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

Re: [mg-rast] mg-rast ftp upload site...
by Andreas Wilke 08 Apr '11

08 Apr '11

Hi Doug , Brian , Tanya thanks for the logfile. I checked some entries and they are looking good but I will go through the logfile thoroughly. You need an account to view the private data , if you don't have one please go to metagenomics.anl.gov/metagenomics.cgi?page=Register and request a login. I need your login information to give you ownership of your data. Andreas On Apr 8, 2011, at 6:47 PM, Doug Wendel wrote: > Data has been sent... Andreas, here's the log. > > <tanya_output.txt.zip> 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] Problem with selecting metagenomes for analysis
by Mark D'Souza 08 Apr '11

08 Apr '11

Hi Sarah, Glad to hear that things are working. We would like to fix this so no one else has this problem, if you identify what is going on please let us know. Regards, Mark ----- Original Message ----- > From: "Sarah Kyker" <src10(a)case.edu> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Friday, April 8, 2011 11:39:07 AM > Subject: Re: [mg-rast] Problem with selecting metagenomes for analysis > Hi Mark, > > Thanks very much for looking into this! I actually tried using a > different computer and it worked great! So, it appears to be a problem > specific to my computer. I'll figure out what's going on! > > Thanks again! > > Sarah :-) > > > > On Fri, Apr 8, 2011 at 10:22 AM, Mark D'Souza < dsouza(a)mcs.anl.gov > > wrote: > > > Hi, > > I was unable to reproduce the problem you had with the site, even > using your metagenomes and login, can you let us know the metagenomes > you selected and the error or warning message you received so that I > can repeat the identical procedure. > > -- > 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: "Sarah Kyker" < src10(a)case.edu > > > To: mg-rast(a)mcs.anl.gov > > Sent: Friday, April 8, 2011 7:22:05 AM > > Subject: [mg-rast] Problem with selecting metagenomes for analysis > > Dear MG-RAST developers, > > > > I am having a problem selecting metagenomes for analysis and am > > hoping > > that you might be able to help me with a quick fix. I have been > > attempting to analyze two metagenomes that our lab uploaded last > > year > > (1N and 2C), but I am continually receiving the error message: "you > > did not select any metagenomes". I am unsure why I am receiving this > > message because I have been following the demonstration in the video > > on the help page under "p-value tool: Sample Grouping." To select > > the > > metagenomes, I have been clicking on the green plus sign, moving > > over > > the metagenomes I am interested in, and clicking "OK" (just as > > demonstrated in the video). But, for some reason, the program is not > > recognizing that I selected any metagenomes. I have tried several > > times with a number of the public metagenomes with no luck. I have > > been using Firefox verson 3.6.16. Any help is appreciated!! Thanks > > very much! > > > > Sarah :-) > > > > -- > > Sarah R. Carrino-Kyker > > Postdoctoral Scholar - Case Western Reserve University > > Visiting Scientist - The Holden Arboretum > > src10(a)cwru.edu > > > > -- > Sarah R. Carrino-Kyker > Postdoctoral Scholar - Case Western Reserve University > Visiting Scientist - The Holden Arboretum > src10(a)cwru.edu

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Re: [mg-rast] Slow processing?
by Mark D'Souza 08 Apr '11

08 Apr '11

Hi, Sorry about that, your jobs were run during a time window when one of the pipeline steps was not functioning correctly and they got stuck in a state which did not flag an error so we were unaware of this status. We have identified the problem and will restart the jobs immediately. ----- Original Message ----- > From: "Tarah Sullivan-Guest" <sullivant(a)ornl.gov> > To: mg-rast(a)mcs.anl.gov > Sent: Friday, April 8, 2011 9:27:23 AM > Subject: [mg-rast] Slow processing? > Hi, I uploaded data on last Thursday, March 31 st , for analysis. > Today it is still in progress and I’m still seeing the message > “Calculating Sims: In progress.” Just wondering if there’s any > particular reason it’s taking so long? The last set of data I uploaded > only took about 3 days, and I know this set is a lot more sequences, > but it doesn’t seem like it was a whole week’s worth more. I very much > appreciate your time and help. > > Thanks, > > Tarah Sullivan > > > > Tarah S. Sullivan > > Postdoctoral Research Associate > > Biosciences Division > > Oak Ridge National Laboratory > > Building 1505, MS-6038 > > Oak Ridge, TN 37831-6038 > > Phone: 865/ 574.0968 > > Fax: 865/ 576.8648 > > E-mail: sullivant(a)ornl.gov -- 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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Slow processing?
by Sullivan-Guest, Tarah 08 Apr '11

