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

problem with the data upload
by Mariya Smit 20 Apr '11

20 Apr '11

Hello, I've tried to upload two metagenomes as zipped sff files. The initial stages seems to be OK, then the system let me know that my input was required, but it did not allow me to access my submission, and since then I could not get a working 'Upload' window (when I open it, it looks empty with all buttons disabled. I am wondering whether there was a problem with the metagenome upload causing all this stalling? My user name is mariyasmit. Thanks a lot, Mariya Mariya Smit, PhD Senior Research Associate Oregon Health & Science University OGI School of Science & Engineering Environmental & Biomolecular Systems 20000 NW Walker Rd. Beaverton, OR 97006 Work (503)-748-2205 Cell (425)-923-6433 Fax: 503-748-1273 Email: smitm(a)ebs.ogi.edu mariyasmit(a)hotmail.com

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Re: [mg-rast] Fwd: Metagenomes
by Folker Meyer 20 Apr '11

20 Apr '11

Tobi: I have given up on names. users will never learn. lets leave it to nikos to fight them on naming. On Apr 20, 2011, at 10:22 AM, Tobias Paczian wrote: > Should we allow renaming of the Metagenomes to the owner? It would not be hard to do and the name is not used as a standalone reference anywhere, so it would probably not hurt. > > At that place we could also propagate a good naming convention, so the name is not too long and still meaningful. > > Cheers > Tobi > > On Apr 19, 2011, at 1:13 PM, Folker Meyer wrote: > >> >> >> Begin forwarded message: >> >>> From: Ana P Barbosa Moreira <apbmoreira(a)gmail.com> >>> Date: April 19, 2011 1:51:03 PM EDT >>> To: Folker Meyer_MG-Rast <folker(a)anl.gov> >>> Subject: Metagenomes >>> >>> Dear Folker Meyer >>> >>> I have some doughts about my metagenomes: >>> >>> IDs: 4461594.3 and 4461593.3. >>> >>> 1- May I rename them? >>> 2- I cannot see the Rank abundance plot that you say should be The plot below this title; >>> 3- Will the Sequence length histogram and Sequence GC Distribution be available soon? My metagenomes were available yesterday. >>> >>> Best regards >>> -- >>> Ana Paula B. Moreira MSc. >>> DSc. Student >>> >>> Federal University of Rio de Janeiro >>> Center of Health Sciences >>> Biology Institute >>> Microbiol Lab - Mar Biol Dept >>> Block A - Annexe >>> Phones: +55 +21 2562-6567/+55 +21 9942-5193 >>> Fax: +55 +21 2259-0753 >>> E-mails: anapaulabm(a)biologia.ufrj.br / apbmoreira(a)gmail.com >>> Skype: anapaulabmoreira >>> >> >

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Fwd: Identical table entries in Functional Classification
by Mark D'Souza 20 Apr '11

20 Apr '11

Begin forwarded message: > From: "Matthew T. Cottrell" <mattcott(a)udel.edu> > Date: April 20, 2011 12:10:48 PM CDT > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Subject: Re: [mg-rast] Identical table entries in Functional Classification > > Mark, > > Thanks for looking into this table glitch. Glad to know that the underlying results are correct. > > Matt > > > On Apr 20, 2011, at 12:45 PM, Mark D'Souza wrote: > >> Hi Matt, >> >> Actually the data is accurate, the same function is found in two different subsystems. The display however is incorrect, for some reason the level 3 column containing two different subsystem names was not displayed. >> >> We are investigating and will fix the code with the next update, thanks for letting us know about the problem. >> >> Regards, >> Mark >> >> >> >> On Apr 20, 2011, at 8:31 AM, Matthew T. Cottrell wrote: >> >>> Folks at MG-RAST, >>> >>> What is the interpretation of duplicate table entries in a Functional Classification report? Downloading the sequences shown in the attached screen shot yields identical FASTA files. Is this a bug or a feature? >>> >>> Thanks, >>> Matt >>> >>> >>> <Duplicate Table Entries.pdf> >>> . . . . . . . . . . . . . . . . . . . . . . . _/) >>> Matthew T. Cottrell, Ph. D. >>> Associate Scientist >>> University of Delaware >>> School of Marine Science and Policy >>> 700 Pilottown Rd. >>> Lewes, DE 19958 >>> >>> 302 645-4383 (office); 302 430-3489 (mobile); 302 645-4007 (fax) >>> http://www.ceoe.udel.edu/people/mattcott >>> >>> >>> >>> >> > > . . . . . . . . . . . . . . . . . . . . . . . _/) > Matthew T. Cottrell, Ph. D. > Associate Scientist > University of Delaware > School of Marine Science and Policy > 700 Pilottown Rd. > Lewes, DE 19958 > > 302 645-4383 (office); 302 430-3489 (mobile); 302 645-4007 (fax) > http://www.ceoe.udel.edu/people/mattcott > > > >

