September 2009 - Mg-rast - mailman3.cels.anl.gov

shutdown
by Robert Olson 30 Sep '09

30 Sep '09

You'll probably want to idle or put a hold on the mg-rast jobs in the queue so that when we shut down early Friday you won't get a bunch of errored jobs. --bob

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Re: [mg-rast] MG-RAST Dataset
by dsouza＠mcs.anl.gov 29 Sep '09

29 Sep '09

Hi, The dataset you refer to: 975 4441115.3 Mediterranean Gutless Worm was obtained from the camera site: http://camera.calit2.net/ http://web.camera.calit2.net/cameraweb/gwt/org.jcvi.camera.web.gwt.download… > Begin forwarded message: > > > From: Manuel Kleiner <mkleiner(a)mpi-bremen.de> > > Date: September 23, 2009 7:53:03 AM CDT > > To: <folker(a)mcs.anl.gov> > > Subject: MG-RAST Dataset > > > > Dear Dr. Meyer > > I am working with the fantastic MG-RAST toolset at the moment and > > had a > > question in that regard. Unfortunatelly the link > > http://www.theseed.org/wiki/Contact does not work and thats why I > am > > contacting you using this e-mailadress. > > I just found the following public dataset on MG-RAST > > Mediterranean Gutless Worm (4441115.3) > > I could not find any background information on where the original > > dataset > > was retrieved from and how it was loaded into MG-RAST. I think it > > might be > > a dataset that we work with a lot, but I wanted to be sure. > > I would be happy if you could give me some hints on the origin of > the > > dataset or tell me where I could find that info. > > Thank you very much (also for providing such an nice tool to the > > community) > > best regards > > Manuel Kleiner > > > > -- > > Manuel Kleiner > > MPI for Marine Microbiology > > Celsiusstr. 1 > > D-28359 Bremen > > Germany > > > > Telefon: +49 (0) 421 2028 905 > > Fax: +49 (0) 421 2028 790 > > > > E-Mail: mkleiner(a)mpi-bremen.de > > http://www.mpi-bremen.de/Manuel_Kleiner.html -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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Re: [mg-rast] MG-RAST Dataset
by Mark D'Souza 29 Sep '09

29 Sep '09

Thanks, Mark ----- "bahador.nosrat" <bahador.nosrat(a)gmail.com> wrote: > From: "bahador.nosrat" <bahador.nosrat(a)gmail.com> > To: dsouza(a)mcs.anl.gov > Cc: mg-rast(a)mcs.anl.gov > Sent: Tuesday, September 29, 2009 4:48:33 PM GMT -06:00 US/Canada Central > Subject: Re: MG-RAST Dataset > > correct > > > 2009/9/29 < dsouza(a)mcs.anl.gov > > > > Hi Bahador, > > I am guessing the metagenome in question (see below) is from the > Camera website, is that right? > > 975 4441115.3 Mediterranean Gutless Worm > > http://web.camera.calit2.net/cameraweb/gwt/org.jcvi.camera.web.gwt.download… > > Thanks, > Mark > > > ----- "Folker Meyer" < folker.meyer(a)googlemail.com > wrote: > > > From: "Folker Meyer" < folker.meyer(a)googlemail.com > > > To: "Mark D'Souza" < dsouza(a)mcs.anl.gov > > > Sent: Tuesday, September 29, 2009 4:16:41 PM GMT -06:00 US/Canada > Central > > Subject: Fwd: MG-RAST Dataset > > > > can you help > > > > Begin forwarded message: > > > > > From: Manuel Kleiner < mkleiner(a)mpi-bremen.de > > > > Date: September 23, 2009 7:53:03 AM CDT > > > To: < folker(a)mcs.anl.gov > > > > Subject: MG-RAST Dataset > > > > > > Dear Dr. Meyer > > > I am working with the fantastic MG-RAST toolset at the moment and > > > had a > > > question in that regard. Unfortunatelly the link > > > http://www.theseed.org/wiki/Contact does not work and thats why I > > am > > > contacting you using this e-mailadress. > > > I just found the following public dataset on MG-RAST > > > Mediterranean Gutless Worm (4441115.3) > > > I could not find any background information on where the original > > > dataset > > > was retrieved from and how it was loaded into MG-RAST. I think it > > > might be > > > a dataset that we work with a lot, but I wanted to be sure. > > > I would be happy if you could give me some hints on the origin of > > the > > > dataset or tell me where I could find that info. > > > Thank you very much (also for providing such an nice tool to the > > > community) > > > best regards > > > Manuel Kleiner > > > > > > -- > > > Manuel Kleiner > > > MPI for Marine Microbiology > > > Celsiusstr. 1 > > > D-28359 Bremen > > > Germany > > > > > > Telefon: +49 (0) 421 2028 905 > > > Fax: +49 (0) 421 2028 790 > > > > > > E-Mail: mkleiner(a)mpi-bremen.de > > > http://www.mpi-bremen.de/Manuel_Kleiner.html > > > > -- > You can't teach a hammer to love nails.

