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

Re: [mg-rast] Your MG-RAST jobs (9927, 9929, 9930, 9933)
by Mark D'Souza 30 Jul '10

30 Jul '10

Hi, Thanks, I deleted the two jobs. 9740 and 9725 have completed the similarity computation, they should be done early next week. Regards, Mark ----- "Gail R" <gailro(a)gmail.com> wrote: > From: "Gail R" <gailro(a)gmail.com> > To: dsouza(a)mcs.anl.gov > Sent: Friday, July 30, 2010 3:41:47 PM GMT -06:00 US/Canada Central > Subject: Re: Your MG-RAST jobs (9927, 9929, 9930, 9933) > > Actually, you can stop 9933 and 9927. > > Do you know why 9740 and 9725 have been running for over a week? > > Thanks, > Gail > > On Fri, Jul 30, 2010 at 12:36 PM, <dsouza(a)mcs.anl.gov> wrote: > > Hi, > > > > The jobs you submitted to MG-RAST (9927, 9929, 9930, 9933) failed as > the sequence files contain mixed end of line characters and could not > be read correctly by the system. > > > > I modified the file for 9927 and restarted the job and it is > proceeding normally. I will delete 9929 and 9930 as they are identical > to 9927. > > > > Please let me know if you wish 9933 to be restarted, otherwise it > too will be 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 (9899, 9900, 9908, 9910, 9912, 9914, 9921, 9922)
by dsouza＠mcs.anl.gov 30 Jul '10

30 Jul '10

Hi, The jobs you submitted to MG-RAST have failed as the sequence files do not conform to the FASTA format standard (http://en.wikipedia.org/wiki/Fasta_format) For example, in the sequence file for 9989 the sequence for contig00710 runs into the sequence identifier line for contig02298 without a newline character, and this occurs for multiple sequences. Please edit your files to fix this and resubmit them to the MG-RAST server. -- 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 (9927, 9929, 9930, 9933)
by dsouza＠mcs.anl.gov 30 Jul '10

30 Jul '10

Hi, The jobs you submitted to MG-RAST (9927, 9929, 9930, 9933) failed as the sequence files contain mixed end of line characters and could not be read correctly by the system. I modified the file for 9927 and restarted the job and it is proceeding normally. I will delete 9929 and 9930 as they are identical to 9927. Please let me know if you wish 9933 to be restarted, otherwise it too will be 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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Re: [mg-rast] MG-RAST job ID 9583
by dsouza＠mcs.anl.gov 30 Jul '10

30 Jul '10

Hi, Sorry for the delay, the job is running and the similarity computation is completed. There are some issues with the site which have to be dealt with before the results can be loaded into the database. I expect this will take a day or two. Regards, Mark ----- "Patricia Ayoubi" <patricia.ayoubi(a)gmail.com> wrote: > From: "Patricia Ayoubi" <patricia.ayoubi(a)gmail.com> > To: dsouza(a)mcs.anl.gov, mg-rast(a)mcs.anl.gov > Cc: "babu fathepure" <babu.fathepure(a)okstate.edu> > Sent: Friday, July 30, 2010 10:15:46 AM GMT -06:00 US/Canada Central > Subject: MG-RAST job ID 9583 > > On July 15th I submitted a batch of sequences for analysis. It has > been uploaded but appears be stalled for some reason. Can you please > check and let me know if it is running or not. The MG-RAST job ID is > 9583. Thank you. > > > > Best Regards, > > Trish > ___________________ > Patricia Ayoubi, Ph.D. > Associate Professor and Academic Advisor > 360A Noble Research Center > Department of Biochemistry and Molecular Biology > Oklahoma State University > Stillwater, OK 74078 > > Phone: 405-744-6199 > Fax: 405-744-7799 > email: patricia.ayoubi(a)okstate.edu > > "Do all you can with what you have, in the time you have, in the place > you are." ~Nkosi Johnson

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MG-RAST job ID 9583
by Patricia Ayoubi 30 Jul '10

