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

Fwd: Status of Uploaded Sequences
by Travis Harrison 24 Jun '11

24 Jun '11

There is currently a backlog, we have had ~500 job submissions in that last 48 hours, some of them big. Additionally there are some jobs rerunning from the failures in the past. - Travis ---------- Forwarded message ---------- From: Mark DSouza <dsouza(a)mcs.anl.gov> Date: Fri, Jun 24, 2011 at 9:53 AM Subject: Re: [mg-rast] Status of Uploaded Sequences To: "Matthew T. Cottrell" <mattcott(a)udel.edu> Cc: MG- Rast <mg-rast(a)mcs.anl.gov> Hi, I will take a look and get back to you, -- 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 ----- Original Message ----- > From: "Matthew T. Cottrell" <mattcott(a)udel.edu> > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > Sent: Thursday, June 23, 2011 4:55:28 PM > Subject: Status of Uploaded Sequences > Mark, > > Yesterday about this time I uploaded sequences that appeared to have > been processed just fine by the uploader, but now 24 h later there is > still not job started. On the "Create job" tab the status is listed as > "upload completed, processing started." Am I missing a step needed to > kick this off? > > Thanks, > Matt > . . . . . . . . . . . . . . . . . . . . . . . _/) > 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] Data selection errors
by Mark D'Souza 24 Jun '11

24 Jun '11

Hi, I am not sure which report you are referring to, can you tell us the steps you use to get the NCBI-nr functional report? Thanks, Mark On Jun 23, 2011, at 5:37 PM, anthony bertagnolli wrote: > Hi Mark, thanks for the reply. I think i figured out what the problem was. However, I have a second question. I noticed that there is now an option to view the NCBI-nr functional report for selected taxa. This is very useful, and i've used it quite a bit. However, I was wondering if there would be a way to download this information for whole samples, rather than just select reference taxa from samples. This would be very useful to have as well, as dowloadiing the report for ever taxa in a given sample would be too time consuming. Thanks again for all the updates to the site, its really quite a nice tool. > > -Anthony Bertagnolli > > > On Jun 15, 2011, at 4:35 PM, Mark D'Souza wrote: > >> Hi, >> >> Can you tell us the mg-rast IDs for the datasets you are viewing, we will check what is the problem. >> >> 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 Jun 14, 2011, at 7:40 PM, anthony bertagnolli wrote: >> >>> Greetings, I've been using MG-RAST to analyze metagenome samples collected from marine environments, and I really like the latest version. However, I've found that when using the Data selection component to change the e-value cutt-off, % ID cuttoff, and min. alignment length, no changes are made to the corresponding data tables below. You would think that when moving from an e-value cutoff 1x10-5, from 0, or 1x10-5 to 1x10-10, you see a difference in the abundance of genes being classified (more stringent the cutt-off, the less reads assigned to a reference organism). However, this does not seem to the case. In fact, it appears as if nothing is occuring at all. Just wondering if maybe this might be a bug, and if it could be fixed. Thanks, >>> >>> -Anthony bertagnolli >> >> >

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Re: [mg-rast] Status of Uploaded Sequences
by Mark DSouza 24 Jun '11

24 Jun '11

Hi, I will take a look and get back to you, -- 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 ----- Original Message ----- > From: "Matthew T. Cottrell" <mattcott(a)udel.edu> > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > Sent: Thursday, June 23, 2011 4:55:28 PM > Subject: Status of Uploaded Sequences > Mark, > > Yesterday about this time I uploaded sequences that appeared to have > been processed just fine by the uploader, but now 24 h later there is > still not job started. On the "Create job" tab the status is listed as > "upload completed, processing started." Am I missing a step needed to > kick this off? > > Thanks, > Matt > . . . . . . . . . . . . . . . . . . . . . . . _/) > 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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Fwd: data processing blocked
by Travis Harrison 24 Jun '11

