Hi Ann,

How long a job is in the waiting state "grey" will let you know how busy the queue (server/cluster) is. How long it is in the executing state "yellow" will let you know how long it takes to process. These are independent.

That said, a ~1% control alignment failure may be reasonable - it just depends on the quality of your data, how strict the mapping parameters are, and how finished the reference genome is. Taking a look at some of the failures might help explain. Maybe run FastQC. Or a tool like Lastz can place a sequence quickly on the genome with control over things like coverage, identity, etc.

Then, tool options can be turned, if you think this is the run-time issue. Keep in mind that making a run less sensitive will speed up processing, but also likely reduce the number of "hits". Help for each tool's form (and link to primary documentation) and testing is the best way to determine the optimal settings per experiment. The defaults are most often those recommended by the tool authors and not optimal for every query/genome.

Hopefully this helps,

Jen
Galaxy team

On 3/7/13 5:24 PM, Ann Holtz-Morris, M.S. wrote:

HI,

Does anyone know how to check whether the Galaxy server(s) load is really high? My alignments, only 200,000 paired end reads seemed to be taking a long time. I read through the archives, and the answers were that 1) alignments take a while and that the server load really affects the turnaround time, and 2) But then again, it could also be your data & settings.

I could not find how users could check whether the server load is really heavy, especially for alignments. I also suspect it could have been be my query being incorrectly set up because when the alignment finally did come back, the ~1% control DNA did not align correctly.

Thanks

aholtzmorris

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