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

different results in version 2 and 3 of MG-RAST
by Laura FANCELLO 22 Apr '11

22 Apr '11

Hi, I'm a phd student and I'm using your new version of MG-RAST on my metagenomes. Actually I realized that the same analysis performed by MG-RAST v2 And by MG-RAST v3 doesn't give the same results. I'm performing phylogenetic annotation on metagenomes 4453567.3, 4453569.3, 4453570.3 against the SEED database with an e-value<1e-05 and I noticed that the number of sequences annotated as Enterobacteriaceae or Streptococcaceae or pseudomonadaceae is absolutely not the same: for example for metagenome 4453567.3 I find 6292 enterobacteriaceae in version 2 and 90 in version 3. I wonder if it is due to an error or rather to a different way to perform the blast search or to an update/new curation of the SEED database... I know that I have a lot od beta-lactamase belonging to cloning/expression vector sequences in my metagenome and maybe these vectorial sequences are considered as bacterial in version 2 and as artificiail sequences in version 3 but this wouldn't explain the differences in the other cases (Burkholderia, Streptococcus, Staphylococcus)... Can you help me?? Thank you very much!!!! Laura -- Laura FANCELLO Universite de la Mediterranee (Aix-Marseille II) http://annuaire.univmed.fr/showuser.php?uid=fancello.l

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Re: [mg-rast] MG-RAST - new data available
by Mark D'Souza 21 Apr '11

21 Apr '11

I believe that was a v2 job and v2 email: > > Fecha: 15-02-2011 09:43 We should check the v3 messages. The nmpdr.org url is not very inspiring. Must have been sent out by mistake, Mark ----- Original Message ----- > From: "Jared Wilkening" <jared.wilkening(a)gmail.com> > To: mg-rast(a)mcs.anl.gov > Sent: Thursday, April 21, 2011 6:23:52 PM > Subject: Re: [mg-rast] MG-RAST - new data available > No sure why this user forwarded us this message without asking > anything but it brings up the point that our old links don't work > anymore. We should think about re-directing the JobDetails page to the > MetagenomeOveriew and Jobs to MetagenomeSelect. > > Jared > > On Thu, Apr 21, 2011 at 2:51 PM, mesparza(a)uantof.cl > <mesparza(a)uantof.cl> wrote: > > > > ----Mensaje original---- > > De: mg-rast(a)mcs.anl.gov > > Fecha: 15-02-2011 09:43 > > Para: <mesparza(a)uantof.cl> > > Asunto: MG-RAST - new data available > > > > Dear Mario Esparza, > > > > you have been granted access to microbial mat_Salar de Huasco > > (4454310.3) by > > Cristina Dorador on our web service MG-RAST. > > > > To directly access the new data, please follow this link: > > http://metagenomics.nmpdr.org/?page=JobDetails&job=13917. > > > > > > -- > > > > This email was automatically generated by the MG-RAST web service. > > Do not > > reply. > > > >

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Re: [mg-rast] MG-RAST - new data available
by Jared Wilkening 21 Apr '11

21 Apr '11

No sure why this user forwarded us this message without asking anything but it brings up the point that our old links don't work anymore. We should think about re-directing the JobDetails page to the MetagenomeOveriew and Jobs to MetagenomeSelect. Jared On Thu, Apr 21, 2011 at 2:51 PM, mesparza(a)uantof.cl <mesparza(a)uantof.cl> wrote: > > ----Mensaje original---- > De: mg-rast(a)mcs.anl.gov > Fecha: 15-02-2011 09:43 > Para: <mesparza(a)uantof.cl> > Asunto: MG-RAST - new data available > > Dear Mario Esparza, > > you have been granted access to microbial mat_Salar de Huasco (4454310.3) by > Cristina Dorador on our web service MG-RAST. > > To directly access the new data, please follow this link: > http://metagenomics.nmpdr.org/?page=JobDetails&job=13917. > > > -- > > This email was automatically generated by the MG-RAST web service. Do not > reply. > >

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Re: [mg-rast] question about KEGG KO numbers and COG numbers
by Mark D'Souza 21 Apr '11

