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

Re: [mg-rast] Problems viewing my metagenomes
by Jared Wilkening 04 Apr '11

04 Apr '11

Nicolas, On a bit closer examination we noticed this is a bug in the browse page. We should have this fixed shortly. Cheers, Jared Wilkening - for the MG-RAST development team On Mon, Apr 4, 2011 at 2:19 PM, <nicorascovan(a)soilgene.net> wrote: > Hi, > > I am having problems viewing shared private metagenomes. There are some > metagenomes that were uploaded by someone else from my group and they were > shared with me in the previous version of MG RAST, now it looks like they > are still shared (it says that there are 6 shared metagenomes) but inside > there are no links. I wonder what the problem could be. > > Thanks, > > Nicolas Rascovan >

1 0

Problems viewing my metagenomes
by nicorascovan＠soilgene.net 04 Apr '11

04 Apr '11

Hi, I am having problems viewing shared private metagenomes. There are some metagenomes that were uploaded by someone else from my group and they were shared with me in the previous version of MG RAST, now it looks like they are still shared (it says that there are 6 shared metagenomes) but inside there are no links. I wonder what the problem could be. Thanks, Nicolas Rascovan

1 0

Re: [mg-rast] progress of uploads...
by Mark D'Souza 04 Apr '11

04 Apr '11

Hi, After logging in, click on the globe icon (browse metagenomes), there is a table labelled 'Your Data Summary' in the top left corner of the next page, clicking on the number listed for 'In Progress' will display the jobs you own which are being processed, they are both queued for similarity calculation. ----- Original Message ----- > From: "mark alston (TGAC)" <mark.alston(a)BBSRC.AC.UK> > To: mg-rast(a)mcs.anl.gov > Sent: Monday, April 4, 2011 8:37:48 AM > Subject: [mg-rast] progress of uploads... > Hi, > > How do I check on the progress of my uploads in MG-RAST v3? > > Thanks. > > > > Best wishes, > > Mark > > > > ################################################ > > Dr Mark Alston, > > Computational Biologist, > > The Genome Analysis Centre, > > Norwich Research Park, > > Norwich, NR4 7UH, UK. > > > > tel +44 (0)1603 450910 > > e-mail mark.alston(a)bbsrc.ac.uk > > web http://www.tgac.bbsrc.ac.uk > > ################################################ -- 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

1 0

Re: [mg-rast] Problem with submitted datasets. Requesting help.
by Mark D'Souza 04 Apr '11

04 Apr '11

Erika, The problem is not with the processing capacity of the system, the V3 system is designed to handle extremely large data sets of the order of Gbp in size and is having trouble with your jobs due to their small size. Could you let us know why you selected to use MG-RAST V3 for your analysis? You could get better results by submitting the sequences to the BLAST server at NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi) which would give a quick accurate results for single sequences. I apologize for not being able to help you out more, the V3 system was designed with large datasets in mind and is really not the correct tool for single or a few small sequences. If it would be of any use, if you concatenate all your sequence files and submit the resulting file to MG-RAST we should be able to push that through quickly. Let us know if you would like to try this option. ----- Original Message ----- > From: "Erica Yashiro" <yashiro(a)wisc.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Monday, April 4, 2011 9:54:48 AM > Subject: [mg-rast] Problem with submitted datasets. Requesting help. > Dear MG-RAST, > > > > I apologize in advance to ask this question. From a previous email, I > understand that you are currently rerunning your older datasets from > v2 through your v3 system and that your server must be running at max > capacity. > > I’m in a situation where I need to defend my phd thesis at the end of > this month, and I’m in dire need of the results that I submitted to > your server over the course of the last 3 weeks. My datasets in > themselves are not very large since I did sanger sequencing. May I ask > if it would be possible for me to obtain analyzable results from my 22 > files sometime in the next week or so? > > > > Thank you very much for your help. > > > > Sincerely, Erika. > > > > ---------------------------------------------- > > Erika Yashiro > > Graduate Research Assistant > > University of Wisconsin - Madison > > Department of Plant Pathology > > 1630 Linden Drive > > 380 Russell Laboratories > > Madison , WI 53706 > > cell: 607-227-4724 > > lab: 608-263-2093 > > email: yashiro(a)wisc.edu > > ---------------------------------------------- -- 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

