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

Re: [mg-rast] linking functional and taxonomic assignments
by Jared Wilkening 05 Apr '11

05 Apr '11

Thanks for the detailed information. We'll take a look into this and get back to you as soon as possible. Cheers, Jared On Tue, Apr 5, 2011 at 3:57 PM, Durso, Lisa <Lisa.Durso(a)ars.usda.gov> wrote: > Hi Jared, > > Thanks for your quick response! I have tried the work flow with a variety > of metagenomes. I am hoping that the problem is that I have overlooked > something obvious. > > Most recently I was using the cattle metagenome:4448367.3. I pick a few > functional genes and add them to my workspace. > > > Next I move to the organism calssification tab, either go with defaults or > pick SEED, choose table for data visualization, and hit generate. > I have also tried with Antartic marine derived lake AntarcticaAquatic_1 > - MARINE DERIVED LAKE (4443683.3). > > Any ideas? Do I need to pick cutoff values in order to get the program to > complete? > > Lisa > > > > ------------------------------ > *From:* Jared Wilkening [mailto:[email protected]] > *Sent:* Tuesday, April 05, 2011 2:32 PM > *To:* Durso, Lisa > *Cc:* mg-rast(a)mcs.anl.gov > *Subject:* Re: [mg-rast] linking functional and taxonomic assignments > > Lisa, > > I'm glad to hear you are excited about version 3 and we're sorry you are > running into issues. We are working are working through bugs and improving > the underlying framework to support larger analyses. To that end would you > be able to send us a list of steps that we could use to reproduce the error > you are getting. Some errors are dataset specific and so its difficult > reproduce without a bit more information. Particularly useful would be the > metagenome name/id, proteins selected, and the tool settings like annotation > source and such. > > In general the page should never more than 5-10 minutes to load. I'm sorry > you waited 24 hours without a result. > > Cheers, > Jared Wilkening > - for the MG-RAST development team > > On Tue, Apr 5, 2011 at 11:56 AM, <lisa.durso(a)ars.usda.gov> wrote: > >> Dear MG-RAST, >> >> I am very excited by the possibility of linking the taxonomic and >> functional assignments. Right now I am doing this by hand, and the new >> version tool would save me a LOT of time. >> >> I am writing because I would like to be able to choose a protein from a >> functional table, move it to workbench, then get the taxonomic assignment. >> I have tried this over the last few weeks, and appear to have success in >> moving a functional protein into the workbench, but when I move to Organism >> Classification, check the "use proteins from workbench" option, the job >> never completes. Even when my workbench only has a few (n=5) proteins, the >> program appears to be stuck. The longest I have waited is a little over 24 >> hours for a set of 8 proteins. >> >> Do you know of anyone else having similar problems? I am using firefox as >> my browser. Could there be other settings on my computer that are >> preventing the program from running? >> >> Thank you, >> Lisa Durso >> > >

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Re: [mg-rast] mg-rast Data In progress
by Travis Harrison 05 Apr '11

05 Apr '11

Marian, Thanks for letting us know about this issue. There is no need to resubmit. I took a look into it and it seems there was a minor glitch with the system and your dataset got stuck in the pipeline. I have reset the pipeline and your data is now being processed. I will let you know when it has completed. Regards, Travis Harrison - for the MG-RAST development team On Tue, Apr 5, 2011 at 1:30 PM, Marianyoly Ortiz <moo(a)email.arizona.edu>wrote: > Hello again, > > I submitted a dataset to the MG-RAST pipeline. It has been going for a week > now and it looks like it is stuck in the same progress bar since it started. > Previous data submitted from our group took just a couple of days to finish > and I was wondering if there is something wrong with the server, our dataset > or if it is matter of time given the large size of this dataset (35 million > reads). > > I was wondering if there is a way that I can cancel this job and resubmit a > job with assembled data which could reduce the data size and hopefully go > faster? > > Thanks, > > Marian > > -- > Marianyoly Ortiz-Ortiz > Graduate Associate, Research > Soil, Water & Environmental Science > The University of Arizona > Tucson, AZ 85721 > FCS 321 > 520-621-9759 >

