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

Re: [mg-rast] data processing blocked
by Mark D'Souza 24 Jun '11

24 Jun '11

Hi, Sorry for the delay, the jobs had got stuck and have now been restarted. They should complete within a day or two. 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 24, 2011, at 4:25 AM, Sebastien Cecillon wrote: > 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] Downloading a LARGE batch of 16S metagenomes
by Andreas Wilke 24 Jun '11

24 Jun '11

Jack has url for download. All metagenomes ate part of the "McMahon Temperate Bog Lake Timeseries" project. Andreas On Jun 23, 2011, at 9:47 PM, Jack Gilbert wrote: > 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) >> 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 Mark D'Souza 24 Jun '11

24 Jun '11

Hi, We had a load spike that is probably causing the delay, let us know if they do not go through over the weekend. Regards, Mark On Jun 24, 2011, at 2:40 PM, Rick White wrote: > Hello Mark, > Most of these samples have few reads and look to be stuck in Dereplication. > Runs 26413 - 26421 and the rest of my stuff? > > It ran some fast the last time, I am worried that its stuck.. > > Sorry to bother... > > Thanks > Rick > > On Fri, Jun 24, 2011 at 1:22 AM, Rick White <raw937(a)gmail.com> wrote: > 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 > > > > > -- > 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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Re: [mg-rast] MGRAST - account request approved
by Rick White 24 Jun '11

24 Jun '11

Hello Mark, Most of these samples have few reads and look to be stuck in Dereplication. Runs 26413 - 26421 and the rest of my stuff? It ran some fast the last time, I am worried that its stuck.. Sorry to bother... Thanks Rick On Fri, Jun 24, 2011 at 1:22 AM, Rick White <raw937(a)gmail.com> wrote: > 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 > > -- 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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Re: [mg-rast] Data selection errors
by Mark D'Souza 24 Jun '11

24 Jun '11

Hi, Thanks, that makes things clear. To get the fasta file for all organisms, you need to: > 1) select a metagenome from the list of options (4440275.3) > > 2) for annnotation, select Genbank (don't select any cut-offs) > > 3) hit generate table > change the group table to domain, select Bacteria (the largest set) > > 6) hit to work bench, moving n proteins to the workbench > > 7) move over to the work bench viewer, here, you should see two options; > > download metagenome dna FASTA annotated by : genbank Repeat for other domains, combining the smaller ones. In principle you should be able to select all domains and create the file for the entire dataset, however, due to a known problem, if the number of sequences is too large you will get a server error so you need to restrict to smaller sets for large metagenomes. Regards, Mark On Jun 24, 2011, at 11:52 AM, bertagna(a)onid.orst.edu wrote: > sure, in the metagenome analysis portion, for organism classification; > > 1) select a metagenome from the list of options (4440275.3) > > 2) for annnotation, select Genbank (don't select any cut-offs) > > 3) hit generate table > > 4) change the group table from class to species > > 5) for the species, select candidatus pelagibacter ubique (the most abundant organism in this sample) > > 6) hit to work bench, moving 1846 proteins to the workbench > > 7) move over to the work bench viewer, here, you should see two options; > > download metagenome dna FASTA annotated by : genbank > > display annotated hits below; > > both of these options allow you to view the genbank annotations for the sequences affiliated with this organism. My question is this, is there a way to download this file for ALL of the organisms detected in given sample. > > Thanks, > > -Anthony > > Quoting Mark D'Souza <dsouza(a)mcs.anl.gov>: > >> 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 >>>> >>>> >>> >> >> >> > > > > Anthony Bertagnolli > Oregon State University > Department of Microbiology > http://www.mcb.oregonstate.edu/giovannoni/projects/subproject/OMZ.htm >

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Re: [mg-rast] First job complete; can't see the output?
by Mark DSouza 24 Jun '11

