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

Re: [mg-rast] KEGG Mapper
by Mark DSouza 19 Jul '11

19 Jul '11

Hi, It sounds like you are using the KEGG mapper correctly, you need to select some metagenomes under the available list, move them to the selected list and then click on 'load data' to add them to the Data A or B sets. Which browser are you using? The MG-RAST site works best on the latest version of FireFox and all the features may not work on other browsers. The Mapper is working correctly for me, let us know which browser you are using. -- 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: "yanwei lim" <ywlim.s(a)gmail.com> > To: mg-rast(a)mcs.anl.gov > Sent: Monday, July 18, 2011 6:27:01 PM > Subject: [mg-rast] KEGG Mapper > Hi, > > > I would like to know whether the KEGG Mapper is functioning. When I > tried to upload my metagenomes into the KEGG Mapper, nothing shows up > on the Data A column, nor Data B. First, I select the metagenomes, > click ok, and click "load data". I assumed there should be something > in the Data A and Data B boxes on the right. > > > Please explain how to use the KEGG Mapper and if it is working. > > > Thank you very much. Your help is very appreciated. > > > Thanks, > Yan Wei Lim

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KEGG Mapper
by yanwei lim 18 Jul '11

18 Jul '11

Hi, I would like to know whether the KEGG Mapper is functioning. When I tried to upload my metagenomes into the KEGG Mapper, nothing shows up on the Data A column, nor Data B. First, I select the metagenomes, click ok, and click "load data". I assumed there should be something in the Data A and Data B boxes on the right. Please explain how to use the KEGG Mapper and if it is working. Thank you very much. Your help is very appreciated. Thanks, Yan Wei Lim

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Sharing MG-RAST jobs
by Mark D'Souza 18 Jul '11

18 Jul '11

Hi, Please reply to this email, no additional text necessary. Share all 90 datasets with: > empr3ss(a)gmail.com > uh25(a)drexel.edu > gcd34(a)drexel.edu Regards, Mark ----- Original Message ----- > From: "Steve Essinger" <sessinger(a)gmail.com> > To: mg-rast(a)mcs.anl.gov > Sent: Monday, July 18, 2011 3:54:12 PM > Subject: [mg-rast] Sharing Datasets with Multiple Users > Hi, > > > I currently have 90 datasets uploaded on MG-RAST. I need to share > these datasets with a few individuals, but cannot give them my > username and password. I see that here is a link to share datasets, > but each one must be shared individual with each person. This is going > to take a long time. Is there anyway to share my datasets as a batch > process? If not, is it an easy fix for you to share the datasets for > me? > > > My username is: sessinger > The datasets need to be shared with: > empr3ss(a)gmail.com > uh25(a)drexel.edu > gcd34(a)drexel.edu > > > Thanks, > Steve Essinger

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Re: [mg-rast] Sharing Datasets with Multiple Users
by Mark DSouza 18 Jul '11

18 Jul '11

Hi, We had a discussion about simplifying this process last week and will be making changes to the website in the future. Right now however, there is no way you can share all the datasets as a batch. I should be able to share the datasets for you, but before I do that we need to verify your identity as this gmail address is not registered with MG-RAST. Please respond to the email I am sending to the address registered with the 'sessinger' account and I will give it a try. -- 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: "Steve Essinger" <sessinger(a)gmail.com> > To: mg-rast(a)mcs.anl.gov > Sent: Monday, July 18, 2011 3:54:12 PM > Subject: [mg-rast] Sharing Datasets with Multiple Users > Hi, > > > I currently have 90 datasets uploaded on MG-RAST. I need to share > these datasets with a few individuals, but cannot give them my > username and password. I see that here is a link to share datasets, > but each one must be shared individual with each person. This is going > to take a long time. Is there anyway to share my datasets as a batch > process? If not, is it an easy fix for you to share the datasets for > me? > > > My username is: sessinger > The datasets need to be shared with: > empr3ss(a)gmail.com > uh25(a)drexel.edu > gcd34(a)drexel.edu > > > Thanks, > Steve Essinger

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Re: [mg-rast] Doubt about MG-Rast annotation
by Mark DSouza 18 Jul '11