24 Jun '11

It looks like load AWE failed on all these on march 19, I will chalk it up to the hard drive failures back then and rerun them. -travis ---------- Forwarded message ---------- From: Sebastien Cecillon <Sebastien.Cecillon(a)ec-lyon.fr> Date: Fri, Jun 24, 2011 at 4:25 AM Subject: [mg-rast] data processing blocked To: mg-rast(a)mcs.anl.gov Dear MG RAST manager,**** seven of my jobs (old data, new MGRAST, private data) are blocked for long time ago, after gene clustering completed.**** Job ID:**** 10707**** 10703**** 10702**** 10701**** 10700**** 10699**** 10696**** Maybe there is a problem with my sequences.**** Thank you for your very good job on MG-RAST.**** Best regards **** ** ** Sebastien CECILLON**** Environmental Microbial Genomics Group**** Laboratoire Ampere**** Ecole Centrale de Lyon**** 36 avenue Guy de Collongue**** F69134 ECULLY cedex**** Phone: +33 4 72 18 60 26**** Mobile: +33 6 26 99 05 28**** web: www.genomenviron.org**** ** **

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Re: [mg-rast] MG-RAST cost
by Folker Meyer 24 Jun '11

24 Jun '11

Dear Reena: to use Shotgun metagenomics, you will need sequence data. Obtaining sequence data is not very difficult, however sampling and DNA isolation protocols will dramatically influence your results. For DNA sequencing the current optimal solution is Illumina sequencing using 75bp or longer. It is both cost optimal as well as optimal in the sense of being error free. Cost for a lane (one 16th of a run on HiSeq2000) should be about US $2000 and it should generate about 10GBp (gigabasepairs). I recommend that you take a look at http://www.earthmicrobiome.org for some more detailed insights into sampling, DNA isolation etc. Best, Folker On Jun 24, 2011, at 12:31 AM, Reena.Khaneja.2007(a)live.rhul.ac.uk wrote: > Dear Sir/ Madam, > > I'm a Phd Student from Simon Cutting's lab in the UK. we are interested in getting a MG-RAST for one of our strains. > > i dont have much idea about the MG-RAST- but if you could clarify some queries i have then i would really appreciate it and may be get MG-RAST for our strain as soon as possible. > > So in order to get MG-RAST, we first need to get a 454 or similar sequencing done? > Then we send you the FASTA format file to you to do the analysis? > I dont know much about programming, but i assume that we get the 454 sequencing as FASTA file and i upload that file to your pipeline and you send us the out put files of the sequence- is this correct? > > Please excuse my lack of knowledge but i really want to know on it and how to get or do this analysis. Your help would be much appreciated. > > Please reply back as soon as possible. > > Many thanks > Reena Khaneja

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data processing blocked
by Sebastien Cecillon 24 Jun '11

24 Jun '11

Dear MG RAST manager, seven of my jobs (old data, new MGRAST, private data) are blocked for long time ago, after gene clustering completed. Job ID: 10707 10703 10702 10701 10700 10699 10696 Maybe there is a problem with my sequences. Thank you for your very good job on MG-RAST. Best regards Sebastien CECILLON Environmental Microbial Genomics Group Laboratoire Ampere Ecole Centrale de Lyon 36 avenue Guy de Collongue F69134 ECULLY cedex Phone: +33 4 72 18 60 26 Mobile: +33 6 26 99 05 28 web: <http://www.genomenviron.org> www.genomenviron.org

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Re: [mg-rast] MGRAST - account request approved
by Rick White 24 Jun '11