24 Jun '11

Hi, The ftp site has the following files: 4650979504 2011-06-23 14:30 run0045_lane3_read1_index0=342.fastq.gz 3726732946 2011-06-23 16:54 run0045_lane3_read2_index0=342.fastq.gz 919207936 2011-06-23 17:36 run0045_lane3_read2_index0=342.2.fastq.gz where the first column is the filesize in bytes. The read2,342.2 upload was certainly truncated, is the earlier read2 file the correct size? Mark ----- Original Message ----- > From: "Vivien Junker" <Vivien.Junker(a)cchmc.org> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Friday, June 24, 2011 12:14:45 PM > Subject: Re: First job complete; can't see the output? > Hi again, > > I'd like to send all the files over the weekend because it take 1-2 > days for the analyses. > > Could you please confirm that the last one I sent to you was > run0045_lane3_read2_index0=360.fastq.gz. > > Thanks again. > Best, > Viv > > >>> Mark D'Souza <dsouza(a)mcs.anl.gov> 6/24/2011 1:01 PM >>> > Hi, > > If you click on the browse metagenomes (globe) icon, the job is now > listed under the 'Available for Analysis List' , or just go to: > http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeOverview&metage… > > Be patient, I loaded a few of the analysis tables and it took some > time. > > Regards, > Mark > > > > On Jun 23, 2011, at 6:24 PM, Vivien Junker wrote: > > > Hi Mark, > > > > My original job is now complete. > > Put I can't see the output. > > > > Have searched for the job ID (26160) but it is not listed. > > > > Advice please? > > > > Many thanks, > > Viv > > > > >>> Mark DSouza <dsouza(a)mcs.anl.gov> 6/23/2011 5:43 PM >>> > > Hi, > > > > Looks goos, the file is 4650979504 bytes in size and the read2 file > > is coming in. Go ahead and upload all the files, drop me an email > > when you are done and I will transfer them over to your account. > > > > Regards, > > Mark > > > > ----- Original Message ----- > > > From: "Vivien Junker" <Vivien.Junker(a)cchmc.org> > > > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > > > Cc: "Mehdi Keddache" <Mehdi.Keddache(a)cchmc.org>, "Prakash > > > Velayutham" <Prakash.Velayutham(a)cchmc.org>, "Vivien Junker" > > > <Vivien.Junker(a)cchmc.org> > > > Sent: Thursday, June 23, 2011 3:39:24 PM > > > Subject: New file for transfer to my account > > > Hi Mark, > > > > > > I've uploaded another file to the incoming/vivien_junker folder > > > name: > > > run0045_lane3_read1_index0=342.fastq.gz. > > > > > > Can you please transfer to my account so I can start the analysis. > > > > > > There will be some 5 more coming. > > > Do you want me to submit on a daily basis or should I submit all > > > at > > > once? > > > > > > Thanks so much for all your help! > > > > > > Best, > > > Viv

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Re: [mg-rast] About some questions/problems of MG-RAST
by Mark D'Souza 24 Jun '11

24 Jun '11

Hi, The abundance counts for the M5NR table (your question two) have been corrected and are now consistent with the barchart from the workbench proteins, thanks for informing us about this. Regards, Mark On Jun 24, 2011, at 11:19 AM, Mark D'Souza wrote: > Hi, > >> 1) I cannot download the data from workbench. It's similar to the problem I asked last time, but not exactly the same. I selected all the annotated data to workbench, and then I tried to download them as the fastafile. However, it cannot be done. The webpage will go back to the main page of MG-RAST or to a page with error message. I doubt if it's related to the size of the file again. > > Unfortunately this is related to the earlier problem you had, we are looking into it. > >> 2) I found the abundance of certain groups are not identical under different functions. What I did was to select the archaea hits (1372 hits and the abundance is 4576) to workbench, and then, I used these hits to make barchart under functional classification. However, the abundance doesn't match these numbers. For example, The first classification on barchart is Cluster-based subsystems, which contains 5964 sequences. That is already more than the total abundance, 4576. And it is less than the barchart from the whole dataset (39830), so I don't know where these numbers were from. > > We are investigating, it looks like the abundance count is not being displayed correctly then the M5NR is selected. > >> 3) This is just a suggestion. Can you design a filter which is related to the abundance? For example, if the abundance is lower than a number, we can ignore them while annotating. > > I believe we have this implemented in the tables, you can specify a lower (or upper) cut-off for the abundance counts displayed. > > Sorry for the delay in responding. > > Regards, > Mark > > > > On Jun 13, 2011, at 10:23 PM, Chih-Ying Lay wrote: > >> Dear Sir/ Madame: >> >> Sorry, it's me again. I still found several problems while using MG-RAST, so I would like to let you know if they can be resolved. >> >> My working metagenome is 4449450.3, and all the problems happened while playing with this dataset. >> >> Here are the problems that I had: >> >> 1) I cannot download the data from workbench. It's similar to the problem I asked last time, but not exactly the same. I selected all the annotated data to workbench, and then I tried to download them as the fastafile. However, it cannot be done. The webpage will go back to the main page of MG-RAST or to a page with error message. I doubt if it's related to the size of the file again. >> >> 2) I found the abundance of certain groups are not identical under different functions. What I did was to select the archaea hits (1372 hits and the abundance is 4576) to workbench, and then, I used these hits to make barchart under functional classification. However, the abundance doesn't match these numbers. For example, The first classification on barchart is Cluster-based subsystems, which contains 5964 sequences. That is already more than the total abundance, 4576. And it is less than the barchart from the whole dataset (39830), so I don't know where these numbers were from. >> >> 3) This is just a suggestion. Can you design a filter which is related to the abundance? For example, if the abundance is lower than a number, we can ignore them while annotating. >> >> So....theses are my questions and problems for now. I really appreciate that you provide us such a good site! >> >> Thank you! >> >> Best Wishes, >> >> Chih-Ying Lay >

