January 2010 - Mg-rast - mailman3.cels.anl.gov

Re: [mg-rast] MG-RAST question
by dsouza＠mcs.anl.gov 27 Jan '10

27 Jan '10

Hi, Sorry about that, we are working on fixing the metabolic maps. About the download page, there is currently no way of accessing the data without going through each subsystem. ----- "Fares Z. Najar, Ph.D." <fznajar(a)ou.edu> wrote: > From: "Fares Z. Najar, Ph.D." <fznajar(a)ou.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Wednesday, January 27, 2010 12:03:59 PM GMT -06:00 US/Canada Central > Subject: [mg-rast] MG-RAST question > > Hi, > I have a question about the processivity of MG-RAST. Upon looking at > > the data, I noticed that the metabolic maps were not constructed and > hence there is no visual tool for this part of the analysis. Is > there > a way to have MG-RAST continue analysis of the data? > > The second question is about the download page. I had to manually > click > on each metabolic category to download the reads' names with the > phylogenetic affiliations. Is there a way to access this > automatically? > > Thank you in advance for your time. > > The data I am looking at is at > 3961 Najar, Fares 4444024.3 YNP_spermpool_singles 126785134 > > -- > ----------------------------------------------- > Fares Z. Najar, Ph.D. > Research Scientist > Chemistry and Biochemistry > Advanced Center for Genome Technology (ACGT) > Stephenson Research and Technology Center > 101 David L. Boren Blvd. Room 2170 > Norman, OK 73019 > > Phone: 405-325-4912 > Fax: 405-325-7762 > E-mail: fznajar(a)ou.edu -- 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 job (4444724.3)
by Pengfei Song 27 Jan '10

27 Jan '10

Thanks, Mark, I'm looking forward to it. I'll check again on Friday! If it can not be solved anytime sooner though (may god forbidden), can you please update my data to a server? Best, Pengfei On 1/27/2010 5:33 PM, dsouza(a)mcs.anl.gov wrote: > Hi, > > I took a look into this, and the problem is with the data acquisition from the database. We are digging deeper into this and hope to have a solution for you in a few days. Sorry for the delay. > > > > ----- "Pengfei Song" <psong(a)oeb.harvard.edu> wrote: > > >> From: "Pengfei Song" <psong(a)oeb.harvard.edu> >> To: mg-rast(a)mcs.anl.gov >> Cc: dsouza(a)mcs.anl.gov >> Sent: Wednesday, January 27, 2010 9:42:01 AM GMT -06:00 US/Canada Central >> Subject: MG-RAST job (4444724.3) >> >> Hello again! >> >> Happy New Year. >> >> I'm still trying (I've been trying since last December) to download >> the SEED bacteria blast data for my job ID 4444724.3, but I guess >> since the dataset is too big, the webpage kept crashing on me (I've >> tried many times on many days). Do you mind sending me the data via >> Email or giving me some suggestions on how to download this? I need >> the E value to be 1E-2. >> >> Many many thanks!! >> Pengfei Song, Ph.D >> Harvard University >> > >

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Re: [mg-rast] MG-RAST job (4444724.3)
by dsouza＠mcs.anl.gov 27 Jan '10

27 Jan '10

Hi, I took a look into this, and the problem is with the data acquisition from the database. We are digging deeper into this and hope to have a solution for you in a few days. Sorry for the delay. ----- "Pengfei Song" <psong(a)oeb.harvard.edu> wrote: > From: "Pengfei Song" <psong(a)oeb.harvard.edu> > To: mg-rast(a)mcs.anl.gov > Cc: dsouza(a)mcs.anl.gov > Sent: Wednesday, January 27, 2010 9:42:01 AM GMT -06:00 US/Canada Central > Subject: MG-RAST job (4444724.3) > > Hello again! > > Happy New Year. > > I'm still trying (I've been trying since last December) to download > the SEED bacteria blast data for my job ID 4444724.3, but I guess > since the dataset is too big, the webpage kept crashing on me (I've > tried many times on many days). Do you mind sending me the data via > Email or giving me some suggestions on how to download this? I need > the E value to be 1E-2. > > Many many thanks!! > Pengfei Song, Ph.D > Harvard University -- 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] question regarding job 6058
by dsouza＠mcs.anl.gov 27 Jan '10

