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

Fwd: [theseed.org Info] CLOUD
by Robert Olson 07 Apr '11

07 Apr '11

----- Forwarded Message ----- From: "Renee Smith" <renee.smith(a)flinders.edu.au> To: info(a)theseed.org Sent: Thursday, April 7, 2011 8:40:49 PM Subject: Re: [theseed.org Info] CLOUD Hi, I have been looking at my samples on the new version of MG-RAST and i have notcied that sequences that hit circoviridae in version 2.0 are now hitting unclassified viruses. Is there a reason for this? Thanks, Renee _______________________________________________ Info mailing list Info(a)lists.theseed.org https://lists.theseed.org/mailman/listinfo/info

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Re: [mg-rast] MGRAST - new data available
by Jared Wilkening 07 Apr '11

07 Apr '11

Sorry about that there seems to be a typo in that email. Here is the correct link: http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeOverview&metage… Thanks for bringing that to our attention. Cheers, Jared Wilkening - for the MG-RAST development team On Thu, Apr 7, 2011 at 6:18 PM, Younghoon Gim <khunny7(a)gmail.com> wrote: > Thank you, yet the link does not work, thank you. > > On Thu, Apr 7, 2011 at 5:12 PM, <mg-rast(a)mcs.anl.gov> wrote: > >> Dear YoungHoon Gim, >> >> you have been granted access to Diamond_fork_biofilm (4460470.3) by Joshua >> Udall on our web service MGRAST. >> >> To directly access the new data, please follow this link: >> >> http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeIverview&metage… >> . >> >> >> -- >> >> This email was automatically generated by the MGRAST web service. Do not >> reply. >> > > > > -- > * > * > *YoungHoon Gim* > >

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Re: [mg-rast] MGRAST - new data available
by Younghoon Gim 07 Apr '11

07 Apr '11

Thank you, yet the link does not work, thank you. On Thu, Apr 7, 2011 at 5:12 PM, <mg-rast(a)mcs.anl.gov> wrote: > Dear YoungHoon Gim, > > you have been granted access to Diamond_fork_biofilm (4460470.3) by Joshua > Udall on our web service MGRAST. > > To directly access the new data, please follow this link: > > http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeIverview&metage… > . > > > -- > > This email was automatically generated by the MGRAST web service. Do not > reply. > -- * * *YoungHoon Gim*

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Re: [mg-rast] Use MG-RAST for taxonomy filter?
by Folker Meyer 07 Apr '11

07 Apr '11

Dear Phillipe, we can provide the functionality you need with MG-RAST, it will require manual effort on our part as it is not automated. However we are happy to help in the context of a collaboration. Best, Folker On Apr 7, 2011, at 10:31 AM, Philippe.gayral02(a)univ-montp2.fr wrote: > Dear colleagues, > I work on a population genomics project based on non-model species transcriptomic data generated from 454 and illumina data (http://162.38.181.25/PopPhyl/) > I would like to use your programm for a cleaning purpose and would like to have your advise before that. > > My goal would be to remove contaminant/parasitic/symbiotic bacterial, fungal and viral sequences from my dataset. Each of our assembled transcriptome came from animals tissues (oyster, hare, worm...), no environmental samples. > > - Do MG-RAST is adapted for that, i.e. can we remove the 'unwanted' sequences based on taxonomy status? > - Otherwise, are you aware of any programm that would do this filter? > > Thank you very much for your help. > Philippe Gayral. > > > > -- > Philippe Gayral > Institut des Sciences de l'Evolution > Universite Montpellier 2 - CC 064 > Place E. bataillon > 34095 Montpellier cedex 5 > FRANCE > Tel: (+33) 4 67 14 32 61 > FAX: (+33) 4 67 14 36 10 > Email: Philippe.gayral02(a)univ-montp2.fr > PopPhyl Project website: http://162.38.181.25/PopPhyl/index.php?section=home > Personal website: https://sites.google.com/site/pgayral/

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Re: [mg-rast] Reporting about the error!
by Mark D'Souza 07 Apr '11

07 Apr '11

Hi, Can you give us some more details about the error you obtained? I took a look at the DF-PD1 data set and did find an error in the analysis. -- Thanks, 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 ----- Original Message ----- > From: "h0992134" <h0992134(a)hku.hk> > To: dsouza(a)mcs.anl.gov > Sent: Saturday, April 2, 2011 6:15:23 AM > Subject: Reporting about the error! > Dear MG-RAST, > > I upload a very small data set (DF-PD1) to MG-Rast V3 recently. But I > found the error. So may I know what is the cause of error and how can > i solve it? > > Best regards, > > Hein Min Tun (Dr.) > BVS, MSc > PhD candidate > HKU > MG-RAST user name- harryhku

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Use MG-RAST for taxonomy filter?
by Philippe.gayral02＠univ-montp2.fr 07 Apr '11

