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

Re: [mg-rast] RAST and mg-rast. .
by Mark D'Souza 30 Nov '09

30 Nov '09

Do you have an estimate of the size (base pairs) of the sequence data? Mark ----- "Caroline Obert" <Caroline.Obert(a)STJUDE.ORG> wrote: > From: "Caroline Obert" <Caroline.Obert(a)STJUDE.ORG> > To: "dsouza(a)mcs.anl.gov" <dsouza(a)mcs.anl.gov> > Cc: mg-rast(a)mcs.anl.gov > Sent: Monday, November 30, 2009 3:35:56 PM GMT -06:00 US/Canada Central > Subject: RE: [mg-rast] RAST and mg-rast. . > > Our original data is from a next gen sequencer. The read lengths are > short (126 bp long) but there are lots of them. Can the server handle > that amount of data? > > Caroline A Obert, PhD. > Genome Sequencing Scientist I > Hartwell Center for Biotechnology and Bioinformatics > St. Jude Children's Research Hospital > D1052G > 262 Danny Thomas Place > Memphis, TN 38105-3678 > > Phone: 901-595-3217 > Email: caroline.obert(a)stjude.org > > -----Original Message----- > From: dsouza(a)mcs.anl.gov [mailto:[email protected]] > Sent: Monday, November 30, 2009 2:54 PM > To: Obert, Caroline > Cc: mg-rast(a)mcs.anl.gov > Subject: Re: [mg-rast] RAST and mg-rast. . > > Hi, > > MG-RAST is designed to analyze metagenomes consisting of short reads > of a few hundred base pairs in length while RAST is designed for > single assembled genomes. MG-RAST will not do a meaningful analysis > for any sequence file which RAST was able to analyze successfully. > Furthermore, because of the different computational tools used by the > two, the MG-RAST processing time would be very long. If you do have a > metagenome made up of short reads then you should submit it to MG-RAST > only, and not to RAST. > > > ----- "Caroline Obert" <Caroline.Obert(a)STJUDE.ORG> wrote: > > > From: "Caroline Obert" <Caroline.Obert(a)STJUDE.ORG> > > To: "mg-rast(a)mcs.anl.gov" <mg-rast(a)mcs.anl.gov> > > Sent: Monday, November 30, 2009 2:15:28 PM GMT -06:00 US/Canada > Central > > Subject: [mg-rast] RAST and mg-rast > > > > Can jobs submitted and analyzed through RAST be uploaded into > MG-RAST? > > > > Yours, > > > > Caroline > > > > > > > > Caroline A Obert, PhD. > > > > Genome Sequencing Scientist I > > > > Hartwell Center for Biotechnology and Bioinformatics > > > > St. Jude Children's Research Hospital > > > > D1052G > > > > 262 Danny Thomas Place > > > > Memphis, TN 38105-3678 > > > > > > > > Phone: 901-595-3217 > > > > Email: caroline.obert(a)stjude.org > > > > > > > > Email Disclaimer: www.stjude.org/emaildisclaimer > > -- > 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] RAST and mg-rast. .
by Obert, Caroline 30 Nov '09

30 Nov '09

Our original data is from a next gen sequencer. The read lengths are short (126 bp long) but there are lots of them. Can the server handle that amount of data? Caroline A Obert, PhD. Genome Sequencing Scientist I Hartwell Center for Biotechnology and Bioinformatics St. Jude Children's Research Hospital D1052G 262 Danny Thomas Place Memphis, TN 38105-3678 Phone: 901-595-3217 Email: caroline.obert(a)stjude.org -----Original Message----- From: dsouza(a)mcs.anl.gov [mailto:[email protected]] Sent: Monday, November 30, 2009 2:54 PM To: Obert, Caroline Cc: mg-rast(a)mcs.anl.gov Subject: Re: [mg-rast] RAST and mg-rast. . Hi, MG-RAST is designed to analyze metagenomes consisting of short reads of a few hundred base pairs in length while RAST is designed for single assembled genomes. MG-RAST will not do a meaningful analysis for any sequence file which RAST was able to analyze successfully. Furthermore, because of the different computational tools used by the two, the MG-RAST processing time would be very long. If you do have a metagenome made up of short reads then you should submit it to MG-RAST only, and not to RAST. ----- "Caroline Obert" <Caroline.Obert(a)STJUDE.ORG> wrote: > From: "Caroline Obert" <Caroline.Obert(a)STJUDE.ORG> > To: "mg-rast(a)mcs.anl.gov" <mg-rast(a)mcs.anl.gov> > Sent: Monday, November 30, 2009 2:15:28 PM GMT -06:00 US/Canada Central > Subject: [mg-rast] RAST and mg-rast > > Can jobs submitted and analyzed through RAST be uploaded into MG-RAST? > > Yours, > > Caroline > > > > Caroline A Obert, PhD. > > Genome Sequencing Scientist I > > Hartwell Center for Biotechnology and Bioinformatics > > St. Jude Children's Research Hospital > > D1052G > > 262 Danny Thomas Place > > Memphis, TN 38105-3678 > > > > Phone: 901-595-3217 > > Email: caroline.obert(a)stjude.org > > > > Email Disclaimer: www.stjude.org/emaildisclaimer -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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Your MG-RAST jobs (5547, 5549)
by dsouza＠mcs.anl.gov 30 Nov '09

