June 2010 - Mg-rast - mailman3.cels.anl.gov

Your MG-RAST job (9128)
by dsouza＠mcs.anl.gov 30 Jun '10

30 Jun '10

Hi, The job you submitted to MG_RAST failed as the space between the '>' character and the sequence ID on the identifier line was not accepted by our fasta checker. I removed the spaces and restarted the job, it should proceed normally, You do not need to take any action. -- 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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Your Mg-RAST jobs (9087, 9088, 9089, 9090)
by dsouza＠mcs.anl.gov 29 Jun '10

29 Jun '10

Hi, The jobs you submitted to MG-RAST failed as the sequence filenames do not have an extension, e.g. '.fasta'. I added this on and restarted the jobs, they should proceed normally, you do not need to take any action. Please add the extension to the filename for future submissions. -- 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] Help on sequences affiliation
by Mark D'Souza 29 Jun '10

29 Jun '10

Hi Fernando, I took a look at the list o jobs under your name and all of them are listed as 'complete'. Please send me the job number or ID for the job you are having trouble with and I will look into this. -- 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 ----- "Fernando Dini Andreote" <fdandreo(a)gmail.com> wrote: > From: "Fernando Dini Andreote" <fdandreo(a)gmail.com> > To: mg-rast(a)mcs.anl.gov > Sent: Tuesday, June 29, 2010 9:40:18 AM GMT -06:00 US/Canada Central > Subject: [mg-rast] Help on sequences affiliation > > Dear colleagues from MG-RAST. > > > > I must say that your website is amazingly useful. > > > > However, in the list of jobs, I have always my metagenomic libraries > with one missing job, entitled: ‘ SEED organism directory creation has > not yet started’. > > > > As a consequence, I cannot see the gene numbers in metabolic routes > allocated. > > > > Can you help me to solve it? > > > > Hope to have this support from you, > > > > My best regards, > > > > Fernando D Andreote > > USP, Brazil > > ____________________________________ > > Fernando Dini Andreote > > Prof. Dr. em Microbiologia do Solo > > Escola Superior de Agricultura "Luiz de Queiroz" > > Universidade de São Paulo > > Departamento de Ciência do Solo > > Avenida Pádua Dias, 11 - Cx. Postal 9 > > Piracicaba, SP, CEP 13418-900 > > Fone: 19 3417-2123 > > ____________________________________

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Help on sequences affiliation
by Fernando Dini Andreote 29 Jun '10

29 Jun '10

Dear colleagues from MG-RAST. I must say that your website is amazingly useful. However, in the list of jobs, I have always my metagenomic libraries with one missing job, entitled: SEED organism directory creation has not yet started. As a consequence, I cannot see the gene numbers in metabolic routes allocated. Can you help me to solve it? Hope to have this support from you, My best regards, Fernando D Andreote USP, Brazil ____________________________________ Fernando Dini Andreote Prof. Dr. em Microbiologia do Solo Escola Superior de Agricultura "Luiz de Queiroz" Universidade de São Paulo Departamento de Ciência do Solo Avenida Pádua Dias, 11 - Cx. Postal 9 Piracicaba, SP, CEP 13418-900 Fone: 19 3417-2123 ____________________________________

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Re: [mg-rast] Question regarding MG-RAST
by Folker Meyer 28 Jun '10