21 Apr '11

Tanya, With the latest code update the tables now contain a column with the KO and COG numbers linked to the relevant websites, thanks for the suggestion. Regards, Mark On Apr 11, 2011, at 4:47 PM, Tanya Yatsunenko wrote: > Thanks Mark. I assume the same applies for COG. > > Tanya > > > On Mon, Apr 11, 2011 at 4:40 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > Hi Tanya, > > We are looking into the best way to do this. In the meantime, if you have just a few functions of interest, the function =is= unique for the KO number, which is available through a search at the KEGG site (http://www.genome.jp/kegg-bin/get_htext?ko00001.keg) > > Regards, > Mark > > > ----- Original Message ----- > > From: "Tanya Yatsunenko" <tyatsun(a)gmail.com> > > To: "Andreas Wilke" <wilke(a)mcs.anl.gov>, "Folker Meyer" <folker.meyer(a)googlemail.com>, "MG- Rast" > > <mg-rast(a)mcs.anl.gov> > > Sent: Monday, April 11, 2011 2:10:01 PM > > Subject: [mg-rast] question about KEGG KO numbers and COG numbers > > Hello MgRast team, and sorry to bug you again. > > > > > > I looked into functional assignments generated for the metagenomes and > > I can't find an assignment to specific KO numbers for KEGG annotation, > > and no COG numbers for COG annotation. > > I can only see functional annotation and sometimes EC numbers, but no > > corresponding KO numbers (I'm aware that not all KOs have EC > > assignment). > > > > > > Is there any way to get KO/COG numbers from those tables, because I'm > > not sure how unique each function name is, and also for other > > purposes? > > > > > > Thanks, > > Tanya > > > > > > > > On Sat, Apr 9, 2011 at 11:06 PM, Tanya < tyatsun(a)gmail.com > wrote: > > > > > > > > > > Hi Andreas > > > > > > I'd like to delete those I uploaded earlier. Thank you for all your > > help! > > > > Tanya. > > > > > > On Apr 9, 2011, at 8:29 PM, Andreas Wilke < wilke(a)mcs.anl.gov > wrote: > > > > > > > > > > > > > > > > Hi Tanya , > > > > > > I noticed that you have submitted some metagenomes with the same name > > as the ones Jesse submitted. Are this the same metagenomes or are they > > different, do you want to add or transfer your metadata to those? > > > > > > > > F3T1pre4 > > F3T2pre4 > > h10A.1 > > h10B.1 > > USchp33Mom > > USchp33Mom > > USchp33Mom > > USinfTw4.1 > > USinfTw4.1 > > USinfTw6.1 > > USinfTw6.1 > > USinfTw6.2 > > <PastedGraphic-4.png> > > > > > > > > > > > > > > > > Andreas >

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Re: [mg-rast] metagenome analysis/organism classification/barchart option does not work 06042011
by Mark D'Souza 21 Apr '11

21 Apr '11

Hi, This problem was fixed with the last code update, thanks for reporting it. Regards, Mark On Apr 6, 2011, at 11:03 AM, Mark D'Souza wrote: > 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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Re: [mg-rast] Downloading sequences from the workbench
by Mark D'Souza 21 Apr '11

21 Apr '11

Hi, This problem has now been fixed, thanks for letting us know about it. There is no way to download data from the recruitment plot tool right now, but we will investigate the feasibility and may add this in a future update. Regards, Mark On Apr 11, 2011, at 5:03 PM, Mark D'Souza wrote: > Hi, > > Sorry about that, we are working on the problem and should have a fix in place within a day or so. > > ----- Original Message ----- >> From: "anthony bertagnolli" <bertagna(a)onid.orst.edu> >> To: mg-rast(a)mcs.anl.gov >> Sent: Monday, April 11, 2011 3:59:00 PM >> Subject: [mg-rast] Downloading sequences from the workbench >> Greetings, I am having trouble downloading sequences that have been >> taxonomically classified as a certain reference organism using the >> workbench feature. When I click on the box to the far right of the >> organism classification table (send proteins to workbench), it sends a >> number of proteins to the workbench. However, when I try to download >> these sequences from the work bench, I end up getting all of the >> classified sequences from the metagenomic data set, rather than the >> sequences that I request specifically. Has anyone else had this >> problem? In addition, is there a way to download sequences/proteins >> from the fragment recruitment tool? >> >> Thanks, >> >> -Anthony Bertagnolli > > -- > 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] MG-RAST - new data available
by mesparza＠uantof.cl 21 Apr '11

21 Apr '11

----Mensaje original----De: mg-rast(a)mcs.anl.govFecha: 15-02-2011 09:43 Para: <mesparza(a)uantof.cl>Asunto: MG-RAST - new data availableDear Mario Esparza,you have been granted access to microbial mat_Salar de Huasco (4454310.3) by Cristina Dorador on our web service MG-RAST.To directly access the new data, please follow this link: http://metagenomics.nmpdr.org/?page=JobDetails&job=13917.--This email was automatically generated by the MG-RAST web service. Do not reply.