30 Jul '10

On July 15th I submitted a batch of sequences for analysis. It has been uploaded but appears be stalled for some reason. Can you please check and let me know if it is running or not. The MG-RAST job ID is 9583. Thank you. Best Regards, Trish ___________________ Patricia Ayoubi, Ph.D. Associate Professor and Academic Advisor 360A Noble Research Center Department of Biochemistry and Molecular Biology Oklahoma State University Stillwater, OK 74078 Phone: 405-744-6199 Fax: 405-744-7799 email: patricia.ayoubi(a)okstate.edu "Do all you can with what you have, in the time you have, in the place you are." ~Nkosi Johnson

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Re: [mg-rast] Your genome 4445126.3 is now publicly available.
by Mark D'Souza 29 Jul '10

29 Jul '10

Hi, Sorry about that, this has now been fixed. ----- "Thibault Varin" <Thibault.Varin(a)genome.ulaval.ca> wrote: > From: "Thibault Varin" <Thibault.Varin(a)genome.ulaval.ca> > To: mg-rast(a)mcs.anl.gov > Sent: Thursday, July 29, 2010 9:37:40 AM GMT -06:00 US/Canada Central > Subject: Re: [mg-rast] Your genome 4445126.3 is now publicly available. > > Dear MG-Rast administrator, > > I tried to make two of my metagenomes (4445126.3 and 4445129.3) public > but it didn't work. > Although, i received two emails of confirmation (see message below) i > can't find them in the public metagenomes list. > Please, could you help me with this issue ? > > Many thanks, > Thibault. > > -----Original Message----- > From: mg-rast(a)mcs.anl.gov [ mailto:[email protected] ] > Sent: Thu 29/07/2010 10:03 > To: Thibault Varin > Subject: Your genome 4445126.3 is now publicly available. > > Dear Thibault Varin, your genome is now public. You can link to the > genome using > http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4445126.3 > . -- 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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Re: [mg-rast] BlackSoudMineMic20050331 (4440282.3)
by dsouza＠mcs.anl.gov 29 Jul '10

29 Jul '10

Hi, This has now been fixed and the metabolic profile works normally. Both the Black and Red jobs were run through an early version of MG-RAST and the analysis may be out of date, if you prefer a more up to date analysis, please feel free to run the jobs through MG-RAST again, we can make the new jobs public under the same project as the old ones if you wish. Regards, Mark ----- "Mark D'Souza" <dsouza(a)mcs.anl.gov> wrote: > From: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > To: "Isabelle Navarro" <orravanisa(a)gmail.com> > Cc: "MG-RAST" <mg-rast(a)mcs.anl.gov> > Sent: Wednesday, July 28, 2010 4:55:26 PM GMT -06:00 US/Canada Central > Subject: Re: [mg-rast] BlackSoudMineMic20050331 (4440282.3) > > Hi, > > Yes, I see what you mean and I have located the source of the problem. > This was done before I was working on MG-RAST so I want to check a few > things before I make any changes, I will get back to you as soon as > things are working correctly. > > Regards, > Mark > > ----- "Isabelle Navarro" <orravanisa(a)gmail.com> wrote: > > > From: "Isabelle Navarro" <orravanisa(a)gmail.com> > > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > > Sent: Wednesday, July 28, 2010 7:53:56 AM GMT -06:00 US/Canada > Central > > Subject: Re: [mg-rast] BlackSoudMineMic20050331 (4440282.3) > > > > Hello, > > > > Yes it's a public job. The job Red Soudan Mine is OK. This work was > > published and the annotation was made with MG-RAST. > > > > > > > > > > Le 28 juil. 2010 à 14:46, Mark D'Souza a écrit : > > > > > Hi, > > > > > > Can you tell me whether the page was accessible at all? This job > has > > no hits against the SEED database, I was able to access the page > but > > the pie chart is not displayed as there are zero SEED hits. > > > > > > > > > > > > ----- "Isabelle Navarro" <orravanisa(a)gmail.com> wrote: > > > > > >> From: "Isabelle Navarro" <orravanisa(a)gmail.com> > > >> To: mg-rast(a)mcs.anl.gov > > >> Sent: Wednesday, July 28, 2010 3:16:43 AM GMT -06:00 US/Canada > > Central > > >> Subject: [mg-rast] BlackSoudMineMic20050331 (4440282.3) > > >> > > >> Hello, > > >> > > >> > > >> It was impossible to access to metabolic profile for the Black > > Soudan > > >> Mine metagenome > > >> > > >> > > >> sincerely > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> Elisabeth Navarro > > >> IRD-LSTM > > >> Environmental Microbial Genomics Group > > >> Laboratoire AMPERE Ecole Centrale de Lyon > > >> 36, avenue Guy de Collongue > > >> 69134 Ecully cedex France > > >> Tél : +33 (0) 4 72 18 62 43 > > >> Fax : +33 (0) 4 78 43 37 17 > > >> > > >> elisabeth.navarro(a)ec-lyon.fr > > >> Elisabeth.Navarro(a)ird.fr > > >> www.genomenviron.org > > > > > > -- > > > 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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Question
by aymé spor 29 Jul '10