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Re: [mg-rast] linking functional and taxonomic assignments
by Jared Wilkening 05 Apr '11

05 Apr '11

Lisa, I'm glad to hear you are excited about version 3 and we're sorry you are running into issues. We are working are working through bugs and improving the underlying framework to support larger analyses. To that end would you be able to send us a list of steps that we could use to reproduce the error you are getting. Some errors are dataset specific and so its difficult reproduce without a bit more information. Particularly useful would be the metagenome name/id, proteins selected, and the tool settings like annotation source and such. In general the page should never more than 5-10 minutes to load. I'm sorry you waited 24 hours without a result. Cheers, Jared Wilkening - for the MG-RAST development team On Tue, Apr 5, 2011 at 11:56 AM, <lisa.durso(a)ars.usda.gov> wrote: > Dear MG-RAST, > > I am very excited by the possibility of linking the taxonomic and > functional assignments. Right now I am doing this by hand, and the new > version tool would save me a LOT of time. > > I am writing because I would like to be able to choose a protein from a > functional table, move it to workbench, then get the taxonomic assignment. > I have tried this over the last few weeks, and appear to have success in > moving a functional protein into the workbench, but when I move to Organism > Classification, check the "use proteins from workbench" option, the job > never completes. Even when my workbench only has a few (n=5) proteins, the > program appears to be stuck. The longest I have waited is a little over 24 > hours for a set of 8 proteins. > > Do you know of anyone else having similar problems? I am using firefox as > my browser. Could there be other settings on my computer that are > preventing the program from running? > > Thank you, > Lisa Durso >

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Re: [mg-rast] MGRAST - new account requested
by Mark D'Souza 05 Apr '11

05 Apr '11

Josh, We have a Andrew Holm registered with the email address 'holmlsice86(a)gmail.com' -- lsice, not slice, he will have to register again if this is wrong. Regards, Mark ----- Original Message ----- > From: "Joshua A Udall" <jaudall(a)gmail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Tuesday, April 5, 2011 12:51:29 PM > Subject: Re: [mg-rast] MGRAST - new account requested > Mark - > > > Thanks for you help. I'm trying to add Andrew, but it doesn't seem to > find his email address when I'm in the admin group page. I get a red > error at the top of the page with both his email address and user id. > > > "Dr. Udall, Hey I registered at MG Rast my login is holm86 and my > email is holmslice86(a)gmail.com im guessing you add me to some kind of > group on there?" > > > Please help. Thanks. > > > > > On Mar 30, 2011, at 9:43 AM, Mark D'Souza wrote: > > > > Josh, > > I created the group, when you log on to MG-RAST if you click on the > 'Account Management' icon (top right-hand corner of the page just > right of your name) the 'Administrate Groups' lets you add users to > the group. The email address you enter is used to identify the MG-RAST > user to be added to the group, so make sure your students supply you > with the address they registered with MG-RAST. > > Regards, > Mark > > ----- Original Message ----- > > > From: "Joshua A Udall" < jaudall(a)gmail.com > > > > To: "Mark D'Souza" < dsouza(a)mcs.anl.gov > > > > Sent: Monday, March 28, 2011 12:53:29 PM > > > Subject: Re: [mg-rast] MGRAST - new account requested > > > Mark - > > > > > > Yes, let's do option c and please use the name Udall_lab for the group > > > name. Thanks. > > > > > > Josh > > > > > > On Mar 28, 2011, at 11:21 AM, Mark D'Souza wrote: > > > > > > > > Hi, > > > > > > > > > > There are a couple of options available, > > > > > a. you could create a single user account under an email address you > > > > > control and give your students the username and password, > > > > > b. you could ask them to register with MG-RAST and then share the > > > > > data sets owned by your account with them, > > > > > c. I can create a formal group with you as the administrator and you > > > > > can ask your students to register and then add them into the group. > > > > > > > > > > Let us know if you would like to go with option c and choose a group > > > > > name and I can set this up. > > > > > > > > > > > > > > > ----- Original Message ----- > > > > > > > From: "Joshua Udall" < joshua_udall(a)byu.edu > > > > > > > > To: mg-rast(a)mcs.anl.gov > > > > > > > Sent: Monday, March 28, 2011 11:23:35 AM > > > > > > > Subject: Re: [mg-rast] MGRAST - new account requested > > > > > > > Thank you. I am a Principle Investigator (Assistant Professor) at > > > > > > > Brigham Young University. I would like to create a group if > > > > > > > possible > > > > > > > and allow my students to work with samples from our lab. I'm new to > > > > > > > this (obviously), and I look forward to hearing from you soon. Any > > > > > > > help or correction is appreciated. > > > > > > > > > > > > > > Josh > > > > > > > > > > > > > > > > > > > > > On Mar 28, 2011, at 9:48 AM, mg-rast(a)mcs.anl.gov wrote: > > > > > > > > > > > > > > > > Dear Joshua Udall, > > > > > > > > > > > > > > > > > > you have successfully requested access to our web service MGRAST. > > > > > > > > > An > > > > > > > > > administrator will review your registration at the earliest > > > > > > > > > opportunity. You will then receive an email with additional > > > > > > > > > information. > > > > > > > > > > > > > > > > > > The following data was sent: > > > > > > > > > Name: Joshua Udall > > > > > > > > > Login: jaudall > > > > > > > > > Email: jaudall(a)byu.edu > > > > > > > > > Group: > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > > > > > > > This email was automatically generated by the MGRAST web service. > > > > > > > > > Do > > > > > > > > > not reply. > > > > > > > > > > -- > > > > > 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 Data In progress
by Marianyoly Ortiz 05 Apr '11

