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

Re: [mg-rast] metagenome analysis/organism classification/barchart option does not work 06042011
by Mark D'Souza 06 Apr '11

06 Apr '11

Hi, We are looking into this, thanks for letting us know about the problem. ----- Original Message ----- > From: "Vladimir Sentchilo" <vladimir.sentchilo(a)unil.ch> > To: mg-rast(a)mcs.anl.gov > Sent: Wednesday, April 6, 2011 8:51:49 AM > Subject: [mg-rast] metagenome analysis/organism classification/barchart option does not work 06042011 > Hello MGRAST team > Thank you for great server... > Today there are some problems with barchart drawing option. > In fact, chart has no bars and also clicking on classification > categories return false unfolding, for example click on Bacteria > returns > Archea group unfolded. > > Best regards -- 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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dataset not moving?
by Scot E Dowd PhD 06 Apr '11

06 Apr '11

Hiya Guys, Submitted a few datasets yesterday. Not sure if there is a problem but the page indicated 10 minutes to process but it is about 18hrs later and still same stage. I have refreshed the page as of this morning and I am using Firefox ;-) username is scotedowd Scot E Dowd PhD Director Research and Testing Laboratory 4321 Marsha Sharp Fwy Lubbock, TX 79407 806-789-6879 sdowd(a)pathogenresearch.org Confidentiality. This electronic transmission is strictly confidential to the sender and intended solely for the addressee. It may contain information which is covered by legal, professional or other privilege. If you are not the intended addressee, or someone authorized by the intended addressee to receive transmissions on behalf of the addressee, you must not retain, disclose in any form, copy or take any action in reliance on this transmission. If you have received this transmission in error, please notify the sender as soon as possible and destroy this message. Research and Testing Laboratory reserves the right to amend statements made herein in the event of a mistake.

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Re: [mg-rast] individual hit annotation
by Mark D'Souza 06 Apr '11

06 Apr '11

Hi, I'm afraid this download is not currently available through version 3 of MG-RAST. We are working on adding the capability and should have it in place in a couple of weeks. Thanks for the feedback. ----- Original Message ----- > From: "Blair Paul" <bgp.marine(a)gmail.com> > To: "mg-rast" <mg-rast(a)mcs.anl.gov> > Sent: Tuesday, April 5, 2011 6:38:22 PM > Subject: [mg-rast] individual hit annotation > To whom this concerns, > > I've been working with mg-rast v3 lately to annotate a few > metagenomes. In doing so, I've noticed some key outputs that were > offered in v2 are missing from v3. Specifically, I'm trying to view > the individual hits (eg. which contigs hit to certain > functions/proteins or to organisms), what those individual > e-values/%identity, and where on my fragment (query start/end) the hit > is located. I was able to look at those details through version 2, > but have found no output through the 'generate' feature (metagenome > analysis), or from any downloadable files offered. If you know of any > solutions that are available through version 3, or plan to update with > those items included (hit id, query location/hit length, scores etc.), > please let me know. > > best, > -Blair Paul > > -- > PhD Candidate, Marine Science > Valentine Lab, UC Santa Barbara > 1006 Webb Hall, Santa Barbara, CA 93106 > 805.893.3036

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metagenome analysis/organism classification/barchart option does not work 06042011
by Vladimir Sentchilo 06 Apr '11

06 Apr '11

Hello MGRAST team Thank you for great server... Today there are some problems with barchart drawing option. In fact, chart has no bars and also clicking on classification categories return false unfolding, for example click on Bacteria returns Archea group unfolded. Best regards

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Re: [mg-rast] MGRAST - new account requested for Udall lab
by Joshua Udall 06 Apr '11

06 Apr '11

Maren - I have you in my group 2x. Try now. I just shared the data with you. I've found that this doesn't happen automatically. On Apr 5, 2011, at 10:54 PM, mg-rast(a)mcs.anl.gov<mailto:[email protected]> wrote: marenj2(a)gmail.com<mailto:[email protected]>

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individual hit annotation
by Blair Paul 05 Apr '11