30 Nov '09

Hi, The sequence files for the two jobs 5547 and 5549 are identical. This is possibly caused by the upload process not functioning correctly, I am placing 5549 on hold and will delete it if I do not hear from you. You do not need to take any action, 5547 will proceed normally. -- 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] RAST and mg-rast
by dsouza＠mcs.anl.gov 30 Nov '09

30 Nov '09

Hi, MG-RAST is designed to analyze metagenomes consisting of short reads of a few hundred base pairs in length while RAST is designed for single assembled genomes. MG-RAST will not do a meaningful analysis for any sequence file which RAST was able to analyze successfully. Furthermore, because of the different computational tools used by the two, the MG-RAST processing time would be very long. If you do have a metagenome made up of short reads then you should submit it to MG-RAST only, and not to RAST. ----- "Caroline Obert" <Caroline.Obert(a)STJUDE.ORG> wrote: > From: "Caroline Obert" <Caroline.Obert(a)STJUDE.ORG> > To: "mg-rast(a)mcs.anl.gov" <mg-rast(a)mcs.anl.gov> > Sent: Monday, November 30, 2009 2:15:28 PM GMT -06:00 US/Canada Central > Subject: [mg-rast] RAST and mg-rast > > Can jobs submitted and analyzed through RAST be uploaded into MG-RAST? > > Yours, > > Caroline > > > > Caroline A Obert, PhD. > > Genome Sequencing Scientist I > > Hartwell Center for Biotechnology and Bioinformatics > > St. Jude Children's Research Hospital > > D1052G > > 262 Danny Thomas Place > > Memphis, TN 38105-3678 > > > > Phone: 901-595-3217 > > Email: caroline.obert(a)stjude.org > > > > Email Disclaimer: www.stjude.org/emaildisclaimer -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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RAST and mg-rast
by Obert, Caroline 30 Nov '09

30 Nov '09

Can jobs submitted and analyzed through RAST be uploaded into MG-RAST? Yours, Caroline Caroline A Obert, PhD. Genome Sequencing Scientist I Hartwell Center for Biotechnology and Bioinformatics St. Jude Children's Research Hospital D1052G 262 Danny Thomas Place Memphis, TN 38105-3678 Phone: 901-595-3217 Email: caroline.obert(a)stjude.org ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer

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Re: [mg-rast] large file upload
by Folker Meyer 30 Nov '09

30 Nov '09

Hi Antonia, I think 300MB is a very moderate size for a data set. The current large file sets are >10GB. There should not be a problem with the upload etc. Just try and send any questions you might have. Best, Folker On Nov 30, 2009, at 8:58 AM, Antonia Mayer wrote: > Dear mg-RAST support - > > I would like to upload three environmental genome samples, fasta and qual files for each, onto the mg-RAST server. Together, three compressed tarballs in another one, they add up to about 300MB. > > Is it possible to analyse this data with you? > > If yes, do you have suggestions as to the upload? > > Thank you, > Antonia Mayer > (mg-RAST account name mayera)

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large file upload
by Antonia Mayer 30 Nov '09

30 Nov '09

Dear mg-RAST support - I would like to upload three environmental genome samples, fasta and qual files for each, onto the mg-RAST server. Together, three compressed tarballs in another one, they add up to about 300MB. Is it possible to analyse this data with you? If yes, do you have suggestions as to the upload? Thank you, Antonia Mayer (mg-RAST account name mayera)

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Re: [mg-rast] meta server
by Robert Olson 27 Nov '09

27 Nov '09

we had some memory issues on bio-big which is where that lives; should be better now ----- "Mark D'Souza" <dsouza(a)mcs.anl.gov> wrote: > Hi, > > Is the meta server down? I am not getting any response to the meta > command. > > Mark

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trouble with the MG-RAST server annotation progress?
by Qichao＠OU 26 Nov '09

26 Nov '09

Hello, I have some trouble with the MG-RAST server annotation progress: I uploaded some files and the MG-RAST began to run the datasets, but it stopped at the 3rd step for almost 3 days, without any indication for the next step (Similarity final check has not yet started). Is there any thing I should do to start the process? Thanks and best! Qichao Tu, Graduate Student Institute for Environmental Genomics University of Oklahoma 101 David L. Boren Blvd. Norman, OK 73019 phone: 405-325-3052 email: qichao(a)ou.edu

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meta server
by Mark D'Souza 25 Nov '09

25 Nov '09

Hi, Is the meta server down? I am not getting any response to the meta command. Mark

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