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Re: [mg-rast] MG-RAST Dataset
by bahador.nosrat 29 Sep '09

29 Sep '09

correct 2009/9/29 <dsouza(a)mcs.anl.gov> > Hi Bahador, > > I am guessing the metagenome in question (see below) is from the Camera > website, is that right? > > 975 4441115.3 Mediterranean Gutless Worm > > > http://web.camera.calit2.net/cameraweb/gwt/org.jcvi.camera.web.gwt.download… > > Thanks, > Mark > > > ----- "Folker Meyer" <folker.meyer(a)googlemail.com> wrote: > > > From: "Folker Meyer" <folker.meyer(a)googlemail.com> > > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > > Sent: Tuesday, September 29, 2009 4:16:41 PM GMT -06:00 US/Canada Central > > Subject: Fwd: MG-RAST Dataset > > > > can you help > > > > Begin forwarded message: > > > > > From: Manuel Kleiner <mkleiner(a)mpi-bremen.de> > > > Date: September 23, 2009 7:53:03 AM CDT > > > To: <folker(a)mcs.anl.gov> > > > Subject: MG-RAST Dataset > > > > > > Dear Dr. Meyer > > > I am working with the fantastic MG-RAST toolset at the moment and > > > had a > > > question in that regard. Unfortunatelly the link > > > http://www.theseed.org/wiki/Contact does not work and thats why I > > am > > > contacting you using this e-mailadress. > > > I just found the following public dataset on MG-RAST > > > Mediterranean Gutless Worm (4441115.3) > > > I could not find any background information on where the original > > > dataset > > > was retrieved from and how it was loaded into MG-RAST. I think it > > > might be > > > a dataset that we work with a lot, but I wanted to be sure. > > > I would be happy if you could give me some hints on the origin of > > the > > > dataset or tell me where I could find that info. > > > Thank you very much (also for providing such an nice tool to the > > > community) > > > best regards > > > Manuel Kleiner > > > > > > -- > > > Manuel Kleiner > > > MPI for Marine Microbiology > > > Celsiusstr. 1 > > > D-28359 Bremen > > > Germany > > > > > > Telefon: +49 (0) 421 2028 905 > > > Fax: +49 (0) 421 2028 790 > > > > > > E-Mail: mkleiner(a)mpi-bremen.de > > > http://www.mpi-bremen.de/Manuel_Kleiner.html > -- You can't teach a hammer to love nails.

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Fwd: MG-RAST Dataset
by dsouza＠mcs.anl.gov 29 Sep '09

29 Sep '09

Hi Bahador, I am guessing the metagenome in question (see below) is from the Camera website, is that right? 975 4441115.3 Mediterranean Gutless Worm http://web.camera.calit2.net/cameraweb/gwt/org.jcvi.camera.web.gwt.download… Thanks, Mark ----- "Folker Meyer" <folker.meyer(a)googlemail.com> wrote: > From: "Folker Meyer" <folker.meyer(a)googlemail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Tuesday, September 29, 2009 4:16:41 PM GMT -06:00 US/Canada Central > Subject: Fwd: MG-RAST Dataset > > can you help > > Begin forwarded message: > > > From: Manuel Kleiner <mkleiner(a)mpi-bremen.de> > > Date: September 23, 2009 7:53:03 AM CDT > > To: <folker(a)mcs.anl.gov> > > Subject: MG-RAST Dataset > > > > Dear Dr. Meyer > > I am working with the fantastic MG-RAST toolset at the moment and > > had a > > question in that regard. Unfortunatelly the link > > http://www.theseed.org/wiki/Contact does not work and thats why I > am > > contacting you using this e-mailadress. > > I just found the following public dataset on MG-RAST > > Mediterranean Gutless Worm (4441115.3) > > I could not find any background information on where the original > > dataset > > was retrieved from and how it was loaded into MG-RAST. I think it > > might be > > a dataset that we work with a lot, but I wanted to be sure. > > I would be happy if you could give me some hints on the origin of > the > > dataset or tell me where I could find that info. > > Thank you very much (also for providing such an nice tool to the > > community) > > best regards > > Manuel Kleiner > > > > -- > > Manuel Kleiner > > MPI for Marine Microbiology > > Celsiusstr. 1 > > D-28359 Bremen > > Germany > > > > Telefon: +49 (0) 421 2028 905 > > Fax: +49 (0) 421 2028 790 > > > > E-Mail: mkleiner(a)mpi-bremen.de > > http://www.mpi-bremen.de/Manuel_Kleiner.html