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Re: [mg-rast] Questions_support
by Mark D'Souza 20 Apr '11

20 Apr '11

No problem, I made the changes. Thanks and Happy Easter to you too. Mark On Apr 20, 2011, at 11:48 AM, Ana Paula B. Moreira wrote: > Hi Mark, > > Thanks for the promptness! > > The Changes I need right now are: > > Metagenome AnaPaula_PE1 (4461594.3) should be renamed AnaPaula_PE14-1, and > > Metagenome AnaPaulaPE_1 (4461593.3) should be renamed AnaPaula_PE22-1. > > Best regards > > Happy Easter > > > 2011/4/20 Mark D'Souza <dsouza(a)mcs.anl.gov> > Hi, > > renaming -- this is not possible right now, but we will be adding this capability as it is clearly needed, if you let me know the changes I can do this for you. > rank abundance and histograms -- we are working on this and will make it available with the next code update, should be within a week. > > Thanks for letting us know about these issues. > > 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 Apr 20, 2011, at 8:49 AM, Ana P Barbosa Moreira wrote: > > > Dear MG-Rast Team > > > > I have some doughts about my metagenomes: > > > > IDs: 4461594.3 and 4461593.3. > > > > 1- May I rename them? > > 2- I cannot see the Rank abundance plot that you say should be The plot below this title; > > 3- Will the Sequence length histogram and Sequence GC Distribution be available soon? My metagenomes were available yesterday. > > > > Best regards > > > > -- > > Ana Paula B. Moreira MSc. > > DSc. Student > > > > Federal University of Rio de Janeiro > > Center of Health Sciences > > Biology Institute > > Microbiol Lab - Mar Biol Dept > > Block A - Annexe > > Phones: +55 +21 2562-6567/+55 +21 9942-5193 > > Fax: +55 +21 2259-0753 > > E-mails: anapaulabm(a)biologia.ufrj.br / apbmoreira(a)gmail.com > > Skype: anapaulabmoreira > > > > > > > -- > Ana Paula B. Moreira MSc. > DSc. Student > > Federal University of Rio de Janeiro > Center of Health Sciences > Biology Institute > Microbiol Lab - BIOMAR > Block A - Annexe (A3) - room 102 > Phones: +55 +21 2562-6567/+55 +21 9942-5193 > Fax: +55 +21 2259-0753 > E-mails: anapaulabm(a)biologia.ufrj.br / apbmoreira(a)gmail.com > Skype: anapaulabmoreira >

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Fwd: Questions_support
by Mark D'Souza 20 Apr '11

20 Apr '11

Begin forwarded message: > From: "Ana Paula B. Moreira" <anapaulabm(a)biologia.ufrj.br> > Date: April 20, 2011 11:48:20 AM CDT > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Subject: Re: [mg-rast] Questions_support > > Hi Mark, > > Thanks for the promptness! > > The Changes I need right now are: > > Metagenome AnaPaula_PE1 (4461594.3) should be renamed AnaPaula_PE14-1, and > > Metagenome AnaPaulaPE_1 (4461593.3) should be renamed AnaPaula_PE22-1. > > Best regards > > Happy Easter > > > 2011/4/20 Mark D'Souza <dsouza(a)mcs.anl.gov> > Hi, > > renaming -- this is not possible right now, but we will be adding this capability as it is clearly needed, if you let me know the changes I can do this for you. > rank abundance and histograms -- we are working on this and will make it available with the next code update, should be within a week. > > Thanks for letting us know about these issues. > > 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 Apr 20, 2011, at 8:49 AM, Ana P Barbosa Moreira wrote: > > > Dear MG-Rast Team > > > > I have some doughts about my metagenomes: > > > > IDs: 4461594.3 and 4461593.3. > > > > 1- May I rename them? > > 2- I cannot see the Rank abundance plot that you say should be The plot below this title; > > 3- Will the Sequence length histogram and Sequence GC Distribution be available soon? My metagenomes were available yesterday. > > > > Best regards > > > > -- > > Ana Paula B. Moreira MSc. > > DSc. Student > > > > Federal University of Rio de Janeiro > > Center of Health Sciences > > Biology Institute > > Microbiol Lab - Mar Biol Dept > > Block A - Annexe > > Phones: +55 +21 2562-6567/+55 +21 9942-5193 > > Fax: +55 +21 2259-0753 > > E-mails: anapaulabm(a)biologia.ufrj.br / apbmoreira(a)gmail.com > > Skype: anapaulabmoreira > > > > > > > -- > Ana Paula B. Moreira MSc. > DSc. Student > > Federal University of Rio de Janeiro > Center of Health Sciences > Biology Institute > Microbiol Lab - BIOMAR > Block A - Annexe (A3) - room 102 > Phones: +55 +21 2562-6567/+55 +21 9942-5193 > Fax: +55 +21 2259-0753 > E-mails: anapaulabm(a)biologia.ufrj.br / apbmoreira(a)gmail.com > Skype: anapaulabmoreira >