24 Jun '11

Hello again This sample in analysis 26349 4466752.3 SB_Mic_Filtered_PS_true Finalizing Data : completed Looks stuck Rest loaded are stuck in Dereplication.. Let me know? Thanks Rick On Thu, Jun 23, 2011 at 6:47 PM, Rick White <raw937(a)gmail.com> wrote: > Hello again, > The analysis is running very slow is their a reason for it? > > Also, one states completed in analysis but looks stuck? > > Whats up with that? > > YOUR #1 FAN > Rick > > On Thu, Jun 23, 2011 at 10:30 AM, <raw937(a)gmail.com> wrote: > >> Thanks buddy! >> Sent from my “contract free” BlackBerry® smartphone on the WIND network. >> >> -----Original Message----- >> From: Mark D'Souza <dsouza(a)mcs.anl.gov> >> Date: Thu, 23 Jun 2011 12:10:11 >> To: Rick White<raw937(a)gmail.com> >> Cc: <mg-rast(a)mcs.anl.gov> >> Subject: Re: [mg-rast] MGRAST - account request approved >> >> Hi Rick, >> >> Sorry about that, I reset the upload and it should work fine now. >> >> 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 Jun 22, 2011, at 11:49 PM, Rick White wrote: >> >> > Hello again, >> > I cant upload any more files... >> > >> > uploaded a RMStromCCMexMic20050722.fa.gz file and its stuck... >> > >> > I can't upload any more? >> > >> > Please help! >> > >> > Thanks >> > rick >> > >> > On Tue, Jun 21, 2011 at 2:16 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> >> wrote: >> > Hi, >> > >> > Give us the metagenome IDs and queries the next time you get an >> undefined tree, we will check into it. We have seen this happen before, >> querying the database for huge amounts of data is the problem and we are >> working on fixing this. >> > >> > What are the parameters you are using for the sequence trimming? >> > >> > Regards, >> > Mark >> > >> > >> > >> > On Jun 21, 2011, at 11:50 AM, Rick White wrote: >> > >> > > I have noticed a bug with the tree output it keeps stating undefined? >> Is this a bug or something else? >> > > >> > > Yes, I will let you know the asap the renaming & deletion. >> > > >> > > Also, when I put in my amplicons & use the trimmer it takes the mean >> 400 bp down to 205 bp. It would be great to reject reads that are shorter >> then the length you want them. >> > > >> > > ONCE AGAIN, I AM A HUGE FAN OF THE SITE! I plan on using from now on. >> > > >> > > Keep up the great work! >> > > Rick >> > > >> > > On Tue, Jun 21, 2011 at 9:32 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> >> wrote: >> > > Hi, and thanks for the compliment, >> > > >> > > The deletion/renaming is something we are working on, if you let me >> know the MG-RAST IDs and changes to be made I can take care of it. >> > > >> > > 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 Jun 20, 2011, at 5:49 PM, Rick White wrote: >> > > >> > > > Mark, >> > > > MG-RAST, is the greatest thing ever!!!!!!!!! >> > > > >> > > > It has saved me so much TIME! I wished I would have known about it >> sooner. >> > > > >> > > > Quick question, how do I delete ones that completed analysis but I >> labeled wrong? >> > > > >> > > > Or how can I edit them? Just rename them it sends me a wierd error >> message. I would like to input pH etc or rename them! >> > > > >> > > > Thanks >> > > > Rick >> > > > >> > > > On Thu, Jun 9, 2011 at 11:59 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> >> wrote: >> > > > Hi, >> > > > >> > > > Can you tell us what you see when you login and the browser you are >> using? You will need to set the preferences for your browser to accept >> cookies (required for login) and we test on FireFox. The URL in the >> notification email you received (http://metagenomics.anl.gov/) points to >> the V3.1 site. >> > > > >> > > > 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 Jun 9, 2011, at 12:46 PM, Rick White wrote: >> > > > >> > > > > Is verison 3 avaliable? >> > > > > >> > > > > I can't login or upload my data on using