1 0

Annotated data download?
by Jon Sanders 04 Apr '11

04 Apr '11

Hey MG-RAST team, Really excited by V3. I would like to download the read-indexed relational annotation data that is used to generate the neat bar charts, functional classification tables, and KEGG pathways, so I can include them as tables in our lab's local database and use them for subsequent statistical analysis and reference. Is this possible in the current release? Or is this the "global data download" that's still under development? If so, any idea when it might be made available? Much appreciated, Jon Sanders PhD Candidate Girguis Lab, Harvard University -- "If you hold a cat by the tail you learn things you cannot learn any other way." --Mark Twain

1 0

Problem with submitted datasets. Requesting help.
by Erica Yashiro 04 Apr '11

04 Apr '11

Dear MG-RAST, I apologize in advance to ask this question. From a previous email, I understand that you are currently rerunning your older datasets from v2 through your v3 system and that your server must be running at max capacity. I'm in a situation where I need to defend my phd thesis at the end of this month, and I'm in dire need of the results that I submitted to your server over the course of the last 3 weeks. My datasets in themselves are not very large since I did sanger sequencing. May I ask if it would be possible for me to obtain analyzable results from my 22 files sometime in the next week or so? Thank you very much for your help. Sincerely, Erika. ---------------------------------------------- Erika Yashiro Graduate Research Assistant University of Wisconsin - Madison Department of Plant Pathology 1630 Linden Drive 380 Russell Laboratories Madison, WI 53706 cell: 607-227-4724 lab: 608-263-2093 email: yashiro(a)wisc.edu ----------------------------------------------

1 0

progress of uploads...
by mark alston (TGAC) 04 Apr '11

04 Apr '11

Hi, How do I check on the progress of my uploads in MG-RAST v3? Thanks. Best wishes, Mark ################################################ Dr Mark Alston, Computational Biologist, The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK. tel +44 (0)1603 450910 e-mail mark.alston(a)bbsrc.ac.uk<mailto:[email protected]> web http://www.tgac.bbsrc.ac.uk<http://www.tgac.bbsrc.ac.uk/> ################################################

1 0

Re: [mg-rast] The bug at KEGG map on MG-RAST
by Tobias Paczian 04 Apr '11

04 Apr '11

Hm, not a bad idea, but no bug. Should I investigate what it would take to display that info? Cheers Tobi On Apr 1, 2011, at 1:52 PM, Chih-Ying Lay wrote: > > Dear Sir/Madame: > > How are you? Thank you for providing the new version of MG-RAST, > which is really beautiful. However, there is probably a bug on the > function of KEGG map. When I use the KEGG map to show which enzymes > I have from my metagenome in the map, the highlightened boxes just > show how many hits in my data, but don't show what are them. I > assume if I click on the box, a window containing all the hits > would jump out, but the window jumping out is just the reference of > that enzyme. > > Could you take a look of this function? It will be very helpful for > the research! > > Thank you very much! > > Have a nice weekend. > > Chih-Ying Lay

1 0

Re: [mg-rast] error message
by Jared Wilkening 02 Apr '11

02 Apr '11

Aline, That will not be necessary. They are likely in that state due to a few transient problems we have been working through with the new system. We'll give them kick and they should be available to you shortly. Cheers, Jared Wilkening - for the MG-RAST Development Team On Sat, Apr 2, 2011 at 5:22 PM, Aline Maria da Silva <almsilva(a)iq.usp.br>wrote: > Hi, > > I have uploaded 2 ssf files (zipped). The initial processing went well but > now their status are “ Finalizing Data: Error”. What that means? > > Should I upload those files again? > > Regards, > > Aline da Silva > > >

1 0

error message
by Aline Maria da Silva 02 Apr '11

02 Apr '11

Hi, I have uploaded 2 ssf files (zipped). The initial processing went well but now their status are " Finalizing Data: Error". What that means? Should I upload those files again? Regards, Aline da Silva

1 0