February 2011 - Mg-rast - mailman3.cels.anl.gov

(Job 9313 , ID 4449583.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 08 Feb '11

08 Feb '11

Min-Soo Kim (WebServerBackend::User=HASH(0xe4d41a0)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4449583.3.

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(Job 9312 , ID 4449584.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 08 Feb '11

08 Feb '11

Min-Soo Kim (WebServerBackend::User=HASH(0x5fe7180)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4449584.3.

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(Job 9311 , ID 4449582.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 08 Feb '11

08 Feb '11

Min-Soo Kim (WebServerBackend::User=HASH(0x1e31e160)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4449582.3.

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(Job 9309 , ID 4449580.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 08 Feb '11

08 Feb '11

Min-Soo Kim (WebServerBackend::User=HASH(0x18c2f160)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4449580.3.

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Re: [mg-rast] (Detailed) progress report on current jobs on the server; Loading more dataset on MG Rast?
by Powell Phd, Amy Jo 07 Feb '11

07 Feb '11

Excellent. Thanks so much for your response. Regards, AJP On 2/7/11 4:21 PM, "Folker Meyer" <folker.meyer(a)gmail.com> wrote: Let's discuss tomorrow. Short answer is yes. We are bottlenecked because new version of mg-RAST is taking off. -- Sent from mobile device On Feb 7, 2011, at 2:07 PM, "Powell Phd, Amy Jo" <ajpowel(a)sandia.gov> wrote: Hi Mark, Thanks so much for the follow up on my query about implementing MG Rast on our machines here. I am looking forward to speaking with you tomorrow afternoon. On a different but related note, I see that the jobs I uploaded to the MG Rast server **do not appear** to have progressed beyond the 3 green squares point (i.e, the progress bar). Are these jobs in fact still being actively computed, i.e., are my current jobs progressing? They **appear** to be stalled. But I could just be seeing a compute power bottle neck ...? Please provide an update on the status of these jobs (beyond what I can see of the server in my account), if possible. Related to this last point, would it be OK with you (& others at MG Rast), if I uploaded more large datasets for analysis on the MG Rast servers? I ask, b/c I don't want to completely choke the MG Rast server. Thanks very much for any guidance you can provide on these points. Regards, AJP On 2/4/11 1:53 PM, "Mark D'Souza" <dsouza(a)mcs.anl.gov <mailto:[email protected]> > wrote: Hi Amy, Sorry for the delay, we will get in touch with you over the phone. Mark ----- Original Message ----- > From: "Powell Phd, Amy Jo" <ajpowel(a)sandia.gov <mailto:[email protected]> > > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov <mailto:[email protected]> > > Sent: Wednesday, February 2, 2011 1:21:15 PM > Subject: Portable/downloadable MG Rast for Sandia bioinformatics servers? > Hi Mark, > > Is there a portable/downloadable/open source version of MG Rast that > we could put on our servers we're building here? > > The main advantage in having a local MG Rast is of course computing > efficiency for big jobs. > > Thanks, AJP > > Amy J. Powell, Ph.D. > > Sandia National Laboratories > Department of Bioenergy & Defense Technology > 1515 Eubank Blvd., SE > Albuquerque, NM 87123 > USA > > Telephone: (505)284-8050 > Fax: (505)284-1323 > > "We are all agreed that your theory is crazy. My own feeling is that > it is not crazy enough." > > Niels Bohr, Nobel Prize winner in Physics Amy J. Powell, Ph.D. Sandia National Laboratories Department of Bioenergy & Defense Technology 1515 Eubank Blvd., SE Albuquerque, NM 87123 USA Telephone: (505)284-8050 Fax: (505)284-1323 "We are all agreed that your theory is crazy. My own feeling is that it is not crazy enough." Niels Bohr, Nobel Prize winner in Physics Amy J. Powell, Ph.D. Sandia National Laboratories Department of Bioenergy & Defense Technology 1515 Eubank Blvd., SE Albuquerque, NM 87123 USA Telephone: (505)284-8050 Fax: (505)284-1323 "We are all agreed that your theory is crazy. My own feeling is that it is not crazy enough." Niels Bohr, Nobel Prize winner in Physics

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Re: [mg-rast] (Detailed) progress report on current jobs on the server; Loading more dataset on MG Rast?
by Folker Meyer 07 Feb '11

07 Feb '11

Let's discuss tomorrow. Short answer is yes. We are bottlenecked because new version of mg-RAST is taking off. -- Sent from mobile device On Feb 7, 2011, at 2:07 PM, "Powell Phd, Amy Jo" <ajpowel(a)sandia.gov> wrote: Hi Mark, Thanks so much for the follow up on my query about implementing MG Rast on our machines here. I am looking forward to speaking with you tomorrow afternoon. On a different but related note, I see that the jobs I uploaded to the MG Rast server **do not appear** to have progressed beyond the 3 green squares point (i.e, the progress bar). Are these jobs in fact still being actively computed, i.e., are my current jobs progressing? They **appear** to be stalled. But I could just be seeing a compute power bottle neck ...? Please provide an update on the status of these jobs (beyond what I can see of the server in my account), if possible. Related to this last point, would it be OK with you (& others at MG Rast), if I uploaded more large datasets for analysis on the MG Rast servers? I ask, b/c I don’t want to completely choke the MG Rast server. Thanks very much for any guidance you can provide on these points. Regards, AJP On 2/4/11 1:53 PM, "Mark D'Souza" <dsouza(a)mcs.anl.gov> wrote: Hi Amy, Sorry for the delay, we will get in touch with you over the phone. Mark ----- Original Message ----- > From: "Powell Phd, Amy Jo" <ajpowel(a)sandia.gov> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Wednesday, February 2, 2011 1:21:15 PM > Subject: Portable/downloadable MG Rast for Sandia bioinformatics servers? > Hi Mark, > > Is there a portable/downloadable/open source version of MG Rast that > we could put on our servers we’re building here? > > The main advantage in having a local MG Rast is of course computing > efficiency for big jobs. > > Thanks, AJP > > Amy J. Powell, Ph.D. > > Sandia National Laboratories > Department of Bioenergy & Defense Technology > 1515 Eubank Blvd., SE > Albuquerque, NM 87123 > USA > > Telephone: (505)284-8050 > Fax: (505)284-1323 > > "We are all agreed that your theory is crazy. My own feeling is that > it is not crazy enough." > > Niels Bohr, Nobel Prize winner in Physics *Amy J. Powell, Ph.D. Sandia National Laboratories Department of Bioenergy & Defense Technology 1515 Eubank Blvd., SE Albuquerque, NM 87123 USA Telephone: (505)284-8050 Fax: (505)284-1323 "We are all agreed that your theory is crazy. My own feeling is that it is not crazy enough." Niels Bohr, Nobel Prize winner in Physics *