18 Jul '11

Hi, The number discrepancy arises from the use of different databases, the original 209 hits is specific to the SEED subsystem, with 66 hits against the proteins in these organisms. When you perform the organism classification against GenBank, the number of hits is higher because of the greater number of organisms in the GenBank database, and so does the abundance counts. The workbench abundance column of the table gives a better breakdown of the taxonomic counts as compared to the 209 count. This is not very intuitive from the display and we are looking into changing the table to make this more explicit. Regards, Mark ----- Original Message ----- > From: "Gustavo B. Gregoracci" <gustavo_biomed(a)yahoo.com> > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > Cc: "MG- Rast" <mg-rast(a)mcs.anl.gov>, "Louisi Oliveira" <louisioliveira(a)gmail.com> > Sent: Monday, July 18, 2011 1:03:28 PM > Subject: Re: Doubt about MG-Rast annotation > Hi there Mark, > > > Thanks for the reply. So, the metagenome ID is 4465448.3 and its > called Forno. The glitch has actually happened in others as well, and > I'm only using this one as an example. > > > I re-checked the numbers and they still don't add. I'm working with > Genbank (e-5) for organism classification, and subsystems (e-5) for > functional classification, for that matter. > > > I have 209 hits in this entire metagenome for photosynthesis. If I > check the number of photosynthesis hits among the bacterial hits I get > 140, while the same for eukaryotic gives me 142 hits. That puzzled me. > When I do the opposite, and check the taxonomic composition of just > the 209 photosynthesis hits the numbers are even more weirder. I get > 245 hits for bacteria and 403 for eukaryotes! > > > Thanks again for the help, > I'm available for any further explanations necessary, > > > Best regards, > Gustavo > > Gustavo Bueno Gregoracci > -- > MSc., Dr. in Microbiology (Genetics and Molecular Biology) > Email: gustavo_biomed(a)yahoo.com > > -- > Pos doc Student > Laboratório de Microbiologia (Prof. Fabiano Thompson) > Centro de Ciências de Saúde - Instituto de Biologia - UFRJ > Tel: +55 (21) 2562-6567 > > > > > > From: Mark DSouza <dsouza(a)mcs.anl.gov> > To: Gustavo B. Gregoracci <gustavo_biomed(a)yahoo.com> > Cc: MG- Rast <mg-rast(a)mcs.anl.gov> > Sent: Monday, July 18, 2011 1:33 PM > Subject: Re: Doubt about MG-Rast annotation > > Hi, > > Can you please send us the MG-RAST ID for the dataset where you > observed this, we will check into it for 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: "Gustavo B. Gregoracci" < gustavo_biomed(a)yahoo.com > > > To: "Mark D'Souza" < dsouza(a)mcs.anl.gov > > > Sent: Saturday, July 16, 2011 10:05:14 AM > > Subject: Doubt about MG-Rast annotation > > Hello there Mark, > > > > > > > > As I was analyzing some metagenomes, I ran into a recurrent problem. > > I > > was trying to cross information from taxonomic and functional > > annotation, and discovered some inconsistencies. I could not figure > > those out so I’m writing you in the hope that you can help me, since > > this will affect my analysis. > > > > > > You see… I wanted to understand the contribution of different > > phylogenetic groups to a given subsystem. So I got the total number > > of > > sequences for the photosynthesis subsystem, for example, which was > > 209 > > hits. Then I went into taxonomy and separated all entries identified > > as eukaryotes, sending them to the workbench. I changed again to > > functional and checked the total number of eukaryotic hits to > > photosynthesis, which was 163. So far so good, but I decided to > > perform the same analysis regarding prokaryotes. Sent all > > prokaryotic > > entries to the workbench and changed to functional to see their > > contribution to photosynthesis as well. I got 174 hits! > > > > > > > > How is this possible? If my whole metagenome has 209 hits to a > > subsystem, how can I have 163 eukaryotic hits within it and 174 > > prokaryotic hits to the same subsystem? Can sequences be annotated > > as > > both eukaryotic and prokaryotic? Cause I was interpreting these > > categories as mutually exclusive… > > > > > > Thanks in advance for the help, > > Looking forward to hear from you, > > > > > > Best regards, > > Gustavo > > > > Gustavo Bueno Gregoracci > > -- > > MSc., Dr. in Microbiology (Genetics and Molecular Biology) > > Email: gustavo_biomed(a)yahoo.com > > > > -- > > Pos doc Student > > Laboratório de Microbiologia (Prof. Fabiano Thompson) > > Centro de Ciências de Saúde - Instituto de Biologia - UFRJ > > Tel: +55 (21) 2562-6567