28 Jun '10

Dear Dagmar, we will update the underlying sequence database with v3 of mg-rast in the next few weeks. Since we use the underlying database to enable comparison it is not as simple as just adding a genome or two, we need to update all similarities for compariso in v2 --> a major hassle. V3 will support that in much smarter ways Best, Folker On Jun 28, 2010, at 7:02 PM, Dagmar Woebken wrote: > Dear Folker, > > We have uploaded our sequences to MG-RAST and they have already been analyzed. The samples our metatranscriptomes were generated from are dominated by the cyanobacterium Microcoleus chthonoplastes. By looking at our data in MG-RAST we have noticed that the SEED database currently does not contain this genome. The Microcoleus genome has recently entered refseq. We have uploaded the data to RAST for annotation and we were wondering now whether the Microcoleus genome could be entered into the SEED database so we could annotate our metatranscriptomic data with that genome information. Would that be possible? > > Thank you very much and best regards, > Dagmar > > > > On May 6, 2010, at 3:06 PM, Folker Meyer wrote: > >> bitte >> On May 6, 2010, at 3:05 PM, Dagmar Woebken wrote: >> >>> Dear Folker, >>> >>> Thank you very much for your reply- we will proceed as you suggested. >>> >>> Best regards, >>> Dagmar >>> >>> >>> >>> On May 6, 2010, at 2:56 PM, Folker Meyer wrote: >>> >>>> Dear Dagmar, >>>> >>>> the system can most certainly be used for such a data set (and has been used several hundred times). >>>> >>>> There might be some features of the new (not yet released version 3.0) that you can benefit from. However I suggest you try using v2.0 first and then contact us again if there are more questions or specific requests. >>>> >>>> Best, >>>> Folker >>>> >>>> On May 6, 2010, at 2:29 PM, Dagmar Woebken wrote: >>>> >>>>> Dear Dr. Meyer, >>>>> >>>>> We are a group of scientists at NASA, Stanford University and the Livermore National Laboratory studying microbial mats and have recently generated two metatranscriptome data sets by 454 sequencing that we want to analyze. We would be very interested in using MG-RAST for this purpose and wanted to ask whether MG-RAST can process metatranscriptome data sets of about 150,000 and 250,000 reads (after rRNA sequence removal; read length of about 390 bp). We would very much appreciate your advice! >>>>> >>>>> Thank you very much and best regards, >>>>> Dagmar Woebken >>>>> >>>>> >>>>> ********************************************* >>>>> Dagmar Woebken, Ph.D. >>>>> Stanford University >>>>> Civil & Env. Engineering Dept. >>>>> James H. Clark Center, E250, MC 5429 >>>>> 318 Campus Drive >>>>> Stanford, CA 94305 >>>>> and >>>>> NASA Ames Research Center >>>>> Exobiology Branch >>>>> Moffett Field, CA 94035 >>>>> Phone: (650) 724-5809 >>>>> Fax: (650) 724-4927 >>>>> Email: dwoebken(a)stanford.edu >>>>> ********************************************* >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Folker Meyer >>>> folker(a)anl.gov >>>> >>>> >>>> >>>> >>> >> >> >> -- >> Folker Meyer >> folker(a)anl.gov >> >> >> >> >

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Re: [mg-rast] Your MG-RAST jobs (9003, 1_40_RL6 and 9004, 1_45_RL7)
by Mark D'Souza 28 Jun '10

28 Jun '10

Sure, RL6 is running. Mark ----- "Jesse Zaneveld" <zaneveld(a)gmail.com> wrote: > From: "Jesse Zaneveld" <zaneveld(a)gmail.com> > To: dsouza(a)mcs.anl.gov > Sent: Monday, June 28, 2010 12:46:22 PM GMT -06:00 US/Canada Central > Subject: Re: Your MG-RAST jobs (9003, 1_40_RL6 and 9004, 1_45_RL7) > > Actually I found the delete job option in your interface and removed > 1_45_RL7, so the only needed action is to start 1_40_RL6 again. > > > Thanks, > Jesse > > > On Thu, Jun 24, 2010 at 1:37 PM, < dsouza(a)mcs.anl.gov > wrote: > > > Hi, > > The two MG-RAST jobs which you submitted recently (9003, 1_40_RL6 and > 9004, 1_45_RL7) have identical sequence files. Please let me know > which one you would like to proceed and I will delete the other, in > the meantime I am putting a hold on both 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

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Your MG-RAST jobs (9044, 9046, 9067)
by Mark D'Souza 28 Jun '10

28 Jun '10

Hi, The jobs you submitted to MG-RAST have been failing as the system requires the sequence file to have an extension (like .fasta). You latest job is progressing normally. -- 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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Your Mg-RAST jobs (9063, 9064, 9065)
by dsouza＠mcs.anl.gov 28 Jun '10

28 Jun '10

Hi, The jobs you submitted to MG-RAST (9063 and 9064) have identical sequence files and seem to be copies of each other. I am going to let 9063 proceed and will delete 9064 unless I hear from you in a day. 9065 will continue as it has different options selected. -- 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] kegg map problem
by Folker Meyer 25 Jun '10

25 Jun '10

We will look into it. -- Sent from mobile device On Jun 25, 2010, at 7:01 PM, Thiago Bruce <thbruce(a)gmail.com> wrote: > hi > my kegg map tool doesnt works happening since my registration (i have already send e- mail) and nothing was done about it. i would like to know whats the problem. > > thanks > > -- > Thiago Bruce MSc. > Phd student > Federal University of Rio de Janeiro > Center of Health Sciences > Biology Institute > Genetics Dept > Lab A2-83 > Phones: +55 +21 2562-6567/+55 +21 7685-1346 >

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kegg map problem
by Thiago Bruce 25 Jun '10

25 Jun '10

hi my kegg map tool doesnt works happening since my registration (i have already send e- mail) and nothing was done about it. i would like to know whats the problem. thanks -- Thiago Bruce MSc. Phd student Federal University of Rio de Janeiro Center of Health Sciences Biology Institute Genetics Dept Lab A2-83 Phones: +55 +21 2562-6567/+55 +21 7685-1346

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