05 Apr '11

Hello again, I submitted a dataset to the MG-RAST pipeline. It has been going for a week now and it looks like it is stuck in the same progress bar since it started. Previous data submitted from our group took just a couple of days to finish and I was wondering if there is something wrong with the server, our dataset or if it is matter of time given the large size of this dataset (35 million reads). I was wondering if there is a way that I can cancel this job and resubmit a job with assembled data which could reduce the data size and hopefully go faster? Thanks, Marian -- Marianyoly Ortiz-Ortiz Graduate Associate, Research Soil, Water & Environmental Science The University of Arizona Tucson, AZ 85721 FCS 321 520-621-9759

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linking functional and taxonomic assignments
by lisa.durso＠ars.usda.gov 05 Apr '11

05 Apr '11

Dear MG-RAST, I am very excited by the possibility of linking the taxonomic and functional assignments. Right now I am doing this by hand, and the new version tool would save me a LOT of time. I am writing because I would like to be able to choose a protein from a functional table, move it to workbench, then get the taxonomic assignment. I have tried this over the last few weeks, and appear to have success in moving a functional protein into the workbench, but when I move to Organism Classification, check the "use proteins from workbench" option, the job never completes. Even when my workbench only has a few (n=5) proteins, the program appears to be stuck. The longest I have waited is a little over 24 hours for a set of 8 proteins. Do you know of anyone else having similar problems? I am using firefox as my browser. Could there be other settings on my computer that are preventing the program from running? Thank you, Lisa Durso

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Re: [mg-rast] Discrepancy in Organisms Annotation
by Jared Wilkening 05 Apr '11