07 Apr '11

Dear colleagues, I work on a population genomics project based on non-model species transcriptomic data generated from 454 and illumina data (http://162.38.181.25/PopPhyl/) I would like to use your programm for a cleaning purpose and would like to have your advise before that. My goal would be to remove contaminant/parasitic/symbiotic bacterial, fungal and viral sequences from my dataset. Each of our assembled transcriptome came from animals tissues (oyster, hare, worm...), no environmental samples. - Do MG-RAST is adapted for that, i.e. can we remove the 'unwanted' sequences based on taxonomy status? - Otherwise, are you aware of any programm that would do this filter? Thank you very much for your help. Philippe Gayral. -- Philippe Gayral Institut des Sciences de l'Evolution Universite Montpellier 2 - CC 064 Place E. bataillon 34095 Montpellier cedex 5 FRANCE Tel: (+33) 4 67 14 32 61 FAX: (+33) 4 67 14 36 10 Email: Philippe.gayral02(a)univ-montp2.fr PopPhyl Project website: http://162.38.181.25/PopPhyl/index.php?section=home Personal website: https://sites.google.com/site/pgayral/

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Re: [mg-rast] Question about barchart and abundances
by Mark D'Souza 07 Apr '11

07 Apr '11

Hi, I was looking at your NREL3 data set and was not able to find the disparity you described. It is possible that this occurred for another data set or I may be looking at the wrong numbers or table. Could you please let us know which data set you found this for and give us an instance where the numbers do not add up. This would make it much simpler for me to figure out what the problem is. -- Thanks, 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 ----- Original Message ----- > From: "Ambarish Nag" <Ambarish.Nag(a)nrel.gov> > To: mg-rast(a)mcs.anl.gov > Sent: Friday, April 1, 2011 2:14:36 PM > Subject: [mg-rast] Question about barchart and abundances > Hi, > I am trying to obtain a level 1 distribution bar chart using the raw > data for the functional classification of a metegenome using > subsystems. When I look at the abundances in the data table (grouped > by clear grouping) for the same metagenome and data selection > parameters, I find that the sum of the abundances in the table differs > from the sum of the number of counts in the data for the raw data bar > chart. This results from the fact that the number of counts for some > level 1 descriptors in the data file for the bar chart is different > from the number of times the level 1 descriptor appears in the > corresponding table. What is the reason behind this disparity? > Thanks > Ambarish

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Re: [mg-rast] Annotated data download?
by Mark D'Souza 07 Apr '11

07 Apr '11

Hi, This is not possible in the current release, but we are working on it and should have something available in a couple of weeks. Thanks for letting us know about this issue. ----- Original Message ----- > From: "Jon Sanders" <jsanders(a)oeb.harvard.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Monday, April 4, 2011 10:31:53 AM > Subject: [mg-rast] Annotated data download? > Hey MG-RAST team, > > > Really excited by V3. I would like to download the read-indexed > relational annotation data that is used to generate the neat bar > charts, functional classification tables, and KEGG pathways, so I can > include them as tables in our lab's local database and use them for > subsequent statistical analysis and reference. Is this possible in the > current release? Or is this the "global data download" that's still > under development? If so, any idea when it might be made available? > > > Much appreciated, > Jon Sanders > PhD Candidate > Girguis Lab, Harvard University > > -- > "If you hold a cat by the tail you learn things you cannot learn any > other way." > --Mark Twain -- 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] uploading 110 metagenomes at once?
by Folker Meyer 07 Apr '11