ubuntu?? >> > > > > >> > > > > On Thu, Jun 9, 2011 at 10:27 AM, <mg-rast(a)mcs.anl.gov> wrote: >> > > > > Dear RIck White, >> > > > > >> > > > > your account request for access to our web service MGRAST has been >> accepted. >> > > > > >> > > > > Your login is: raw937 >> > > > > Your password is: v307SsCD >> > > > > >> > > > > We recommend to change the password immediately. To do so please >> go to our web service http://metagenomics.anl.gov/ and change your >> password from the account management. >> > > > > >> > > > > >> > > > > -- >> > > > > >> > > > > This email was automatically generated by the MGRAST web service. >> Do not reply. >> > > > > >> > > > > >> > > > > >> > > > > -- >> > > > > Richard Allen White III M.S. >> > > > > PhD Student - Suttle Lab >> > > > > Department of Microbiology & Immunology >> > > > > The University of British Columbia >> > > > > Vancouver, BC, Canada >> > > > > V6T 1Z4 >> > > > > ph.(604) 827-5715 >> > > > > cell. ***My new number is 604-440-5150*** >> > > > > http://www.ocgy.ubc.ca/~suttle/ >> > > > > >> > > > > For Shipping: >> > > > > Richard Allen White III & Amy Chan >> > > > > Suttle Lab >> > > > > UBC-Botany/zoology/micro >> > > > > 1316-6270 University Blvd. >> > > > > Vancouver, BC >> > > > > V6T 1Z4 >> > > > > 1.604.827.5715 >> > > > > >> > > > >> > > > >> > > > >> > > > >> > > > -- >> > > > Richard Allen White III M.S. >> > > > PhD Student - Suttle Lab >> > > > Department of Microbiology & Immunology >> > > > The University of British Columbia >> > > > Vancouver, BC, Canada >> > > > V6T 1Z4 >> > > > ph.(604) 827-5715 >> > > > cell. ***My new number is 604-440-5150*** >> > > > http://www.ocgy.ubc.ca/~suttle/ >> > > > >> > > > For Shipping: >> > > > Richard Allen White III & Amy Chan >> > > > Suttle Lab >> > > > UBC-Botany/zoology/micro >> > > > 1316-6270 University Blvd. >> > > > Vancouver, BC >> > > > V6T 1Z4 >> > > > 1.604.827.5715 >> > > > >> > > >> > > >> > > >> > > >> > > -- >> > > Richard Allen White III M.S. >> > > PhD Student - Suttle Lab >> > > Department of Microbiology & Immunology >> > > The University of British Columbia >> > > Vancouver, BC, Canada >> > > V6T 1Z4 >> > > ph.(604) 827-5715 >> > > cell. ***My new number is 604-440-5150*** >> > > http://www.ocgy.ubc.ca/~suttle/ >> > > >> > > For Shipping: >> > > Richard Allen White III & Amy Chan >> > > Suttle Lab >> > > UBC-Botany/zoology/micro >> > > 1316-6270 University Blvd. >> > > Vancouver, BC >> > > V6T 1Z4 >> > > 1.604.827.5715 >> > > >> > >> > >> > >> > >> > -- >> > Richard Allen White III M.S. >> > PhD Student - Suttle Lab >> > Department of Microbiology & Immunology >> > The University of British Columbia >> > Vancouver, BC, Canada >> > V6T 1Z4 >> > ph.(604) 827-5715 >> > cell. ***My new number is 604-440-5150*** >> > http://www.ocgy.ubc.ca/~suttle/ >> > >> > For Shipping: >> > Richard Allen White III & Amy Chan >> > Suttle Lab >> > UBC-Botany/zoology/micro >> > 1316-6270 University Blvd. >> > Vancouver, BC >> > V6T 1Z4 >> > 1.604.827.5715 >> > >> >> > > > -- > Richard Allen White III M.S. > PhD Student - Suttle Lab > Department of Microbiology & Immunology > The University of British Columbia > Vancouver, BC, Canada > V6T 1Z4 > ph.(604) 827-5715 > cell. ***My new number is 604-440-5150*** > http://www.ocgy.ubc.ca/~suttle/ > > For Shipping: > Richard Allen White III & Amy Chan > Suttle Lab > UBC-Botany/zoology/micro > 1316-6270 University Blvd. > Vancouver, BC > V6T 1Z4 > 1.604.827.5715 > > -- Richard Allen White III M.S. PhD Student - Suttle Lab Department of Microbiology & Immunology The University of British Columbia Vancouver, BC, Canada V6T 1Z4 ph.(604) 827-5715 cell. ***My new number is 604-440-5150*** http://www.ocgy.ubc.ca/~suttle/ For Shipping: Richard Allen White III & Amy Chan Suttle Lab UBC-Botany/zoology/micro 1316-6270 University Blvd. Vancouver, BC V6T 1Z4 1.604.827.5715