08 Apr '11

Hi, I uploaded data on last Thursday, March 31st, for analysis. Today it is still in progress and I'm still seeing the message "Calculating Sims: In progress." Just wondering if there's any particular reason it's taking so long? The last set of data I uploaded only took about 3 days, and I know this set is a lot more sequences, but it doesn't seem like it was a whole week's worth more. I very much appreciate your time and help. Thanks, Tarah Sullivan Tarah S. Sullivan Postdoctoral Research Associate Biosciences Division Oak Ridge National Laboratory Building 1505, MS-6038 Oak Ridge, TN 37831-6038 Phone: 865/ 574.0968 Fax: 865/ 576.8648 E-mail: sullivant(a)ornl.gov<mailto:[email protected]>

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Re: [mg-rast] Problem with selecting metagenomes for analysis
by Mark D'Souza 08 Apr '11

08 Apr '11

Hi, I was unable to reproduce the problem you had with the site, even using your metagenomes and login, can you let us know the metagenomes you selected and the error or warning message you received so that I can repeat the identical procedure. -- 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: "Sarah Kyker" <src10(a)case.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Friday, April 8, 2011 7:22:05 AM > Subject: [mg-rast] Problem with selecting metagenomes for analysis > Dear MG-RAST developers, > > I am having a problem selecting metagenomes for analysis and am hoping > that you might be able to help me with a quick fix. I have been > attempting to analyze two metagenomes that our lab uploaded last year > (1N and 2C), but I am continually receiving the error message: "you > did not select any metagenomes". I am unsure why I am receiving this > message because I have been following the demonstration in the video > on the help page under "p-value tool: Sample Grouping." To select the > metagenomes, I have been clicking on the green plus sign, moving over > the metagenomes I am interested in, and clicking "OK" (just as > demonstrated in the video). But, for some reason, the program is not > recognizing that I selected any metagenomes. I have tried several > times with a number of the public metagenomes with no luck. I have > been using Firefox verson 3.6.16. Any help is appreciated!! Thanks > very much! > > Sarah :-) > > -- > Sarah R. Carrino-Kyker > Postdoctoral Scholar - Case Western Reserve University > Visiting Scientist - The Holden Arboretum > src10(a)cwru.edu

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Re: [mg-rast] mg rast question
by Folker Meyer 08 Apr '11

08 Apr '11

Dear Carla, we will add the blast against a single metageome functionality again in the coming weeks Best, Folker On Apr 8, 2011, at 12:52 PM, carla nartuhi mavian wrote: > Hello, > > I'm a PhD student working in genomes sequencing, annotation etc.. and I > found very useful the BLAST tool of the second version of the MG Rast that > allowed to find any sequence among all the reads uploaded. > I was searching for this tool in the new version, but I can't find it! > Maybe it's me that I'm not able to find it, or is that there's no such > tool yet? > If there is not the BLAST tool, are you going to put it again? > > Thank you for your attention, > > Best regards, > > Carla Mavian > > > LAB.227 > Group Leader A.Alcamì > CBMSO-UAM > C/Nicolás Cabrera 1 > Campus de Cantoblanco > 28049-MADRID > > >

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Problem with selecting metagenomes for analysis
by Sarah Kyker 08 Apr '11

