Hi Mark, Thanks for all the previous help. At the moment I have one file stuck at finalizing for a long time, is there something I can do? Thanks Omry On Tue, Jul 5, 2011 at 9:57 AM, Omry Koren <[email protected]> wrote:

Hi Mark, A few of my files are stuck with an error. Is there anything I should do? Thank you very much for all your help and time, Omry

On Wed, Jun 29, 2011 at 12:50 PM, Mark DSouza <[email protected]> wrote:

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Hi Omry,

There is no way to delete jobs from the web interface right now, we will be adding this in the future. In the meantime I can delete the jobs, is this the correct list? 25749 4466152.3 1234 25892 4466295.3 1264 25853 4466256.3 2264 25747 4466150.3 2264 25687 4466090.3 2195

We will check the job 1303 (25745, 4466148.3) which is showing an error.

Regards, Mark

----- Original Message -----

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From: "Omry Koren" <[email protected]> To: [email protected] Sent: Wednesday, June 29, 2011 10:36:21 AM Subject: [mg-rast] Fwd: Submission to MG-RAST ---------- Forwarded message ---------- From: Omry Koren < [email protected] > Date: Tue, Jun 21, 2011 at 12:18 PM Subject: Re: Submission to MG-RAST To: Mark DSouza < [email protected] >

Hi Mark, I went over all of the files and I have a few questions: 1. How do I delete files? I have a few duplicates (1234,1264, and 2195) and I would also like to delete both 2264 since the sequencing center just notified me that they are very bad quality. 2. A few files are showing errors, anything I can do?

Thank you very much for your time, Omry

On Mon, Jun 13, 2011 at 8:24 PM, Omry Koren < [email protected] > wrote:

I am really sorry about that, I thought some of the files were corrupted. This is my first time using MG-RAST and I will contact you next time I run into trouble. Thank you and sorry again, Omry

On Mon, Jun 13, 2011 at 5:32 PM, Mark DSouza < [email protected] > wrote:

Hi,

I am still seeing multiple uploads for the same file, 2195 was uploaded four times, including once today, 2264 has been uploaded thrice, including once today, 1234 and 1264 were uploaded twice with an upload of 1264 today. Check if a dataset is already running before uploading it and contact us if a job is not progressing, we can fix things on our side. Creating duplicate jobs loads our compute machines unnecessarily and affects the processing times for all our users. These datasets are each multiple Gbp in size and will not get completed in a day, if you are patient and work with us the jobs will get processed.

Regards, Mark

----- Original Message -----

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From: "Omry Koren" < [email protected] > To: "Mark DSouza" < [email protected] >

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Sent: Friday, June 10, 2011 5:09:17 PM Subject: Re: Submission to MG-RAST okay, thank you very much

On Fri, Jun 10, 2011 at 6:06 PM, Mark DSouza < [email protected] > wrote:

Hi,

No problem. I deleted the duplicated jobs. I also noticed that the upload for 2342 seems to be truncated, please compare the file size from the upload page against your local file, you probably need to redo the upload for this job.

Regards, Mark

----- Original Message -----

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From: "Omry Koren" < [email protected] > To: "Mark DSouza" < [email protected] > Sent: Friday, June 10, 2011 3:26:17 PM Subject: Re: Submission to MG-RAST Hi, Yes those are duplicates and can be deleted, thank you. Besides what I am uploading now I only have one more file to upload so will save the ftp option for next time. Thank you very much Omry

On Fri, Jun 10, 2011 at 4:24 PM, Mark DSouza < [email protected]

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wrote:

Hi,

It appears that you are uploading a large amount of sequence data to MG-RAST. While this is not a problem, it would make the process easier for both of us if we coordinate these uploads. If you have more data to submit we can create an ftp site where you can dump your data files and we can then use the files to complete the submission.

From the jobs which have been created the files 2195.txt and 2264.txt have been uploaded multiple times and seem to be running multiple jobs. If you can confirm that these are identical datasets I will delete the duplicated jobs.

Please let us know about the ftp option, this will make the upload process easier for you as well as help us in balancing the load on our machines and avoid duplicating jobs.

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

[email protected] http://metagenomics.anl.gov/

If you need to respond to this email please address it to the mailing-list [email protected]

-- Omry Koren, Ph.D. Postdoctoral Associate Department of Microbiology 467 Biotechnology building Cornell University Ithaca, NY 14853 Email: [email protected]

-- Omry Koren, Ph.D. Postdoctoral Associate Department of Microbiology 467 Biotechnology building Cornell University Ithaca, NY 14853 Email: [email protected]

--

Omry Koren, Ph.D. Postdoctoral Associate Department of Microbiology 467 Biotechnology building Cornell University Ithaca, NY 14853 Email: [email protected]

--

Omry Koren, Ph.D. Postdoctoral Associate Department of Microbiology 467 Biotechnology building Cornell University Ithaca, NY 14853 Email: [email protected]

-- Omry Koren, Ph.D. Postdoctoral Associate Department of Microbiology 467 Biotechnology building Cornell University Ithaca, NY 14853 Email: [email protected]

-- Omry Koren, Ph.D. Postdoctoral Associate Department of Microbiology 467 Biotechnology building Cornell University Ithaca, NY 14853 Email: [email protected]

-- Omry Koren, Ph.D. Postdoctoral Associate Department of Microbiology 467 Biotechnology building Cornell University Ithaca, NY 14853 Email: [email protected]