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Sharing Datasets with Multiple Users
by Steve Essinger 18 Jul '11

18 Jul '11

Hi, I currently have 90 datasets uploaded on MG-RAST. I need to share these datasets with a few individuals, but cannot give them my username and password. I see that here is a link to share datasets, but each one must be shared individual with each person. This is going to take a long time. Is there anyway to share my datasets as a batch process? If not, is it an easy fix for you to share the datasets for me? My username is: sessinger The datasets need to be shared with: empr3ss(a)gmail.com uh25(a)drexel.edu gcd34(a)drexel.edu Thanks, Steve Essinger

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Re: [mg-rast] Doubt about MG-Rast annotation
by Gustavo B. Gregoracci 18 Jul '11

18 Jul '11

Hi there Mark, Thanks for the reply. So, the metagenome ID is 4465448.3 and its called Forno. The glitch has actually happened in others as well, and I'm only using this one as an example. I re-checked the numbers and they still don't add. I'm working with Genbank (e-5) for organism classification, and subsystems (e-5) for functional classification, for that matter. I have 209 hits in this entire metagenome for photosynthesis. If I check the number of photosynthesis hits among the bacterial hits I get 140, while the same for eukaryotic gives me 142 hits. That puzzled me. When I do the opposite, and check the taxonomic composition of just the 209 photosynthesis hits the numbers are even more weirder. I get 245 hits for bacteria and 403 for eukaryotes! Thanks again for the help, I'm available for any further explanations necessary, Best regards, Gustavo Gustavo Bueno Gregoracci -- MSc., Dr. in Microbiology (Genetics and Molecular Biology) Email: gustavo_biomed(a)yahoo.com -- Pos doc Student Laboratório de Microbiologia (Prof. Fabiano Thompson) Centro de Ciências de Saúde - Instituto de Biologia - UFRJ Tel: +55 (21) 2562-6567 >________________________________ >From: Mark DSouza <dsouza(a)mcs.anl.gov> >To: Gustavo B. Gregoracci <gustavo_biomed(a)yahoo.com> >Cc: MG- Rast <mg-rast(a)mcs.anl.gov> >Sent: Monday, July 18, 2011 1:33 PM >Subject: Re: Doubt about MG-Rast annotation > >Hi, > >Can you please send us the MG-RAST ID for the dataset where you observed this, we will check into it for 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: "Gustavo B. Gregoracci" <gustavo_biomed(a)yahoo.com> >> To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> >> Sent: Saturday, July 16, 2011 10:05:14 AM >> Subject: Doubt about MG-Rast annotation >> Hello there Mark, >> >> >> >> As I was analyzing some metagenomes, I ran into a recurrent problem. I >> was trying to cross information from taxonomic and functional >> annotation, and discovered some inconsistencies. I could not figure >> those out so I’m writing you in the hope that you can help me, since >> this will affect my analysis. >> >> >> You see… I wanted to understand the contribution of different >> phylogenetic groups to a given subsystem. So I got the total number of >> sequences for the photosynthesis subsystem, for example, which was 209 >> hits. Then I went into taxonomy and separated all entries identified >> as eukaryotes, sending them to the workbench. I changed again to >> functional and checked the total number of eukaryotic hits to >> photosynthesis, which was 163. So far so good, but I decided to >> perform the same analysis regarding prokaryotes. Sent all prokaryotic >> entries to the workbench and changed to functional to see their >> contribution to photosynthesis as well. I got 174 hits! >> >> >> >> How is this possible? If my whole metagenome has 209 hits to a >> subsystem, how can I have 163 eukaryotic hits within it and 174 >> prokaryotic hits to the same subsystem? Can sequences be annotated as >> both eukaryotic and prokaryotic? Cause I was interpreting these >> categories as mutually exclusive… >> >> >> Thanks in advance for the help, >> Looking forward to hear from you, >> >> >> Best regards, >> Gustavo >> >> Gustavo Bueno Gregoracci >> -- >> MSc., Dr. in Microbiology (Genetics and Molecular Biology) >> Email: gustavo_biomed(a)yahoo.com >> >> -- >> Pos doc Student >> Laboratório de Microbiologia (Prof. Fabiano Thompson) >> Centro de Ciências de Saúde - Instituto de Biologia - UFRJ >> Tel: +55 (21) 2562-6567 > > >

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Re: [mg-rast] Doubt about MG-Rast annotation
by Mark DSouza 18 Jul '11