08 Apr '11

Dear MG-RAST developers, I am having a problem selecting metagenomes for analysis and am hoping that you might be able to help me with a quick fix. I have been attempting to analyze two metagenomes that our lab uploaded last year (1N and 2C), but I am continually receiving the error message: "you did not select any metagenomes". I am unsure why I am receiving this message because I have been following the demonstration in the video on the help page under "p-value tool: Sample Grouping." To select the metagenomes, I have been clicking on the green plus sign, moving over the metagenomes I am interested in, and clicking "OK" (just as demonstrated in the video). But, for some reason, the program is not recognizing that I selected any metagenomes. I have tried several times with a number of the public metagenomes with no luck. I have been using Firefox verson 3.6.16. Any help is appreciated!! Thanks very much! Sarah :-) -- Sarah R. Carrino-Kyker Postdoctoral Scholar - Case Western Reserve University Visiting Scientist - The Holden Arboretum src10(a)cwru.edu <sarah.carrino(a)cwru.edu>

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mg rast question
by carla nartuhi mavian 08 Apr '11

08 Apr '11

Hello, I'm a PhD student working in genomes sequencing, annotation etc.. and I found very useful the BLAST tool of the second version of the MG Rast that allowed to find any sequence among all the reads uploaded. I was searching for this tool in the new version, but I can't find it! Maybe it's me that I'm not able to find it, or is that there's no such tool yet? If there is not the BLAST tool, are you going to put it again? Thank you for your attention, Best regards, Carla Mavian LAB.227 Group Leader A.Alcamì CBMSO-UAM C/Nicolás Cabrera 1 Campus de Cantoblanco 28049-MADRID

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Fwd: Fwd: [theseed.org Info] CLOUD
by Folker Meyer 08 Apr '11

08 Apr '11

Travis: please take a look. Begin forwarded message: > From: Renee Smith <renee.smith(a)flinders.edu.au> > Date: April 8, 2011 8:45:29 AM GMT+02:00 > To: Folker Meyer <folker(a)anl.gov> > Subject: RE: [mg-rast] Fwd: [theseed.org Info] CLOUD > > Hi, > > The metagenomes i am looking at are "A5" job ID: 4453083.3 and "A1" job ID: 4453064.3. > > Thanks for your help, > > Renee > > ________________________________________ > From: Folker Meyer [folker(a)anl.gov] > Sent: Friday, 8 April 2011 4:07 PM > To: Renee Smith > Cc: M. G. Rast; info(a)theseed.org; Robert Olson > Subject: Re: [mg-rast] Fwd: [theseed.org Info] CLOUD > > Dear Renee, > > that is a database problem (with the sequence databases we import). Let me explain at bit more: > > The same happened with 16s. We foolishly believed that updating databases like RDP, Silva and > Greengenes was a good idea. However the new versions of those databases now contain large quantities of "unclassified" sequences that in many real world tests "overlay" the signal. > > There are so many of them that in many cases we got the result you described. We fixed this by removing unclassified sequences from the 16s databases. I suspect the same thing has happened here for the protein world. > > There seem to be quite a few unclassified virus sequences in the archives and they are more similar to your query. In a way that is the correct behavior, but it is certainly less than useful. > > I have an idea for a solution in mind that we will explore today. > > We will get back to you once we have investigated (NOTE: we need the Job ID (or the 444xx ID of your data). > > Best, > Folker > > > On Apr 8, 2011, at 3:44 AM, Robert Olson wrote: > >> >> >> ----- 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] Fwd: [theseed.org Info] CLOUD
by Folker Meyer 08 Apr '11

08 Apr '11

Dear Renee, that is a database problem (with the sequence databases we import). Let me explain at bit more: The same happened with 16s. We foolishly believed that updating databases like RDP, Silva and Greengenes was a good idea. However the new versions of those databases now contain large quantities of "unclassified" sequences that in many real world tests "overlay" the signal. There are so many of them that in many cases we got the result you described. We fixed this by removing unclassified sequences from the 16s databases. I suspect the same thing has happened here for the protein world. There seem to be quite a few unclassified virus sequences in the archives and they are more similar to your query. In a way that is the correct behavior, but it is certainly less than useful. I have an idea for a solution in mind that we will explore today. We will get back to you once we have investigated (NOTE: we need the Job ID (or the 444xx ID of your data). Best, Folker On Apr 8, 2011, at 3:44 AM, Robert Olson wrote: > > > ----- 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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