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

Re: [mg-rast] Your MG-RAST jobs (13949 bacterial shotgun data and 14071 human stool)
by Mark D'Souza 07 Feb '11

07 Feb '11

Thanks, Mark ----- Original Message ----- > From: "Rohini Sinha" <rsinha(a)mail.med.upenn.edu> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Monday, February 7, 2011 2:15:27 PM > Subject: Re: Your MG-RAST jobs (13949 bacterial shotgun data and 14071 human stool) > Hi, > > I deleted one of the jobs. > > Thanks, > Rohini > > On Mon, Feb 7, 2011 at 3:07 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> > wrote: > > Hi, > > > > The sequence files for the two jobs (13949 bacterial shotgun data > > and 14071 human stool) you submitted are identical, I will put a > > hold on both for now. Please let me know which one you wish to > > delete. > > > > -- > > 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 > > > > > > -- > Programmer Analyst > University of Pennsylvania School of Medicine > Phone : 215-573-3141

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Re: [mg-rast] Your MG-RAST jobs (14032 MH0034, 14033 MH0049)
by Mark D'Souza 07 Feb '11

07 Feb '11

Done, No problem Mark ----- Original Message ----- > From: "Omer Eilam" <omereila(a)post.tau.ac.il> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Monday, February 7, 2011 2:06:08 PM > Subject: Re: Your MG-RAST jobs (14032 MH0034, 14033 MH0049) > Please delete job # 14032. > > > Thanks much! > omer > > > On Mon, Feb 7, 2011 at 10:03 PM, Mark D'Souza < dsouza(a)mcs.anl.gov > > wrote: > > > Hi, > > The sequence files for the two jobs 14032 MH0034 and 14033 MH0049 are > identical, I will put a hold on both jobs for now, please let me know > which one you wish to proceed and which one to delete. > > -- > 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 > > > > -- > > > Omer Eilam > Complex Network Systems > Prof. Eytan Ruppin > Tel-Aviv University > http://cns.cs.tau.ac.il/

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Your MG-RAST jobs (13940 WT control merge and 14100 WT con B)
by Mark D'Souza 07 Feb '11

07 Feb '11

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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Your MG-RAST jobs (13949 bacterial shotgun data and 14071 human stool)
by Mark D'Souza 07 Feb '11

07 Feb '11

Hi, The sequence files for the two jobs (13949 bacterial shotgun data and 14071 human stool) you submitted are identical, I will put a hold on both for now. Please let me know which one you wish to delete. -- 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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Your MG-RAST jobs (14032 MH0034, 14033 MH0049)
by Mark D'Souza 07 Feb '11

07 Feb '11

Hi, The sequence files for the two jobs 14032 MH0034 and 14033 MH0049 are identical, I will put a hold on both jobs for now, please let me know which one you wish to proceed and which one to delete. -- 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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Your MG-RAST jobs (14020, 14074, 14021, 14076, 14022, 14075)
by Mark D'Souza 07 Feb '11

07 Feb '11

Hi, Some of the data sets you submitted to MG-RAST are identical, perhaps they were submitted multiple times by mistake. To conserve our computing resources, I will delete 14020,14021 and 14022, the other jobs will proceed normally. -- 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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(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

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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Re: [mg-rast] MG-RAST Job 13872 seems to have stalled
by Mark D'Souza 07 Feb '11

07 Feb '11

Hi, There is no problem with the job, it is queued for similarity computation. The volume of new data sets on the MG-RAST system has been high recently at the same time we have had a shortage of compute cycles, resulting in longer than usual processing time. We are working to rectify this. ----- Original Message ----- > From: "Rolf Alexander Prade" <rolf.prade(a)okstate.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Monday, February 7, 2011 12:45:44 PM > Subject: [mg-rast] MG-RAST Job 13872 seems to have stalled > Dear Sir, > MG-RAST Job 13872 seems to have stalled it has not yet started the > Similarity final check for over 7 days. > Thanks > R Prade -- 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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MG-RAST Job 13872 seems to have stalled
by Prade, Rolf Alexander 07 Feb '11

07 Feb '11

Dear Sir, MG-RAST Job 13872 seems to have stalled it has not yet started the Similarity final check for over 7 days. Thanks R Prade

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Re: [mg-rast] data submission problem
by Mark D'Souza 07 Feb '11

07 Feb '11

Hi, As I said in my previous two emails, "The problem is with the uncompressed fasta file, the ^Z end of file character needs to be removed as it is being treated as part of the last sequence.". Try editing your uncompressed fasta file with a text editor like vi, go to the last line and delete the last character and newline then reenter them, save, compress to tarred gzipped file and submit. Regards, Mark ----- Original Message ----- > From: "Xiangzhen Li" <lixz(a)illinois.edu> > To: dsouza(a)mcs.anl.gov > Sent: Monday, February 7, 2011 11:52:39 AM > Subject: data submission problem > Dear Mark > I submitted several big files using .tgz file (Linux and Unix system). > It is not successful. These task already was removed from MG RAST. I > am not sure which compress software is suitable for this work. Do you > accept compressed file by windows-version software, like TugZip? Can > we send the files to you, and ask your help for submission? > Thanks > > -- > Xiangzhen Li > Department of Civil and Environmental Engineering > University of Illinois at Urbana-Champaign > 205 N. Mathews > Urbana, IL 61802

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