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Re: [mg-rast] MG-RAST - new password requested
by Mark D'Souza 29 Sep '09

29 Sep '09

Hi, Sorry about that, I changed your password to: qwerty Please log in and change this as soon as you receive this email. ----- "Stefan Sievert" <ssievert(a)whoi.edu> wrote: > From: "Stefan Sievert" <ssievert(a)whoi.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Tuesday, September 29, 2009 2:37:19 PM GMT -06:00 US/Canada Central > Subject: Re: [mg-rast] MG-RAST - new password requested > > Hi: > I am currently trying to log in to use MG-RAST and the server does not > seem to respond. I always get back to the login website. Thanks in > advance. > Best, > Stefan > > > > On Sep 29, 2009, at 9:14 AM, mg-rast(a)mcs.anl.gov wrote: > > > > A request to reset the password for your login 'ssievert' has been > issued. If you have not requested a new password via the web > interface, please contact us at mg-rast(a)mcs.anl.gov . > > Your new password is: d.rvUAx/ > > We recommend to change the password immediately. To do so please go to > our web service http://metagenomics.nmpdr.org/ and change your > password from the account management. > > -- > > This email was automatically generated by the MG-RAST web service. Do > not reply. > > > > > > ************************************************* > > > Dr. Stefan Sievert > Associate Scientist > Biology Department, Mail Stop 52 > Stanley W. Watson Laboratory for Biogeochemistry > Woods Hole Oceanographic Institution > Woods Hole, MA 02543, USA > Phone: (508) 289-2305 > Fax: (508) 457-2076 > e-mail: ssievert(a)whoi.edu > Sievert Lab for Microbial Ecology and Physiology > > > ************************************************** -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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Re: [mg-rast] MG-RAST - new password requested
by Stefan Sievert 29 Sep '09

29 Sep '09

Hi: I am currently trying to log in to use MG-RAST and the server does not seem to respond. I always get back to the login website. Thanks in advance. Best, Stefan On Sep 29, 2009, at 9:14 AM, mg-rast(a)mcs.anl.gov wrote: > A request to reset the password for your login 'ssievert' has been > issued. If you have not requested a new password via the web > interface, please contact us at mg-rast(a)mcs.anl.gov. > > Your new password is: d.rvUAx/ > > We recommend to change the password immediately. To do so please go > to our web service http://metagenomics.nmpdr.org/ and change your > password from the account management. > > -- > > This email was automatically generated by the MG-RAST web service. > Do not reply. > ************************************************* Dr. Stefan Sievert Associate Scientist Biology Department, Mail Stop 52 Stanley W. Watson Laboratory for Biogeochemistry Woods Hole Oceanographic Institution Woods Hole, MA 02543, USA Phone: (508) 289-2305 Fax: (508) 457-2076 e-mail: ssievert(a)whoi.edu Sievert Lab for Microbial Ecology and Physiology **************************************************

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Re: [mg-rast] Please delete
by Mark D'Souza 29 Sep '09

