Helen, I believe you wandered onto the RAST site and tried the upload there -- there are traces of this happening, and RAST does impose a contig length limit. The sites look very similar below the banner. No harm done, the job did get loaded to MG-RAST and is now being processed. Regards, Mark On Mon, 27 Apr 2009, Helen White wrote:

Mark Yes, that is the file of mine in the queue. When I tried to upload it at one point I received the below error, which led me to think there was a length problem. Can you explain the error as I clearly am missing something here. Thanks so much. Helen

Format: fasta

Found 492 contigs.

Found 388127 characters sequence data.

Found 0 ambiguous characters.

Found GC content to be 56.7

min length = 500, median length = 671, mean length = 788.9, max length = 2695

*Failed:*

The mean sequence length is below 2k chars.

Mark D'Souza wrote:

...

Hi Helen,

I see a new MG-RAST job under your name which is queued for the first processing step. Until this step is completed the job will not be visible to you, are you interpreting this as a failed upload?

There should be no contig length limit to 2Kbp for submission to MG-RAST, in fact the current version works best with small fragments.

Regards, Mark D'Souza -- for the MG-RAST team

[email protected] http://metagenomics.nmpdr.org/

On Mon, 27 Apr 2009, Helen White wrote:

...

Hi I am trying to upload a fasta file to MG-RAST of a metagenome, but my contigs are only ~800bp. Is it possible to make an exception to the 2Kbp contig length rule for this sample? Thanks for any help you can offer Best, Helen