ditto. depends on the data. we can not know this in advance, but 1 peg per fragment is not unreasonable. peg to frag ration is an interesting way to look at metagenomes. wonder if low ration means diverse biome or just means we have not seen a lot of this before. FOlker On Apr 24, 2008, at 9:00 AM, Robert Olson wrote:
I was talking about the fraction that got called as pegs.
On Apr 24, 2008, at 8:56 AM, Folker Meyer wrote:
yes. it is reasonable. people can simply combine to mid-sized 454 runs and get to 600k reads...
Folker On Apr 24, 2008, at 8:43 AM, Robert Olson wrote:
This job has 445585 reads, from which it created 282K pegs. Does this seem remarkable to anyone? Wonder what's going on. Rob - does it seem reasonable?
--bob
On Apr 24, 2008, at 8:36 AM, Robert Olson wrote:
This is the actual problem.
root@treponema:/vol/mg-rast-prod/jobs/540# wc -l rp/4440668.3/ Features/peg/tbl 282879 rp/4440668.3/Features/peg/tbl
This job produced 282K peg features. FIGV is just not up for that. we will have to put a fix in soon for this.
--bob
On Apr 24, 2008, at 8:22 AM, Folker Meyer wrote:
Sean:
in the process of getting the new version of the server up and running on the production hardware we ran into resource issues. This killed both the new and the old version.
THe old version will be up and running shortly.
Sorry for the inconvienience, FOlker On Apr 24, 2008, at 7:56 AM, Sean Norman wrote:
Hi Folker,
Sorry to take more of your time but I am trying to view the features of one of my metagenomics jobs analyzed by the MG-RAST using the SEED viewer and keep getting the error message below. I've emailed the contact listed in the error message a few times but have not yet received a reply. The user is snorman and the job# is 540 (4440668.3). Please let me know if there is anything I can do to remedy this problem. Thanks and have a good day.
Cheers,
Sean
"Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator, [email protected] and inform them of the time the error occurred, and anything you might have done that may have caused the error.
More information about this error may be available in the server error log."
R. Sean Norman, Ph.D. Assistant Professor Dept. of Environmental Health Sciences Arnold School of Public Health University of South Carolina 921 Assembly St. Columbia, SC 29208 Phone: 803.777.0940 Email: [email protected]
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Folker Meyer