29 Sep '09

Done, Thanks for letting us know about it. ----- "Torsten Thomas" <t.thomas(a)unsw.edu.au> wrote: > From: "Torsten Thomas" <t.thomas(a)unsw.edu.au> > To: mg-rast(a)mcs.anl.gov > Sent: Wednesday, September 23, 2009 6:44:27 PM GMT -06:00 US/Canada Central > Subject: [mg-rast] Please delete > > Hi. > > > Please delete my job 4864 as I accidently submitted the same sequences > twice. > > > Thanks > > > Torsten > > > > > > Dr. Torsten Thomas > Senior Research Fellow > Centre for Marine Bio-Innovation > School of Biotechnology and Biomolecular Sciences > The University of New South Wales > Sydney, NSW 2052 > Australia > Ph + 61 (0) 2 938 53467 > Mob +61 (0) 410159525 > Fax + 61 (0) 2 938 51779 > > > "Anyone who believes exponential growth can go on forever in a finite > world is either a madman or an economist" (Kenneth Boulding, > economist) -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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Re: [mg-rast] Missing Files "Nine Biomes" paper
by dsouza＠mcs.anl.gov 29 Sep '09

29 Sep '09

Hi, I apologize for the delay in answering, we are in the process of creating the files you requested and will contact you when they are ready for download. ----- "Lucas Brouwers" <lucasbrouwers(a)gmail.com> wrote: > From: "Lucas Brouwers" <lucasbrouwers(a)gmail.com> > To: mg-rast(a)mcs.anl.gov > Sent: Tuesday, September 29, 2009 10:26:01 AM GMT -06:00 US/Canada Central > Subject: Re: [mg-rast] Missing Files "Nine Biomes" paper > > Dear Reader, > > > I am curious as to whether you received my following request. > > > If not, could you please look into it? > > > If so, could you please get back to me concerning my question? > > > Thanks in advance for your efforts! > > > Best wishes, > > > Lucas > > > On Thu, Sep 3, 2009 at 9:45 AM, Lucas Brouwers < > lucasbrouwers(a)gmail.com > wrote: > > > > Dear Reader, > > > Currently I am involved in a project on a new pathway prediction > approach in functional comparative metagenomics. > I am trying to download all metagenomes that are described i n your > article "Functional metagenomic profiling of nine biomes" (Nature, > april 2008). > The files I'm especially interested in are the tar files that contain > all internal data (metagenomeID.all_internal_data.tar.gz). > For most metagenomes, these are readily available from the download > pages. > However, for some of the metagenomes this file seems to be missing > (e.g. > http://metagenomics.nmpdr.org/metagenomics.cgi?page=DownloadMetagenome&meta… > ). > Below is a list of metagenomes for which the file is missing. I would > like to kindly ask you if it is possible that these files can be > uploaded. > > > > > • 4440060.4 > • 4441682.3 > • 4441681.3 > • 4441680.3 > • 4441679.3 > • 4440463.3 > • 4440464.3 > • 4440283.3 > • 4440284.3 > > Another thing I noticed: for the last metagenomes (from cow rumen & > chicken cecum), the links from > http://www.theseed.org/DinsdaleSupplementalMaterial/ are broken. > > > Thanks in advance! > > > Best wishes, > > > Lucas Brouwers > NCMLS, Nijmegen > > > -- > > Lucas Brouwers > lucasbrouwers(a)gmail.com > 06 26 92 83 25 > > > > > -- > > Lucas Brouwers > lucasbrouwers(a)gmail.com > 06 26 92 83 25 -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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Re: [mg-rast] A question about MG rast
by dsouza＠mcs.anl.gov 29 Sep '09

29 Sep '09

Dear Dr. Sun, We have been having longer than usual processing times recently due to some required maintenance as our machines get moved to a new location. Seeing as your metagenome is realtively small, I increased it's priority and it should complete within a day or two. ----- "Yijun Sun" <sunyijun(a)ufl.edu> wrote: > From: "Yijun Sun" <sunyijun(a)ufl.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Tuesday, September 29, 2009 8:54:01 AM GMT -06:00 US/Canada Central > Subject: [mg-rast] A question about MG rast > > Dear sir: > > I submitted a job to mg-rast to perform the annotation of 16S > sequences. The submitted dataset is quite small, consisting of only > 57973 sequences. The job was submitted on Sep 22, and I am still > waiting for the result. I am wondering if you could check the job to > see if there is something wrong with it. The job ID is 4444929.3. > Thank you very much. > > Best, > > ---- > Yijun Sun, Ph.D. > University of Florida > URL: plaza.ufl.edu/sunyijun > Email: sunyijun(a)biotech.ufl.edu -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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