where allocating more could help). Please keep all replies on the mailing list with a cc.


Galaxy team

On 12/10/13 12:07 PM, Michael Mason wrote:

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.

Jennifer Hillman-Jackson

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