18 Jul '11

Hi, Can you please send us the MG-RAST ID for the dataset where you observed this, we will check into it for 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: "Gustavo B. Gregoracci" <gustavo_biomed(a)yahoo.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Saturday, July 16, 2011 10:05:14 AM > Subject: Doubt about MG-Rast annotation > Hello there Mark, > > > > As I was analyzing some metagenomes, I ran into a recurrent problem. I > was trying to cross information from taxonomic and functional > annotation, and discovered some inconsistencies. I could not figure > those out so I’m writing you in the hope that you can help me, since > this will affect my analysis. > > > You see… I wanted to understand the contribution of different > phylogenetic groups to a given subsystem. So I got the total number of > sequences for the photosynthesis subsystem, for example, which was 209 > hits. Then I went into taxonomy and separated all entries identified > as eukaryotes, sending them to the workbench. I changed again to > functional and checked the total number of eukaryotic hits to > photosynthesis, which was 163. So far so good, but I decided to > perform the same analysis regarding prokaryotes. Sent all prokaryotic > entries to the workbench and changed to functional to see their > contribution to photosynthesis as well. I got 174 hits! > > > > How is this possible? If my whole metagenome has 209 hits to a > subsystem, how can I have 163 eukaryotic hits within it and 174 > prokaryotic hits to the same subsystem? Can sequences be annotated as > both eukaryotic and prokaryotic? Cause I was interpreting these > categories as mutually exclusive… > > > Thanks in advance for the help, > Looking forward to hear from you, > > > Best regards, > Gustavo > > Gustavo Bueno Gregoracci > -- > MSc., Dr. in Microbiology (Genetics and Molecular Biology) > Email: gustavo_biomed(a)yahoo.com > > -- > Pos doc Student > Laboratório de Microbiologia (Prof. Fabiano Thompson) > Centro de Ciências de Saúde - Instituto de Biologia - UFRJ > Tel: +55 (21) 2562-6567

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QIIME Report in MG-RAST v3.1
by Deepak Sharma 18 Jul '11

18 Jul '11

Hi Mark, I hope you are doing great. I have a small question regarding the QIIME report feature in MGRAST. MGRAST website doesn't give much information about the QIIME feature like how to use the file and what the two files means. Could you give me some information about how *data and *metadata can be used by QIIME? Thanks -- *Deepak Sharma, M.Sc* *Microbial Research Tech.* West Virginia State University PO Box 1000 - 102 Hamblin Hall Institute, WV 25112 Telephone: (304) 766-5239 E-mail: dsharma(a)wvstateu.edu

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Re: [mg-rast] images
by Tobias Paczian 18 Jul '11