27 Jan '10

Hi, The job has been queued for similarity computation. We have over 20 Gbp of sequence data in the queue right now, and our processing times have been over 4 weeks. However, we are in the process of bringing additional compute resources online which will cut down this time. ----- "Jia Liu" <jliu(a)jcvi.org> wrote: > From: "Jia Liu" <jliu(a)jcvi.org> > To: mg-rast(a)mcs.anl.gov > Sent: Wednesday, January 27, 2010 4:04:08 PM GMT -06:00 US/Canada Central > Subject: [mg-rast] question regarding job 6058 > > Hello, Dear Researchers, > > > > I submitted 1 metagenomics annotation job since last Friday. It seems > still running, but not making much progress for the past several days. > > http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=6058 > > > > I wonder whether there is anything wrong with my job or it is > completely normal? I wonder how long normally it will take to run the > annotation pipeline for 1 million 454 reads? > > > > Thank you for your help. I am looking forward to your response. > > > > Best Regards, > > > > Jia Liu, Ph. D., > > Senior Bioinformatics Analysis > > J Craig Venter Institute > > 9704 Medical Center Dr > > Rockville, MD 20850 -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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question regarding job 6058
by Liu, Jia 27 Jan '10

27 Jan '10

Hello, Dear Researchers, I submitted 1 metagenomics annotation job since last Friday. It seems still running, but not making much progress for the past several days. http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=6058 I wonder whether there is anything wrong with my job or it is completely normal? I wonder how long normally it will take to run the annotation pipeline for 1 million 454 reads? Thank you for your help. I am looking forward to your response. Best Regards, Jia Liu, Ph. D., Senior Bioinformatics Analysis J Craig Venter Institute 9704 Medical Center Dr Rockville, MD 20850

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MG-RAST question
by Fares Z. Najar, Ph.D. 27 Jan '10

27 Jan '10

Hi, I have a question about the processivity of MG-RAST. Upon looking at the data, I noticed that the metabolic maps were not constructed and hence there is no visual tool for this part of the analysis. Is there a way to have MG-RAST continue analysis of the data? The second question is about the download page. I had to manually click on each metabolic category to download the reads' names with the phylogenetic affiliations. Is there a way to access this automatically? Thank you in advance for your time. The data I am looking at is at 3961 Najar, Fares 4444024.3 YNP_spermpool_singles 126785134 -- ----------------------------------------------- Fares Z. Najar, Ph.D. Research Scientist Chemistry and Biochemistry Advanced Center for Genome Technology (ACGT) Stephenson Research and Technology Center 101 David L. Boren Blvd. Room 2170 Norman, OK 73019 Phone: 405-325-4912 Fax: 405-325-7762 E-mail: fznajar(a)ou.edu

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MG-RAST job (4444724.3)
by Pengfei Song 27 Jan '10

27 Jan '10

Hello again! Happy New Year. I'm still trying (I've been trying since last December) to download the SEED bacteria blast data for my job ID 4444724.3, but I guess since the dataset is too big, the webpage kept crashing on me (I've tried many times on many days). Do you mind sending me the data via Email or giving me some suggestions on how to download this? I need the E value to be 1E-2. Many many thanks!! Pengfei Song, Ph.D Harvard University

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Re: [mg-rast] mg-rast KEGG question
by Folker Meyer 27 Jan '10

27 Jan '10

Antonia, I was under the assumption it was working again. PLease send details of what is not working for which data set. Best, FOlker On Jan 27, 2010, at 6:21 AM, Antonia Mayer wrote: > Hello! > > Do you have a sense of how long it might take until the KEGG-mapping works again? > > Thank you, > Antonia > > > On 04/01/2010 22:46, Folker Meyer wrote: >> We are looking into this. >> >> Folker > >> On Jan 4, 2010, at 9:47 AM, Antonia Mayer <antonia.mayer(a)unil.ch> wrote: >> >>> Folker, hi - >>> Thanks a lot for your last response. >>> >>> One of the samples I have uploaded has completed (job #5512) or nearly >>> so ("Exportable data creation has not yet started" remains.) but KEGG >>> map results are 0. Is there anything I have to do to allow mapping >>> onto KEGG? >>> >>> All the best and a good new year to you, >>> Antonia > > >

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Re: [mg-rast] mg-rast KEGG question
by Antonia Mayer 27 Jan '10

27 Jan '10

Hello! Do you have a sense of how long it might take until the KEGG-mapping works again? Thank you, Antonia On 04/01/2010 22:46, Folker Meyer wrote: > We are looking into this. > > Folker > On Jan 4, 2010, at 9:47 AM, Antonia Mayer <antonia.mayer(a)unil.ch> wrote: > >> Folker, hi - >>Thanks a lot for your last response. >> >> One of the samples I have uploaded has completed (job #5512) or nearly >> so ("Exportable data creation has not yet started" remains.) but KEGG >> map results are 0. Is there anything I have to do to allow mapping >> onto KEGG? >> >> All the best and a good new year to you, >> Antonia

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Your MG-RAST jobs (6102, 6103, 6104, 6105)
by dsouza＠mcs.anl.gov 26 Jan '10

26 Jan '10

Hi, The jobs you submitted to MG-RAST have failed at the upload stage, please resubmit them to the MG-RAST server, making sure that you reach the last page of the submission process with the job number listed on it, if you encounter an error message page please let us know. -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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