05 Apr '11

Hi Vicente, Since we released version 3 we have had to made a few changes address bugs but the fundamental annotations and the counts should be relatively unchanged. One important thing to note with the analysis in v3 is that sequences are mapped to proteins that can occur in multiple organisms. Unlike in version 2 there is not a 1 to 1 relationship between sequence and organism abundance. This is especially the case with proteins from core metabolism. Additionally the table on the analysis page when it groups by a taxa level it aggregates all the counts from lower taxa levels and so unless you have the table set the same way the abundances can appear different. I'm not sure if this is related to what you were seeing but currently there is a bug if the annotation source set to M5NR. It will include all of the protein sources as individual rows on when the table grouping is cleared but aggravate the counts together on grouping. We are fixing this with an update that will go live later today. In the case of the rna annotations (SSU, RDP, Greengenes) we dropped sequences without taxonomic annotations from our rna database because we found the data sources have included large numbers of un-annotationed environmental sequences. The result is that you should find more of the rna hits having a full taxa annotation but the counts should remain relatively the same. I hope this addresses your questions. If something is still unclear please do no hesitate to ask. Cheers, Jared Wilkening - for the MG-RAST development team On Tue, Apr 5, 2011 at 10:10 AM, <Gomez-Alvarez.Vicente(a)epamail.epa.gov>wrote: > Dear MG-RAST; > > > > Hi, back in March 24 I download the results of the "Organism > Classification" (class and species) analysis for the following projects > 4459783.3<http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeOverview&metage…>, > 4459784.3<http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeOverview&metage…>, > 4459792.3<http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeOverview&metage…>and > 4459793.3<http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeOverview&metage…>. > I used the SSU, RDP and SEED annotation sources. Today I download again > the results/analysis using the same parameters as before and for my surprise > the number of sequences annotated as organisms were different and in some > cases decrease by more than half from the original analysis of 03-24-2011. > > Do they reanalyzed the Organisms Annotation? Or change the parameters for > annotation? Since the Functional Classification (Subsystem, COG, and KO) do > not suffer any change that I notice. > > If any time I redo the analysis it will show a different results? At least > for the Organisms Annotation? > > > Thanks again for this service > > > > Vicente Gomez-Alvarez > Federal Post-Doctoral fellow > Microbial Contaminants Control Branch > Ph: 513-569-7362 > Room: 302 > > Mail: > *U.S. Environmental Protection Agency** - ORD* > *National Risk Management Research Laboratory* > *Water Supply and Water Resources Division* > *26 W. Martin Luther King Dr. [Mail Stop - MLK 387]* > *Cincinnati, Ohio 45268*

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Discrepancy in Organisms Annotation
by Gomez-Alvarez.Vicente＠epamail.epa.gov 05 Apr '11

05 Apr '11

Dear MG-RAST; Hi, back in March 24 I download the results of the "Organism Classification" (class and species) analysis for the following projects 4459783.3, 4459784.3, 4459792.3 and 4459793.3. I used the SSU, RDP and SEED annotation sources. Today I download again the results/analysis using the same parameters as before and for my surprise the number of sequences annotated as organisms were different and in some cases decrease by more than half from the original analysis of 03-24-2011. Do they reanalyzed the Organisms Annotation? Or change the parameters for annotation? Since the Functional Classification (Subsystem, COG, and KO) do not suffer any change that I notice. If any time I redo the analysis it will show a different results? At least for the Organisms Annotation? Thanks again for this service Vicente Gomez-Alvarez Federal Post-Doctoral fellow Microbial Contaminants Control Branch Ph: 513-569-7362 Room: 302 Mail: U.S. Environmental Protection Agency - ORD National Risk Management Research Laboratory Water Supply and Water Resources Division 26 W. Martin Luther King Dr. [Mail Stop - MLK 387] Cincinnati, Ohio 45268

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Re: [mg-rast] Juliana_RL4 (4453376.3) metagenome
by Jared Wilkening 05 Apr '11

05 Apr '11

Cristiane, Thanks for letting us know about this issue. I took a look into it and it seems there was a momentary glitch with the system and so only 16s results were loaded into the database. We are resetting the load stage and so that should be fixed shortly. Cheers, Jared Wilkening - for the MG-RAST development team On Tue, Apr 5, 2011 at 9:14 AM, <thompson(a)ioc.fiocruz.br> wrote: > Dear mg-rast team, > Juliana_RL4 (4453376.3)metagenome does not allow any kind of analysis after > you recompute the data. There is an error message and a message saying no > data is found. Please, could check this problem? > > thank you in advance > > Cristiane Thompson >

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Juliana_RL4 (4453376.3) metagenome
by thompson＠ioc.fiocruz.br 05 Apr '11

05 Apr '11

Dear mg-rast team, Juliana_RL4 (4453376.3)metagenome does not allow any kind of analysis after you recompute the data. There is an error message and a message saying no data is found. Please, could check this problem? thank you in advance Cristiane Thompson

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