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MG-RAST cost
by Reena.Khaneja.2007＠live.rhul.ac.uk 24 Jun '11

24 Jun '11

Dear Sir/ Madam, I'm a Phd Student from Simon Cutting's lab in the UK. we are interested in getting a MG-RAST for one of our strains. i dont have much idea about the MG-RAST- but if you could clarify some queries i have then i would really appreciate it and may be get MG-RAST for our strain as soon as possible. So in order to get MG-RAST, we first need to get a 454 or similar sequencing done? Then we send you the FASTA format file to you to do the analysis? I dont know much about programming, but i assume that we get the 454 sequencing as FASTA file and i upload that file to your pipeline and you send us the out put files of the sequence- is this correct? Please excuse my lack of knowledge but i really want to know on it and how to get or do this analysis. Your help would be much appreciated. Please reply back as soon as possible. Many thanks Reena Khaneja

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Re: [mg-rast] Downloading a LARGE batch of 16S metagenomes
by Jack Gilbert 23 Jun '11

23 Jun '11

Okay awesome thanks andi Dr Jack A Gilbert Argonne National Laboratory 9700 S. Cass Avenue Building 202, Room B373 Argonne, Illinois, 60439 Tel: +1 630 252 7489 Cell: +1 630 915 2383 Email: gilbertjack(a)anl.gov sent from my iPad On Jun 23, 2011, at 7:46 PM, Andreas Wilke <wilke(a)mcs.anl.gov> wrote: Hi Jack, Hunter and I are working on a solution tomorrow. Adding all related metagenomes to a project is only part of a solution since Let's touch base tomorrow please. Andreas On Jun 23, 2011, at 6:19 PM, Jack Gilbert wrote: Whats happening with this? I would like to push this through to the collaborator asap. Cheers Jack On Tue, Jun 21, 2011 at 4:27 PM, Mark DSouza <dsouza(a)mcs.anl.gov> wrote: > Andi, > > The attached file contains the list of jobs for this project. > > Mark > > ----- Original Message ----- > > From: "Jack Gilbert" <gilbertjack(a)gmail.com> > > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > > Cc: mg-rast(a)mcs.anl.gov, "Sarah Owens" <sarah.owens(a)anl.gov> > > Sent: Tuesday, June 21, 2011 8:02:45 AM > > Subject: Re: [mg-rast] Downloading a LARGE batch of 16S metagenomes > > Thanks mark > > > > Bonnie samples are not part of the project. > > > > Project title should be "McMahon Temperate Bog Lake Timeseries" > > > > Cheers > > > > Jack > > > > Jack A Gilbert > > Argonne National Laboratory > > Building 202, Room B373 > > 9700, South Cass Avenue > > Lemont, IL, 60439 > > Email: gilbertjack(a)ANL.gov > > Office: +1 630 252 7489 > > Cell: +1 630-915-2383 > > Sent from my iPhone > > > > On Jun 21, 2011, at 8:57 AM, Mark DSouza <dsouza(a)mcs.anl.gov> wrote: > > > > > Hi Jack, > > > > > > We can take care of this, give us a project name, also is the Bonnie > > > run part of this project. > > > > > > Mark > > > > > > ----- Original Message ----- > > >> From: "Jack Gilbert" <gilbertjack(a)gmail.com> > > >> To: mg-rast(a)mcs.anl.gov, "Sarah Owens" <sarah.owens(a)anl.gov> > > >> Sent: Tuesday, June 21, 2011 6:49:26 AM > > >> Subject: [mg-rast] Downloading a LARGE batch of 16S metagenomes > > >> Hey Guys, > > >> > > >> One of our collaborators would like to download the data processed > > >> by > > >> MGrast for their project, but there are ALOT of them. Every > > >> Metagenome > > >> thats starts with McMahon needs to be placed in a project. Is there > > >> a > > >> quick and easy way to do this? OR do I have to do it manually ;-(? > > >> > > >> Additionally, When I go to download there does not seem to be a way > > >> of > > >> downloading all metagenomes in a collection? There is however this > > >> for > > >> project - can I make a project? > > >> > > >> We would like to give Trina the opportunity to move forward with > > >> this > > >> asap, so let me know how we can proceed asap ;-) > > >> > > >> Cheers from the Long Island Wine Country ;-) > > >> > > >> J > > >> > > >> > > >> ---------- Forwarded message ---------- > > >> From: Jack Gilbert < gilbertjack(a)gmail.com > > > >> Date: Tue, Jun 21, 2011 at 6:40 AM > > >> Subject: Re: Analyses > > >> To: Trina McMahon < tmcmahon(a)cae.wisc.edu > > > >> Cc: Sarah Owens < Sarah.Owens(a)anl.gov > > > >> > > >> > > >> Hey Trina, > > >> > > >> All these have been QCd via QIIME for the Illumina protocol. But I > > >> agree taxonomic annotation against the freshwater tribes would be > > >> useful. > > >> > > >> We will get them onto a portal for full download. > > >> > > >> Cheers > > >> > > >> Jack > > >> > > >> > > >> > > >> > > >> > > >> On Tue, Jun 21, 2011 at 6:33 AM, Trina McMahon < > > >> tmcmahon(a)cae.wisc.edu > > >>> wrote: > > >> > > >> > > >> > > >> Hey you two, > > >> > > >> > > >> First of all, THANKS Sarah for figuring out how to make these data > > >> accessible in MG-RAST. I have been poking at them here and there. > > >> But > > >> now I'd actually like to download them and run some analyses > > >> locally. > > >> > > >> > > >> A couple questions: > > >> > > >> > > >> 1) Who should I contact at MG-RAST to ask about modifying the > > >> interface to download sets of metagenomes?! Currently, each sample > > >> is > > >> listed as a separate entry to so download them all I would have to > > >> click on each one individually and there are > 600!! > > >> > > >> > > >> 2) Any idea when the other ~380 will be processed thru MG-RAST? I'd > > >> like to look at them all together if possible. > > >> > > >> > > >> If it's easier to just post all the data somewhere in raw or > > >> semi-processed form, that would be fine too. I actually have a > > >> pipeline setup here at Uppsala university with QIIME, and I'd like > > >> to > > >> run my own taxonomic binning (using a hand-curated database of > > >> freshwater sequences with more resolved taxonomies). > > >> > > >> > > >> THANKS again! > > >> trina > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> On May 23, 2011, at 1:36 PM, Trina McMahon wrote: > > >> > > >> > > >> > > >> Wow!!! > > >> > > >> > > >> Do you mean the metagenomes??? Or just the tags?? I know Ashley has > > >> her hands on the tag sequences already.... > > >> > > >> > > >> I have a student starting in July who will work on it... in the > > >> meantime I would love to look at them. And of course you are > > >> welcome > > >> to also. Maybe we can check in to compare notes next month? Please > > >> please share with me on MG-RAST! > > >> > > >> > > >> trina > > >> > > >> > > >> > > >> > > >> > > >> > > >> On May 20, 2011, at 7:11 PM, Jack Gilbert wrote: > > >> > > >> > > >> Hey Trina, > > >> > > >> About half or more of your 987 samples we did sequencing for are > > >> processed through MG-RAST already and available for analysis. What > > >> shall we do now? Do you have someone to work on these or do you > > >> want > > >> us to start the analysis? > > >> > > >> Jack > > >> > > >> -- > > >> Dr. Jack A. Gilbert B.Sc. Ph.D. > > >> Argonne National Laboratory > > >> Bldg. 202, Biosciences > > >> Room B373 > > >> 9700 South Cass Avenue > > >> Argonne, IL, 60430 > > >> Tel: +1 630 252-7489 > > >> Cell: +1 630 915 2383 > > >> Email: gilbertjack(a)gmail.com > > >> Twitter: @gilbertjacka > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > ------------------------------------------------------------------------------------- > > >> Katherine (Trina) McMahon, Associate Professor > > >> Goddess of Funkosity > > >> Departments of Civil and Environmental Engineering and Bacteriology > > >> Environmental Chemistry and Technology Program > > >> Limnology and Marine Science Program > > >> Microbiology Doctoral Training Program > > >> > > >> > > >> **On sabbatical leave starting August 20, 2010** > > >> > > >> > > >> Mailing Address: > > >> 3204 Engineering Hall, 1415 Engineering Drive > > >> University of Wisconsin - Madison, Madison, WI 53706-1691 > > >> > > >> > > >> Alternate Office: 5552 Microbial Sciences Building > > >> > > >> > > >> Phone: 608/890-2836 Fax: 608/262-9865 > > >> Email: tmcmahon(a)engr.wisc.edu > > >> McMahon Lab: > > >> http://www.engr.wisc.edu/cee/faculty/mcmahon_katherine.html > > >> North Temperate Lakes Microbial Observatory: > > >> http://microbes.limnology.wisc.edu/ > > >> > > >> > > >> > ------------------------------------------------------------------------------------- > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > ------------------------------------------------------------------------------------- > > >> Katherine (Trina) McMahon, Associate Professor > > >> Goddess of Funkosity > > >> Departments of Civil and Environmental Engineering and Bacteriology > > >> Environmental Chemistry and Technology Program > > >> Limnology and Marine Science Program > > >> Microbiology Doctoral Training Program > > >> > > >> > > >> **On sabbatical leave starting August 20, 2010** > > >> > > >> > > >> Mailing Address: > > >> 3204 Engineering Hall, 1415 Engineering Drive > > >> University of Wisconsin - Madison, Madison, WI 53706-1691 > > >> > > >> > > >> Alternate Office: 5552 Microbial Sciences Building > > >> > > >> > > >> Phone: 608/890-2836 Fax: 608/262-9865 > > >> Email: tmcmahon(a)engr.wisc.edu > > >> McMahon Lab: > > >> http://www.engr.wisc.edu/cee/faculty/mcmahon_katherine.html > > >> North Temperate Lakes Microbial Observatory: > > >> http://microbes.limnology.wisc.edu/ > > >> > > >> > > >> > ------------------------------------------------------------------------------------- > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> -- > > >> Dr. Jack A. Gilbert B.Sc. Ph.D. > > >> Argonne National Laboratory > > >> Bldg. 202, Biosciences > > >> Room B373 > > >> 9700 South Cass Avenue > > >> Argonne, IL, 60430 > > >> Tel: +1 630 252-7489 > > >> Cell: +1 630 915 2383 > > >> Email: gilbertjack(a)gmail.com > > >> Twitter: @gilbertjacka > > >> > > >> > > >> > > >> > > >> -- > > >> Dr. Jack A. Gilbert B.Sc. Ph.D. > > >> Argonne National Laboratory > > >> Bldg. 202, Biosciences > > >> Room B373 > > >> 9700 South Cass Avenue > > >> Argonne, IL, 60430 > > >> Tel: +1 630 252-7489 > > >> Cell: +1 630 915 2383 > > >> Email: gilbertjack(a)gmail.com > > >> Twitter: @gilbertjacka > -- Dr. Jack A. Gilbert B.Sc. Ph.D. Argonne National Laboratory Bldg. 202, Biosciences Room B373 9700 South Cass Avenue Argonne, IL, 60430 Tel: +1 630 252-7489 Cell: +1 630 915 2383 Email: gilbertjack(a)gmail.com Twitter: @gilbertjacka Andreas Wilke Argonne National Laboratory Mathematics and Computer Science Division Bldg. 240 , 4F8 9700 South Cass Avenue Argonne, IL 60439 (630) 252-3190 (phone) (630) 252-5986.(fax)