05 Apr '11

To whom this concerns, I've been working with mg-rast v3 lately to annotate a few metagenomes. In doing so, I've noticed some key outputs that were offered in v2 are missing from v3. Specifically, I'm trying to view the individual hits (eg. which contigs hit to certain functions/proteins or to organisms), what those individual e-values/%identity, and where on my fragment (query start/end) the hit is located. I was able to look at those details through version 2, but have found no output through the 'generate' feature (metagenome analysis), or from any downloadable files offered. If you know of any solutions that are available through version 3, or plan to update with those items included (hit id, query location/hit length, scores etc.), please let me know. best, -Blair Paul -- PhD Candidate, Marine Science Valentine Lab, UC Santa Barbara 1006 Webb Hall, Santa Barbara, CA 93106 805.893.3036

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Re: [mg-rast] question about MG-RAST 3
by Jared Wilkening 05 Apr '11

05 Apr '11

Marcio, You are right there is something a little bit odd about these jobs. >From the website I do see that that the protein search came up with about just as many hits as the rna search ( http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeOverview&metage…) Is this amplicon or shotgun metagenomic data? The other odd thing is later run through the system (4454965.3) only 2104 sequences passed the quality filtering. Which actually lines up nicely with the combine number of hits found between protein and rna. Potentially this could be a sequence quality issue? I'm having trouble logging into our system from home tonight so I can't get at any more details than that but I will take closer look tomorrow. A side note, in the future if you could address emails to mg-rast(a)mcs.anl.gov we would appreciate it. This will make sure you get an answer quickly in case one of us it on vacation or unavailable. Cheers, Jared On Tue, Apr 5, 2011 at 5:00 PM, Marcio Costa <costam(a)uoguelph.ca> wrote: > Dear Jared, > > I have a question about a metagenomic study of the bacterial 16S r-RNA that > we had uploaded (4454965.3) on MG-RAST. This job just became available to me > on the new version, however, despite been showed that it had 17,593 > sequences analyzed on the browse metagenomes page, it gives only around 1000 > reads on the metagenome analysis page. In addition, when I compare the > results with the previous version of MG-RAST, they are completely different, > even using the same dataset (RDP). This same file has been uploaded in the > new version (4459773.3), but even less sequences are showed (around 600). > > The same issue has happened with several other files we had previously > loaded. > > Please let me know your thoughts. > > Thank you, > > Marcio. > >

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

05 Apr '11

Cristiane, I just checked on your jobs and now see both rna and protein data for you jobs. Cheers, Jared On Tue, Apr 5, 2011 at 9:42 AM, Cristiane Thompson <thompson(a)ioc.fiocruz.br>wrote: > Dear Jared Wilkening, > thanks. > > Cristiane Thompson, PhD > Laboratory of Molecular Genetics of Microrganisms > Oswaldo Cruz Institute (IOC) - Oswaldo Cruz Fundation (FIOCRUZ) > Rio de Janeiro, RJ, Brazil > > Phone no.: + 55 21 38658168 (Lab) > Fax no.: + 55 21 22604282 > E-mail:[email protected] > > > > 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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Re: [mg-rast] Problems viewing my metagenomes
by Nicolás Rascovan 05 Apr '11

05 Apr '11

Excelent, it's working fine now! Thanks Jared, Best, Nicolas. El 5 de abril de 2011 18:56, Jared Wilkening <jared(a)mcs.anl.gov> escribió: > Nicolas, > > Should be fixed. Could you take a look? > > Cheers, > Jared > > 2011/4/4 Nicolás Rascovan <nicorascovan(a)soilgene.net> > >> Excelent, >> >> Thanks a lot. >> >> Nicolas. >> >> >> 2011/4/4 Jared Wilkening <jared.wilkening(a)gmail.com> >> >>> 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 >>>> >>> >>> >> >

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Re: [mg-rast] Problems viewing my metagenomes
by Jared Wilkening 05 Apr '11

05 Apr '11

Nicolas, Should be fixed. Could you take a look? Cheers, Jared 2011/4/4 Nicolás Rascovan <nicorascovan(a)soilgene.net> > Excelent, > > Thanks a lot. > > Nicolas. > > > 2011/4/4 Jared Wilkening <jared.wilkening(a)gmail.com> > >> 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 >>> >> >> >

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