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Fwd: Problems with MG RAST CLOUD
by Mark D'Souza 20 Apr '11

20 Apr '11

Begin forwarded message: > From: "Delmont Tom" <Tom.Delmont(a)ec-lyon.fr> > Date: April 20, 2011 2:40:06 AM CDT > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Subject: Re: [mg-rast] Problems with MG RAST CLOUD > > Hi Mark, > > thank you for looking at the solexa runs... > > For the names of metagenomes / projects, I can wait , no problems > > best > > Tom Delmont, PhD student > Environmental Microbial Genomics Group > Laboratoire AMPERE > Ecole Centrale de Lyon > 36 avenue Guy de Collongue > 69134 ECULLY > Tel: 33 (0)4 72 18 61 17 > ----- Original Message ----- From: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > To: "Delmont Tom" <Tom.Delmont(a)ec-lyon.fr> > Cc: <mg-rast(a)mcs.anl.gov> > Sent: Tuesday, April 19, 2011 6:30 PM > Subject: Re: [mg-rast] Problems with MG RAST CLOUD > > > Hi Tom, > > The recruitment plot is available to map metagenomes to sequenced genomes -- on the analysis page, it is one of the options in the 'Analysis Views' table. > > > > > -------------------------------------------------------------------------------- > > > > > The jobs which have not completed seem to be halted for some reason, I will check what is going on with them and get them restarted. > > Changing the names of metagenomes/projects is clearly something which is desirable, but is not possible through the web interface at this time. We will be adding it in the future, let me know if you have some changes to make right now and I can take care of them. > > 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 Apr 19, 2011, at 6:46 AM, Delmont Tom wrote: > >> Hi, >> >> I have several problems witht the new version: >> >> 1/ can we still map metagenomes to already sequenced genomes (I don't find the way)? >> 2/ can you really annotate solexa sequences (all my pyrosequences were annotated quickly, but the solexa runs are not...)? >> 4/Can we change the name of projects / metagenomes before making them public (to help scientists understand what a metagenome is but also to help my own analysis)? >> >> best >> >> tom >> >> Tom Delmont, PhD student >> Environmental Microbial Genomics Group >> Laboratoire AMPERE >> Ecole Centrale de Lyon >> 36 avenue Guy de Collongue >> 69134 ECULLY >> Tel: 33 (0)4 72 18 61 17 > > >

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Re: [mg-rast] Fwd: Metagenomes
by Mark D'Souza 20 Apr '11