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Re: [mg-rast] MGRAST - account request approved
by Rick White 23 Jun '11

23 Jun '11

Hello again, The analysis is running very slow is their a reason for it? Also, one states completed in analysis but looks stuck? Whats up with that? YOUR #1 FAN Rick On Thu, Jun 23, 2011 at 10:30 AM, <raw937(a)gmail.com> wrote: > Thanks buddy! > Sent from my “contract free” BlackBerry® smartphone on the WIND network. > > -----Original Message----- > From: Mark D'Souza <dsouza(a)mcs.anl.gov> > Date: Thu, 23 Jun 2011 12:10:11 > To: Rick White<raw937(a)gmail.com> > Cc: <mg-rast(a)mcs.anl.gov> > Subject: Re: [mg-rast] MGRAST - account request approved > > Hi Rick, > > Sorry about that, I reset the upload and it should work fine now. > > 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 Jun 22, 2011, at 11:49 PM, Rick White wrote: > > > Hello again, > > I cant upload any more files... > > > > uploaded a RMStromCCMexMic20050722.fa.gz file and its stuck... > > > > I can't upload any more? > > > > Please help! > > > > Thanks > > rick > > > > On Tue, Jun 21, 2011 at 2:16 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> > wrote: > > Hi, > > > > Give us the metagenome IDs and queries the next time you get an undefined > tree, we will check into it. We have seen this happen before, querying the > database for huge amounts of data is the problem and we are working on > fixing this. > > > > What are the parameters you are using for the sequence trimming? > > > > Regards, > > Mark > > > > > > > > On Jun 21, 2011, at 11:50 AM, Rick White wrote: > > > > > I have noticed a bug with the tree output it keeps stating undefined? > Is this a bug or something else? > > > > > > Yes, I will let you know the asap the renaming & deletion. > > > > > > Also, when I put in my amplicons & use the trimmer it takes the mean > 400 bp down to 205 bp. It would be great to reject reads that are shorter > then the length you want them. > > > > > > ONCE AGAIN, I AM A HUGE FAN OF THE SITE! I plan on using from now on. > > > > > > Keep up the great work! > > > Rick > > > > > > On Tue, Jun 21, 2011 at 9:32 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> > wrote: > > > Hi, and thanks for the compliment, > > > > > > The deletion/renaming is something we are working on, if you let me > know the MG-RAST IDs and changes to be made I can take care of it. > > > > > > 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 Jun 20, 2011, at 5:49 PM, Rick White wrote: > > > > > > > Mark, > > > > MG-RAST, is the greatest thing ever!!!!!!!!! > > > > > > > > It has saved me so much TIME! I wished I would have known about it > sooner. > > > > > > > > Quick question, how do I delete ones that completed analysis but I > labeled wrong? > > > > > > > > Or how can I edit them? Just rename them it sends me a wierd error > message. I would like to input pH etc or rename them! > > > > > > > > Thanks > > > > Rick > > > > > > > > On Thu, Jun 9, 2011 at 11:59 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> > wrote: > > > > Hi, > > > > > > > > Can you tell us what you see when you login and the browser you are > using? You will need to set the preferences for your browser to accept > cookies (required for login) and we test on FireFox. The URL in the > notification email you received (http://metagenomics.anl.gov/) points to > the V3.1 site. > > > > > > > > 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 Jun 9, 2011, at 12:46 PM, Rick White wrote: > > > > > > > > > Is verison 3 avaliable? > > > > > > > > > > I can't login or upload my data on using ubuntu?? > > > > > > > > > > On Thu, Jun 9, 2011 at 10:27 AM, <mg-rast(a)mcs.anl.gov> wrote: > > > > > Dear RIck White, > > > > > > > > > > your account request for access to our web service MGRAST has been > accepted. > > > > > > > > > > Your login is: raw937 > > > > > Your password is: v307SsCD > > > > > > > > > > We recommend to change the password immediately. To do so please go > to our web service http://metagenomics.anl.gov/ and change your password > from the account management. > > > > > > > > > > > > > > > -- > > > > > > > > > > This email was automatically generated by the MGRAST web service. > Do not reply. > > > > > > > > > > > > > > > > > > > > -- > > > > > Richard Allen White III M.S. > > > > > PhD Student - Suttle Lab > > > > > Department of Microbiology & Immunology > > > > > The University of British Columbia > > > > > Vancouver, BC, Canada > > > > > V6T 1Z4 > > > > > ph.(604) 827-5715 > > > > > cell. ***My new number is 604-440-5150*** > > > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > > > > > For Shipping: > > > > > Richard Allen White III & Amy Chan > > > > > Suttle Lab > > > > > UBC-Botany/zoology/micro > > > > > 1316-6270 University Blvd. > > > > > Vancouver, BC > > > > > V6T 1Z4 > > > > > 1.604.827.5715 > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > Richard Allen White III M.S. > > > > PhD Student - Suttle Lab > > > > Department of Microbiology & Immunology > > > > The University of British Columbia > > > > Vancouver, BC, Canada > > > > V6T 1Z4 > > > > ph.(604) 827-5715 > > > > cell. ***My new number is 604-440-5150*** > > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > > > For Shipping: > > > > Richard Allen White III & Amy Chan > > > > Suttle Lab > > > > UBC-Botany/zoology/micro > > > > 1316-6270 University Blvd. > > > > Vancouver, BC > > > > V6T 1Z4 > > > > 1.604.827.5715 > > > > > > > > > > > > > > > > > > > -- > > > Richard Allen White III M.S. > > > PhD Student - Suttle Lab > > > Department of Microbiology & Immunology > > > The University of British Columbia > > > Vancouver, BC, Canada > > > V6T 1Z4 > > > ph.(604) 827-5715 > > > cell. ***My new number is 604-440-5150*** > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > For Shipping: > > > Richard Allen White III & Amy Chan > > > Suttle Lab > > > UBC-Botany/zoology/micro > > > 1316-6270 University Blvd. > > > Vancouver, BC > > > V6T 1Z4 > > > 1.604.827.5715 > > > > > > > > > > > > > -- > > Richard Allen White III M.S. > > PhD Student - Suttle Lab > > Department of Microbiology & Immunology > > The University of British Columbia > > Vancouver, BC, Canada > > V6T 1Z4 > > ph.(604) 827-5715 > > cell. ***My new number is 604-440-5150*** > > http://www.ocgy.ubc.ca/~suttle/ > > > > For Shipping: > > Richard Allen White III & Amy Chan > > Suttle Lab > > UBC-Botany/zoology/micro > > 1316-6270 University Blvd. > > Vancouver, BC > > V6T 1Z4 > > 1.604.827.5715 > > > > -- Richard Allen White III M.S. PhD Student - Suttle Lab Department of Microbiology & Immunology The University of British Columbia Vancouver, BC, Canada V6T 1Z4 ph.(604) 827-5715 cell. ***My new number is 604-440-5150*** http://www.ocgy.ubc.ca/~suttle/ For Shipping: Richard Allen White III & Amy Chan Suttle Lab UBC-Botany/zoology/micro 1316-6270 University Blvd. Vancouver, BC V6T 1Z4 1.604.827.5715

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