07 Apr '11

Tanya: we have a set of web services that Rob KNights team has used to submit several thousands. But it requires some coding on your end. Alternatively, we can work out another solution for getting your data in. I wanted to visit Jeff's lab anyway that might be an option or you can just stop by at Argonne and we help creating the upload scripts. Do you have all the metadata already encoded. Best, Folker On Apr 6, 2011, at 7:46 PM, Mark D'Souza wrote: > Hi, > > What is the size of the data sets? > > Uploading as a a single zipped file should be fine, though smaller batches may be easier. > > -- > 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 > > > ----- Original Message ----- >> From: "Tanya Yatsunenko" <yata(a)go.wustl.edu> >> To: "MG- Rast" <mg-rast(a)mcs.anl.gov> >> Cc: "Folker Meyer" <folker.meyer(a)googlemail.com> >> Sent: Wednesday, April 6, 2011 1:37:01 PM >> Subject: [mg-rast] uploading 110 metagenomes at once? >> Hi again, and sorry to bug you so much. >> I'm in a need to annotate 110 metagenomes (soon). Can I zip them in 1 >> file and upload once, instead of uploading 1 at a time? And will mg >> rast be able to handle so many at once? >> thank yoU! >> >> >> Tanya. >> >> >> >> On Wed, Mar 30, 2011 at 12:41 PM, Andreas Wilke < wilke(a)mcs.anl.gov > >> wrote: >> >> >> >> Hi Tanya , >> >> unfortunately we had to change the location of a logfile for our >> database. This required a restart of the database. This does not >> require a re-annotation of your metagenomes. >> >> >> Please let us know if you have still problems to access your >> metagenomes. >> >> >> Regards, >> >> >> Andreas Wilke >> >> >> >> >> >> >> >> >> >> >> >> On Mar 30, 2011, at 11:42 AM, Tanya Yatsunenko wrote: >> >> >> Hi >> >> >> I've used MG RAST long time ago, and still have several metagenomes >> uploaded. However, when I tried to open "DAta Analysis" tab, I got >> this message: Can't locate auto/DBI/ error.al in @INC (@INC contains: >> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_0_2/common/lib >> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_0_2/common/lib/FigKernelPackages >> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_0_2/common/lib/WebApplication >> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_0_2/common/lib/FortyEight >> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_0_2/common/lib/PPO >> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_0_2/common/lib/RAST >> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_0_2/common/lib/MGRAST >> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_0_2/common/lib/SeedViewer >> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_0_2/common/lib/ModelSEED >> /mcs/bio/mg-rast/prod/FIGDisk/dist/dev/common/lib >> /mcs/bio/mg-rast/prod/FIGDisk/dist/dev/common/lib/FigKernelPackages >> /mcs/bio/mg-rast/prod/FIGDisk/config >> /mcs/bio/mg-rast/test/FIGDisk/dist/releases/current/common/lib >> /mcs/bio/mg-rast/test/FIGDisk/dist/releases/current/common/lib/FigKernelPackages >> /mcs/bio/mg-rast/test/FIGDisk/dist/releases/current/common/lib/WebApplication >> /mcs/bio/mg-rast/test/FIGDisk/dist/releases/current/common/lib/FortyEight >> /mcs/bio/mg-rast/test/FIGDisk/dist/releases/current/common/lib/PPO >> /mcs/bio/mg-rast/test/FIGDisk/config >> /soft/packages/perl/5.12.1/lib/site_perl/5.12.1/x86_64-linux-thread-multi >> /soft/packages/perl/5.12.1/lib/site_perl/5.12.1 >> /soft/packages/perl/5.12.1/lib/5.12.1/x86_64-linux-thread-multi >> /soft/packages/perl/5.12.1/lib/5.12.1 .) at >> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_0_2/common/lib/Babel/lib/Babel.pm >> line 29 >> >> >> Does that mean that I have to re-annotate all my metagenomes, i.e. >> submit them as new jobs? >> Thank you >> >> Tanya. >> >> >> >> >> Andreas Wilke >> Argonne National Laboratory >> Mathematics and Computer Science Division >> Bldg. 240 , 4F8 >> 9700 South Cass Avenue >> Argonne, IL 60439 >> (630) 252-3190 (phone) >> >> (630) 252-5986 .(fax)

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Re: [mg-rast] Unable to upload data
by Mark D'Souza 06 Apr '11

06 Apr '11

Hi, Do you see the 'Jumploader' box with the 'Add' button? If you do, try clicking on the Add button to select the file you want to upload. If not, let us know, the browser sometimes gets into a state where it does not display the applet and restarting it may help. Regards, Mark ----- Original Message ----- > From: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > To: amarots(a)iqsc.usp.br > Cc: mg-rast(a)mcs.anl.gov, "Jared Wilkening" <jared.wilkening(a)gmail.com> > Sent: Wednesday, April 6, 2011 2:50:46 PM > Subject: Re: [mg-rast] Unable to upload data > Hi, > > I will take a look into this and get back to you. > > -- > 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 > > ----- Original Message ----- > > From: amarots(a)iqsc.usp.br > > To: "Jared Wilkening" <jared.wilkening(a)gmail.com> > > Cc: mg-rast(a)mcs.anl.gov > > Sent: Wednesday, April 6, 2011 2:47:39 PM > > Subject: [mg-rast] Unable to upload data > > Dear MG-Rast developing team, > > I've been trying to upload data for hours and can't get it done. The > > "upload" link isn't performing as presented at the tutorial. In fact > > I > > can't even post the files to be loaded. Instead the following > > message > > is > > showing up: [please wait for your upload to complete before viewing > > other > > tabs]. Although, I have no upload in progress. > > What should I do to upload the data? > > Thanks, > > Amaro > > > > > > > > > > > > > > > > > > > Amaro, > > > > > > We are about ready to finalized the last round of recomputes so I > > > would > > > expect they would be done by the end week or at latest early next > > > week. > > > New > > > jobs are generally taking about a week at the moment due to our > > > heavy load > > > and the recomputing. > > > > > > Cheers, > > > Jared Wilkening > > > - for the MG-RAST development team > > > > > > On Tue, Mar 29, 2011 at 4:53 PM, <amarots(a)iqsc.usp.br> wrote: > > > > > >> Dear MG-Rast developing team, > > >> > > >> I wonder if you have an estimated time for releasing the > > >> metagenomes > > >> which > > >> are still recomputing at the new MG-RAST version 3? I'm > > >> particularly > > >> interested in the two metagenomes I'm signed as a user: 4453373.3 > > >> - > > >> Amaro_RL1 and 4453374.3 - Amaro_RL2. > > >> Also, I would like to know how long will it take to process new > > >> data, > > >> which is about to be loaded into the MG-RAST? > > >> > > >> I thank you in advance for the attention, > > >> Best regards, > > >> Amaro Trindade-Silva > > >> > > >> > > >> > > >> > > >

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