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[Fwd: help MG-RAST jobs (13876, 13877)]]
by vbrahma＠imtech.res.in 07 Feb '11

07 Feb '11

------------------------------- Original Message ------------------------------- Subject: help MG-RAST jobs (13876, 13877)] From: vbrahma(a)imtech.res.in Date: Tue, February 8, 2011 4:13 am To: dsouza(a)mcs.anl.gov -------------------------------------------------------------------------------- Hi My job #13876 was submitted on 27jan 2011 and yet Similarity final check has not yet started. SEED organism directory creation has not yet started. Exportable data creation has not yet started. Final processing has not yet started. As suggested I have dleted Job #13877 Kindly help regards VBR ------------------------------- Original Message ------------------------------- Subject: Re: Your MG-RAST jobs (13876, 13877) From: vbrahma(a)imtech.res.in Date: Sat, January 29, 2011 1:06 am To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> -------------------------------------------------------------------------------- hi thanks for bringing this to notice. Kindly proceed with only one fasta file. both are identical.If you would kindly know how to delete one file I can do that too.Thanks I appreciate. regards VBR > Hi, > > The two jobs 13876 and 13877 appear to be identical and are both named > 'Kaziranga', probably the sequence file got uploaded twice by mistake. To > conserve our compute resources I will let 13876 complete and put a hold on the > processing of 13877 and delete it in two days if I do not hear from you. > > -- > Regards, > Mark D'Souza > -- for the MG-RAST team > > mg-rast(a)mcs.anl.gov > http://metagenomics.anl.gov/ > > If you need to respond to this email please address it to the mailing-list > mg-rast(a)mcs.anl.gov >

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status shows completed but can't access metagenome in mg-rast beta
by Daniel Barshis 07 Feb '11

07 Feb '11

Hi There, I currently have a metagenome analysis running on the MG-RASTBeta server under the user name danbarshis and job ID 4452340.3. Its status is listed as "In Progress: sims: completed" but when I try to click to view it gives me the following error message "Failure in component: Can't call method "id" on an undefined value at /mcs/bio/mg-rast/test/FIGDisk/dist/releases/dev/common/lib/MGRAST/WebPage/MetagenomeSelect.pm line 426. " Are you familiar with this error and/or is there something wrong with the analysis of this job or is it still running? Any information and advice on if the job is stuck and needs to be resubmitted would be appreciated. many thanks, dan p.s. also I just noticed that the email address specified in the beta version help/contact section is "mg-rast.mcs.anl.gov" which I believe should be "mg-rast(a)mcs.anl.gov" in case this was a typo -- ><((º> ><((º> ><((º> ><((º> ><((º> Daniel Barshis, Ph.D. Postdoctoral Scholar, Palumbi Lab Hopkins Marine Station of Stanford University Pacific Grove, California 93950 USA Phone: (831) 655-6210 Fax: (831) 655-6215

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Re: [mg-rast] MG-RAST version 3.0 beta test
by Petr Baldrian 07 Feb '11

07 Feb '11

Dear MG-Rast team, I am unable to upload files in the beta test MG-RAST version 3.0. When I open the "Upload" page, there is no form to input the name and location of files to be uploaded. I am using Windows 7 / Mozilla Firefox 3.6.13. Could you please check what is wrong? Thank you, Petr Baldrian baldrian(a)biomed.cas.cz

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Re: [mg-rast] Your MG-RAST jobs (13940 WT control merge and 14100 WT con B)
by Mark D'Souza 07 Feb '11

07 Feb '11

Done, Thanks, Mark ----- Original Message ----- > From: "Clarissa Schwab" <clarissa.schwab(a)univie.ac.at> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Monday, February 7, 2011 2:44:52 PM > Subject: Re: Your MG-RAST jobs (13940 WT control merge and 14100 WT con B) > Hi Mark > Thanks for your mail. The 14100 WT con B can be deleted. > Clarissa > > Mo, 7.02.2011, 21:13, Mark D'Souza wrote: > > Hi, > > > > The sequence files for two jobs you submitted (13940 WT control > > merge and > > 14100 WT con B) are identical. I am holding both for now, please let > > me > > know which one you would like deleted. > > > > > > -- > > Regards, > > Mark D'Souza > > -- for the MG-RAST team > > > > mg-rast(a)mcs.anl.gov > > http://metagenomics.anl.gov/ > > > > If you need to respond to this email please address it to the > > mailing-list > > mg-rast(a)mcs.anl.gov > > > > > >

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