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Re: [mg-rast] Date access
by Gary Xie 21 Apr '11

21 Apr '11

Thanks Mark for your help. Gary On Apr 21, 2011, at 12:31 PM, Mark D'Souza wrote: > Hi Gary, > > This job was run under both version 2 of MG-RAST (at http://metagenomics.anl.gov/v2/metagenomics.cgi) > as well as version 3 (http://metagenomics.anl.gov/ > metagenomics.cgi), the job is shared with Felicia under both > versions, but yes, she will have to log in through the front page > before accessing it. I tried this using both your accounts, in both > versions and had no problem, though Felicia will have to agree to > the terms of service in version 3 before viewing the analysis. If > you'll continue to have any problems accessing this or other jobs > let us know. > > Regards, > Mark > > > > On Apr 21, 2011, at 1:09 PM, Gary Xie wrote: > >> I believe you have to login first. If you have the same issue, you >> might want to contact the MG-rast team at mg-rast(a)mcs.anl.gov >> This site is maintained by them. >> Gary >> >> On Apr 21, 2011, at 11:59 AM, Felicia Qi wrote: >> >>> Gary, >>> >>> I cannot open any of these pages. here is the message I got: >>> >>> An error has occured: >>> >>> Unable to retrieve the job for metagenome '4453939.3'. >>> >>> To continue please go back to the start page. >>>

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Re: [mg-rast] Early access of NIH HMP oral metagenome data
by Felicia Qi 21 Apr '11

21 Apr '11

It worked. Thanks. Felicia On Apr 21, 2011, at 1:31 PM, Mark D'Souza wrote: > Hi Gary, > > This job was run under both version 2 of MG-RAST (at http:// > metagenomics.anl.gov/v2/metagenomics.cgi) as well as version 3 > (http://metagenomics.anl.gov/metagenomics.cgi) the job is shared > with Felicia under both versions, but yes, she will have to log in > through the front page before accessing it. I tried this using both > your accounts, in both versions and had no problem, though Felicia > will have to agree to the terms of service in version 3 before > viewing the analysis. If you'll continue to have any problems > accessing this or other jobs let us know. > > Regards, > Mark > > > > On Apr 21, 2011, at 1:09 PM, Gary Xie wrote: > >> I believe you have to login first. If you have the same issue, you >> might want to contact the MG-rast team at mg-rast(a)mcs.anl.gov >> This site is maintained by them. >> Gary >> >> On Apr 21, 2011, at 11:59 AM, Felicia Qi wrote: >> >>> Gary, >>> >>> I cannot open any of these pages. here is the message I got: >>> >>> An error has occured: >>> >>> Unable to retrieve the job for metagenome '4453939.3'. >>> >>> To continue please go back to the start page. >>> >>> On Apr 21, 2011, at 12:07 PM, Gary Xie wrote: >>> >>>> Hi, Felicia, >>>> I just grant you to have an early access of our NIH oral HMP >>>> contigs >>>> (>300bp) and 454 reads. >>>> Please be aware that we should not publish anything using these >>>> data >>>> until the main NIH/HMP science/nature paper came out. >>>> Let me know if you have any question. Thanks, >>>> Gary >>> >> >

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Re: [mg-rast] Early access of NIH HMP oral metagenome data
by Mark D'Souza 21 Apr '11

21 Apr '11

Hi Gary, This job was run under both version 2 of MG-RAST (at http://metagenomics.anl.gov/v2/metagenomics.cgi) as well as version 3 (http://metagenomics.anl.gov/metagenomics.cgi) the job is shared with Felicia under both versions, but yes, she will have to log in through the front page before accessing it. I tried this using both your accounts, in both versions and had no problem, though Felicia will have to agree to the terms of service in version 3 before viewing the analysis. If you'll continue to have any problems accessing this or other jobs let us know. Regards, Mark On Apr 21, 2011, at 1:09 PM, Gary Xie wrote: > I believe you have to login first. If you have the same issue, you might want to contact the MG-rast team at mg-rast(a)mcs.anl.gov > This site is maintained by them. > Gary > > On Apr 21, 2011, at 11:59 AM, Felicia Qi wrote: > >> Gary, >> >> I cannot open any of these pages. here is the message I got: >> >> An error has occured: >> >> Unable to retrieve the job for metagenome '4453939.3'. >> >> To continue please go back to the start page. >> >> On Apr 21, 2011, at 12:07 PM, Gary Xie wrote: >> >>> Hi, Felicia, >>> I just grant you to have an early access of our NIH oral HMP contigs >>> (>300bp) and 454 reads. >>> Please be aware that we should not publish anything using these data >>> until the main NIH/HMP science/nature paper came out. >>> Let me know if you have any question. Thanks, >>> Gary >> >

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