18 Jul '11

Yeah, kinda. This has to do with the handling of the hover overs. I could check this out again. As for the image format, I do not think we should offer more formats. Cheers Tobi On Jul 14, 2011, at 5:33 PM, Mark D'Souza wrote: > Tobi, > > I figured this is a Raphael bug, is this right? > > Thanks, > Mark > > > > Begin forwarded message: > >> From: Julian Marchesi <MarchesiJR(a)cardiff.ac.uk> >> Date: July 14, 2011 3:39:36 AM CDT >> To: Mark DSouza <dsouza(a)mcs.anl.gov> >> Subject: Re: [mg-rast] images >> >> Hi Mark >> >> Thanks for helping with the other issue but I have another one - >> sorry >> >> When I have processed some data and I'm analysing it some of the >> dynamic figures e.g. rank abundance can be made static for >> downloading, but I don't get a "clean image" (see example) The >> pointer comes up when I hit the static button >> >> Also are there any plans to save it in a different format to PNG >> e.g. EMF or SVG >> >> cheers >> >> Julian >> >> <Mail Attachment.gif> >> >> >> >> Dr Julian R. Marchesi >> School of Biosciences >> Museum Avenue >> Cardiff University >> Cardiff >> CF10 3AT >> Telephone: +44 (0)29 208 74188 >> Fax: +44 (0)29 20874305 >> Mobile 07885 569144 >> >> The information contained in this e-mail message and any >> attachments is strictly confidential and is intended for the >> person or organisation to whom it is addressed. >> If you are not the intended recipient, you must not read, use, >> copy or disseminate the information contained in this message and >> must delete it. Please advise us >> immediately if you are not the named addresses or the person >> responsible for delivering the message to the named addressee. >> >> Although Cardiff University believes this e-mail and any >> attachments are free of any virus or defect which may affect a >> computer, it is the responsibility of the recipient >> to ensure that it is virus free. Cardiff university will not >> accept any liability for any loss or damage arising in any way >> from its use. >> >> >> >> From: Mark DSouza <dsouza(a)mcs.anl.gov> >> To: Julian Marchesi <MarchesiJR(a)cardiff.ac.uk> >> Cc: MG- Rast <mg-rast(a)mcs.anl.gov> >> Date: 13/07/2011 22:11 >> Subject: Re: [mg-rast] re job hanging >> >> >> >> Hi, >> >> There was a problem with the demultiplexing, I ran this step and >> all your sequences got classified under the 'no_MID_tag' status as >> all the sequences in the sff file begin with 'tcag' which does not >> match any of the MID tags. You can modify your MID tags to include >> this prefix and resubmit the dataset, let me know if you have >> trouble with the demultiplexing again. >> >> Regards, >> Mark >> >> >> >> ----- Original Message ----- >> > From: "Julian Marchesi" <MarchesiJR(a)cardiff.ac.uk> >> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> >> > Sent: Tuesday, July 12, 2011 9:41:34 AM >> > Subject: Re: [mg-rast] re job hanging >> > cheers >> > >> > Julian >> > >> > >> > >> > Dr Julian R. Marchesi >> > School of Biosciences >> > Museum Avenue >> > Cardiff University >> > Cardiff >> > CF10 3AT >> > Telephone: +44 (0)29 208 74188 >> > Fax: +44 (0)29 20874305 >> > Mobile 07885 569144 >> > >> > The information contained in this e-mail message and any >> attachments >> > is strictly confidential and is intended for the person or >> > organisation to whom it is addressed. >> > If you are not the intended recipient, you must not read, use, >> copy or >> > disseminate the information contained in this message and must >> delete >> > it. Please advise us >> > immediately if you are not the named addresses or the person >> > responsible for delivering the message to the named addressee. >> > >> > Although Cardiff University believes this e-mail and any >> attachments >> > are free of any virus or defect which may affect a computer, it >> is the >> > responsibility of the recipient >> > to ensure that it is virus free. Cardiff university will not accept >> > any liability for any loss or damage arising in any way from its >> use. >> > >> > >> > >> > From: Mark D'Souza <dsouza(a)mcs.anl.gov> >> > To: Julian Marchesi <MarchesiJR(a)cardiff.ac.uk> >> > Cc: mg-rast(a)mcs.anl.gov >> > Date: 12/07/2011 15:30 >> > Subject: Re: [mg-rast] re job hanging >> > >> > >> > >> > >> > Hi, >> > >> > No, that is not normal, we will take a look 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 >> > >> > >> > >> > >> > On Jul 12, 2011, at 8:18 AM, Julian Marchesi wrote: >> > >> > > Hi Guys >> > > >> > > I've uploaded my data (16S rRNA gene) and have supplied the >> MIDS and >> > > have been waiting >24 hours for it to demultiplex >> > > >> > > job number 42129 here is the status >> > > >> > > my login name is jugsy67 >> > > >> > > filename status next step progress >> > > GPFRVDY05.sff.fasta demultiplex demultiplexing waiting for >> > > demultiplexing ... >> > > >> > > Is this normal? The file is an sff file approx 216 Mb in size >> > > >> > > Dr Julian R. Marchesi >> > > School of Biosciences >> > > Museum Avenue >> > > Cardiff University >> > > Cardiff >> > > CF10 3AT >> > > Telephone: +44 (0)29 208 74188 >> > > Fax: +44 (0)29 20874305 >> > > Mobile 07885 569144 >> > > >> > > The information contained in this e-mail message and any >> attachments >> > > is strictly confidential and is intended for the person or >> > > organisation to whom it is addressed. >> > > If you are not the intended recipient, you must not read, use, >> copy >> > > or disseminate the information contained in this message and must >> > > delete it. Please advise us >> > > immediately if you are not the named addresses or the person >> > > responsible for delivering the message to the named addressee. >> > > >> > > Although Cardiff University believes this e-mail and any >> attachments >> > > are free of any virus or defect which may affect a computer, >> it is >> > > the responsibility of the recipient >> > > to ensure that it is virus free. Cardiff university will not >> accept >> > > any liability for any loss or damage arising in any way from its >> > > use. >> >

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