29 Jul '10

Dear colleague, I've recently uploaded some metagenomics datasets onto the MG-rast server in order to annotate my sequences. Apparently, the annotation process is stuck at step 3 (over 7) since several days. Could you please tell me if that's normal or if there is something wrong with the sequences I have submitted ? Thank you very much for your help, Best wishes, Aymé -- Aymé Spor, PhD. Department of Microbiology 257 Wing Hall Cornell University Ithaca, NY 14853 email: as2354(a)cornell.edu

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Re: [mg-rast] metabolic profile for BlackSoudMineMic20050331 (4440282.3) not working correctly
by dsouza＠mcs.anl.gov 29 Jul '10

29 Jul '10

Thanks all, I will let the user know. It looks like there was an attempt to update the sims and change the databases at some point which was not pushed to completion so the database table contains the old sims and the meta.xml file had wrong information. Since this is a public (and published) metagenome I corrected the meta.xml file and things work normally now. Mark ----- "Rob Edwards" <redwards(a)mcs.anl.gov> wrote: > From: "Rob Edwards" <redwards(a)mcs.anl.gov> > To: "Robert Olson" <olson(a)mcs.anl.gov> > Cc: dsouza(a)mcs.anl.gov > Sent: Thursday, July 29, 2010 9:31:58 AM GMT -06:00 US/Canada Central > Subject: Re: metabolic profile for BlackSoudMineMic20050331 (4440282.3) not working correctly > > No idea why its not in sync, go ahead and change it. > > But its a pretty old sample, you should probably tell the user to > rerun them through the system again and make them public. Any results > they get will likely be suspicious anyway. > > > Rob > > On Wed, Jul 28, 2010 at 7:20 PM, Robert Olson <olson(a)mcs.anl.gov> > wrote: > > I have no idea; I don't think I had anything to do with the > "database upgrade" stuff. > > --bob > > > > ----- dsouza(a)mcs.anl.gov wrote: > > > >> Hi, > >> > >> A user pointed out that the metabolic profile for the job > >> BlackSoudMineMic20050331 (14, 4440282.3) is not displaying > subsystem > >> counts, though RedSoudMineMic20050331 (13, 4440281.3) is OK. I > traced > >> this to the meta.xml file which has the wrong version for the SEED > >> database which results in the database table containing the blast > hits > >> not being identified correctly. > >> > >> This job has the SEED database information in 'sims.database_list' > set > >> as: > >> { abbr: u, dir: sims.seed, fasta: > >> /vol/mg-rast-prod/Data/upgrades/OLD_to_018c/nr, name: nr, > >> peg_synonyms: /vol/mg-rast-test/Data/db/seed/018c/peg.synonyms, > type: > >> protein, uspib: 11337 } ], from: OLD, inhibit_sims: 1, name: > >> SEED_Upgrade, size_of_new: 945932029, size_of_old: 1449319901, to: > >> 018c, version: OLD-to-018c }, ... > >> > >> which is different from jobs around it, 13 has: > >> { files: [ { abbr: s, dir: sims.seed, fasta: /vol/48-hour/Data/nr, > >> name: nr, peg_synonyms: /vol/48-hour/Data/peg.synonyms, type: > protein, > >> uspib: 11308 } ], name: SEED, version: OLD } > >> > >> The table in postgres looks OK (though I have no idea what the > >> subsystem counts are like) and I believe changing the version from > >> 'OLD-to-018c' to 'OLD' will fix things. > >> > >> I just wanted to know if there was any reason for the difference > >> before I make the change. > >> > >> Thanks, > >> Mark > >> > >> ----- "Mark D'Souza" <dsouza(a)mcs.anl.gov> wrote: > >> > >> > From: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > >> > To: "Isabelle Navarro" <orravanisa(a)gmail.com> > >> > Cc: "MG-RAST" <mg-rast(a)mcs.anl.gov> > >> > Sent: Wednesday, July 28, 2010 4:55:26 PM GMT -06:00 US/Canada > >> Central > >> > Subject: Re: [mg-rast] BlackSoudMineMic20050331 (4440282.3) > >> > > >> > Hi, > >> > > >> > Yes, I see what you mean and I have located the source of the > >> problem. > >> > This was done before I was working on MG-RAST so I want to check > a > >> few > >> > things before I make any changes, I will get back to you as soon > as > >> > things are working correctly. > >> > > >> > Regards, > >> > Mark > >> > > >> > ----- "Isabelle Navarro" <orravanisa(a)gmail.com> wrote: > >> > > >> > > From: "Isabelle Navarro" <orravanisa(a)gmail.com> > >> > > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > >> > > Sent: Wednesday, July 28, 2010 7:53:56 AM GMT -06:00 US/Canada > >> > Central > >> > > Subject: Re: [mg-rast] BlackSoudMineMic20050331 (4440282.3) > >> > > > >> > > Hello, > >> > > > >> > > Yes it's a public job. The job Red Soudan Mine is OK. This > work > >> was > >> > > published and the annotation was made with MG-RAST. > >> > > > >> > > > >> > > > >> > > > >> > > Le 28 juil. 2010 à 14:46, Mark D'Souza a écrit : > >> > > > >> > > > Hi, > >> > > > > >> > > > Can you tell me whether the page was accessible at all? This > >> job > >> > has > >> > > no hits against the SEED database, I was able to access the > page > >> > but > >> > > the pie chart is not displayed as there are zero SEED hits. > >> > > > > >> > > > > >> > > > > >> > > > ----- "Isabelle Navarro" <orravanisa(a)gmail.com> wrote: > >> > > > > >> > > >> From: "Isabelle Navarro" <orravanisa(a)gmail.com> > >> > > >> To: mg-rast(a)mcs.anl.gov > >> > > >> Sent: Wednesday, July 28, 2010 3:16:43 AM GMT -06:00 > US/Canada > >> > > Central > >> > > >> Subject: [mg-rast] BlackSoudMineMic20050331 (4440282.3) > >> > > >> > >> > > >> Hello, > >> > > >> > >> > > >> > >> > > >> It was impossible to access to metabolic profile for the > Black > >> > > Soudan > >> > > >> Mine metagenome > >> > > >> > >> > > >> > >> > > >> sincerely > >> > > >> > >> > > >> > >> > > >> > >> > > >> > >> > > >> > >> > > >> > >> > > >> > >> > > >> > >> > > >> > >> > > >> > >> > > >> > >> > > >> Elisabeth Navarro > >> > > >> IRD-LSTM > >> > > >> Environmental Microbial Genomics Group > >> > > >> Laboratoire AMPERE Ecole Centrale de Lyon > >> > > >> 36, avenue Guy de Collongue > >> > > >> 69134 Ecully cedex France > >> > > >> Tél : +33 (0) 4 72 18 62 43 > >> > > >> Fax : +33 (0) 4 78 43 37 17 > >> > > >> > >> > > >> elisabeth.navarro(a)ec-lyon.fr > >> > > >> Elisabeth.Navarro(a)ird.fr > >> > > >> www.genomenviron.org > >> > > > > >> > > > -- > >> > > > 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 analysis question
by Kathleen Barry 29 Jul '10

29 Jul '10

Dear MG-RAST specialist, When I use MG-RAST to identify phylogeny using SEED, I am confused about where these data come from. Does the SEED use a non-redundant database, or does it check against all known microbial and metagenomic sequences? Best, Kathleen -- ------------------------------------------------- Kathleen A. Barry Graduate Research and Teaching Assistant Ph.D. Candidate--Companion Animal Nutrition M.S. Comparative Animal Nutrition B.S. Animal Sciences email: kbarry1(a)illinois.edu phone: (773)817-4362 --------------------------------------------------

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