Hi Stuart, I will leave some of your questions to be answered by people on the mg-rast list. It does look like something is not right with the data you downloaded, the people who wrote the genbank file code would know better. I don't think a resubmission should be necessary, if there is something wrong we can fix it, and if our file format is incorrect we can change that. There is no size limit on the data you submit, if we have a problem processing it we will contact you. Regards, Mark D'Souza -- for the MG-RAST team http://metagenomics.nmpdr.org/ On Thu, 31 Jul 2008 [email protected] wrote:

Hi Mark

I have a few questions regarding the results from our data that we sent to your server (job # 956 genome 4441094.3 - ENvironmental_enrichment).

I have downloaded the annotated genbank file for the genome annotation, when I open the file I can only count 136982 sequences compared to 465226 called after preprocessing. From the other data that we have sent up and got back we normally get the same number of sequences in the annotated file as that which appears in the job details summary for the number of sequences after preprocessing. Is this what you would normally expect?

We normally download the genbank file and use this for some of our analysis here. Can we get a hold of the complete annotation or do we need to resend the data (this took 30 days to calculate)? It would appear if we use the seed viewer to view the annotated genome all the sequence fragments are there we just don't get them all when we download the file.

Also for this data set the server seems to time out when we request to view the features table is this due to the file size?

Thanks for any help with this. Do you have a size limit on the data set that could be submitted?

Regards

Stuart

Stuart Denman

CSIRO Livestock Industries 306 Carmody Rd, St Lucia QLD 4067, Australia Ph: +61-7-3214 2273 Fax: +61-7-3214 2900

[email protected]