20 Apr '11

Hi, I think we should make this possible. A number of users have asked for this. It appears that some put in a crappy working name on submission and then want to rename it when they make the data public. Mark On Apr 20, 2011, at 3:22 AM, Tobias Paczian wrote: > Should we allow renaming of the Metagenomes to the owner? It would not be hard to do and the name is not used as a standalone reference anywhere, so it would probably not hurt. > > At that place we could also propagate a good naming convention, so the name is not too long and still meaningful. > > Cheers > Tobi > > On Apr 19, 2011, at 1:13 PM, Folker Meyer wrote: > >> >> >> Begin forwarded message: >> >>> From: Ana P Barbosa Moreira <apbmoreira(a)gmail.com> >>> Date: April 19, 2011 1:51:03 PM EDT >>> To: Folker Meyer_MG-Rast <folker(a)anl.gov> >>> Subject: Metagenomes >>> >>> Dear Folker Meyer >>> >>> I have some doughts about my metagenomes: >>> >>> IDs: 4461594.3 and 4461593.3. >>> >>> 1- May I rename them? >>> 2- I cannot see the Rank abundance plot that you say should be The plot below this title; >>> 3- Will the Sequence length histogram and Sequence GC Distribution be available soon? My metagenomes were available yesterday. >>> >>> Best regards >>> -- >>> Ana Paula B. Moreira MSc. >>> DSc. Student >>> >>> Federal University of Rio de Janeiro >>> Center of Health Sciences >>> Biology Institute >>> Microbiol Lab - Mar Biol Dept >>> Block A - Annexe >>> Phones: +55 +21 2562-6567/+55 +21 9942-5193 >>> Fax: +55 +21 2259-0753 >>> E-mails: anapaulabm(a)biologia.ufrj.br / apbmoreira(a)gmail.com >>> Skype: anapaulabmoreira >>> >> >

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Re: [mg-rast] Identical table entries in Functional Classification
by Mark D'Souza 20 Apr '11

20 Apr '11

Hi Matt, Actually the data is accurate, the same function is found in two different subsystems. The display however is incorrect, for some reason the level 3 column containing two different subsystem names was not displayed. We are investigating and will fix the code with the next update, thanks for letting us know about the problem. Regards, Mark On Apr 20, 2011, at 8:31 AM, Matthew T. Cottrell wrote: > Folks at MG-RAST, > > What is the interpretation of duplicate table entries in a Functional Classification report? Downloading the sequences shown in the attached screen shot yields identical FASTA files. Is this a bug or a feature? > > Thanks, > Matt > > > <Duplicate Table Entries.pdf> > . . . . . . . . . . . . . . . . . . . . . . . _/) > Matthew T. Cottrell, Ph. D. > Associate Scientist > University of Delaware > School of Marine Science and Policy > 700 Pilottown Rd. > Lewes, DE 19958 > > 302 645-4383 (office); 302 430-3489 (mobile); 302 645-4007 (fax) > http://www.ceoe.udel.edu/people/mattcott > > > >

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Re: [mg-rast] Questions_support
by Mark D'Souza 20 Apr '11

20 Apr '11

Hi, renaming -- this is not possible right now, but we will be adding this capability as it is clearly needed, if you let me know the changes I can do this for you. rank abundance and histograms -- we are working on this and will make it available with the next code update, should be within a week. Thanks for letting us know about these issues. 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 Apr 20, 2011, at 8:49 AM, Ana P Barbosa Moreira wrote: > Dear MG-Rast Team > > I have some doughts about my metagenomes: > > IDs: 4461594.3 and 4461593.3. > > 1- May I rename them? > 2- I cannot see the Rank abundance plot that you say should be The plot below this title; > 3- Will the Sequence length histogram and Sequence GC Distribution be available soon? My metagenomes were available yesterday. > > Best regards > > -- > Ana Paula B. Moreira MSc. > DSc. Student > > Federal University of Rio de Janeiro > Center of Health Sciences > Biology Institute > Microbiol Lab - Mar Biol Dept > Block A - Annexe > Phones: +55 +21 2562-6567/+55 +21 9942-5193 > Fax: +55 +21 2259-0753 > E-mails: anapaulabm(a)biologia.ufrj.br / apbmoreira(a)gmail.com > Skype: anapaulabmoreira >

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Re: [mg-rast] login trouble
by Mark D'Souza 20 Apr '11

20 Apr '11

Hi, I changed your password to 'changethis' and verified that it works correctly with your username, please select a new password as soon as you get this email -- after logging on, click on the icon (account management) to the right of your name to get a page where this can be done, or use this URL: http://metagenomics.anl.gov/metagenomics.cgi?page=AccountManagement 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 Apr 20, 2011, at 3:46 AM, paula.sapereira(a)inrb.pt wrote: > I am tying to login without success, can you plese show me how to do it correctly > > Dear Paula Sa Pereira, > > your account request for access to our web service MG-RAST has been accepted. > > Your login is: PaulaSaPereira > Your password is: .bSUC4V3 > > We recommend to change the password immediately. To do so please go to our web service http://metagenomics.nmpdr.org/ and change your password from the account management. > > >

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