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Re: [mg-rast] First job complete; can't see the output?
by Mark D'Souza 24 Jun '11

24 Jun '11

Hi, If you click on the browse metagenomes (globe) icon, the job is now listed under the 'Available for Analysis List' , or just go to: http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeOverview&metage… Be patient, I loaded a few of the analysis tables and it took some time. Regards, Mark On Jun 23, 2011, at 6:24 PM, Vivien Junker wrote: > Hi Mark, > > My original job is now complete. > Put I can't see the output. > > Have searched for the job ID (26160) but it is not listed. > > Advice please? > > Many thanks, > Viv > > >>> Mark DSouza <dsouza(a)mcs.anl.gov> 6/23/2011 5:43 PM >>> > Hi, > > Looks goos, the file is 4650979504 bytes in size and the read2 file is coming in. Go ahead and upload all the files, drop me an email when you are done and I will transfer them over to your account. > > Regards, > Mark > > ----- Original Message ----- > > From: "Vivien Junker" <Vivien.Junker(a)cchmc.org> > > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > > Cc: "Mehdi Keddache" <Mehdi.Keddache(a)cchmc.org>, "Prakash Velayutham" <Prakash.Velayutham(a)cchmc.org>, "Vivien Junker" > > <Vivien.Junker(a)cchmc.org> > > Sent: Thursday, June 23, 2011 3:39:24 PM > > Subject: New file for transfer to my account > > Hi Mark, > > > > I've uploaded another file to the incoming/vivien_junker folder name: > > run0045_lane3_read1_index0=342.fastq.gz. > > > > Can you please transfer to my account so I can start the analysis. > > > > There will be some 5 more coming. > > Do you want me to submit on a daily basis or should I submit all at > > once? > > > > Thanks so much for all your help! > > > > Best, > > Viv

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Re: [mg-rast] About some questions/problems of MG-RAST
by Mark D'Souza 24 Jun '11

24 Jun '11

Hi, > 1) I cannot download the data from workbench. It's similar to the problem I asked last time, but not exactly the same. I selected all the annotated data to workbench, and then I tried to download them as the fastafile. However, it cannot be done. The webpage will go back to the main page of MG-RAST or to a page with error message. I doubt if it's related to the size of the file again. Unfortunately this is related to the earlier problem you had, we are looking into it. > 2) I found the abundance of certain groups are not identical under different functions. What I did was to select the archaea hits (1372 hits and the abundance is 4576) to workbench, and then, I used these hits to make barchart under functional classification. However, the abundance doesn't match these numbers. For example, The first classification on barchart is Cluster-based subsystems, which contains 5964 sequences. That is already more than the total abundance, 4576. And it is less than the barchart from the whole dataset (39830), so I don't know where these numbers were from. We are investigating, it looks like the abundance count is not being displayed correctly then the M5NR is selected. > 3) This is just a suggestion. Can you design a filter which is related to the abundance? For example, if the abundance is lower than a number, we can ignore them while annotating. I believe we have this implemented in the tables, you can specify a lower (or upper) cut-off for the abundance counts displayed. Sorry for the delay in responding. Regards, Mark On Jun 13, 2011, at 10:23 PM, Chih-Ying Lay wrote: > Dear Sir/ Madame: > > Sorry, it's me again. I still found several problems while using MG-RAST, so I would like to let you know if they can be resolved. > > My working metagenome is 4449450.3, and all the problems happened while playing with this dataset. > > Here are the problems that I had: > > 1) I cannot download the data from workbench. It's similar to the problem I asked last time, but not exactly the same. I selected all the annotated data to workbench, and then I tried to download them as the fastafile. However, it cannot be done. The webpage will go back to the main page of MG-RAST or to a page with error message. I doubt if it's related to the size of the file again. > > 2) I found the abundance of certain groups are not identical under different functions. What I did was to select the archaea hits (1372 hits and the abundance is 4576) to workbench, and then, I used these hits to make barchart under functional classification. However, the abundance doesn't match these numbers. For example, The first classification on barchart is Cluster-based subsystems, which contains 5964 sequences. That is already more than the total abundance, 4576. And it is less than the barchart from the whole dataset (39830), so I don't know where these numbers were from. > > 3) This is just a suggestion. Can you design a filter which is related to the abundance? For example, if the abundance is lower than a number, we can ignore them while annotating. > > So....theses are my questions and problems for now. I really appreciate that you provide us such a good site! > > Thank you! > > Best Wishes, > > Chih-Ying Lay

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Re: [mg-rast] M5NR
by Mark D'Souza 24 Jun '11

24 Jun '11

Hi, You are right, it is not being displayed correctly, we will get it fixed and get back to you. Glad to hear that you find MG-RAST useful. 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 23, 2011, at 8:01 PM, sophie.davidson(a)dpi.vic.gov.au wrote: > Hi, > > I am fiddling around with MG-RAST and have come across a bit of a problem when using M5NR as my annotation source. If I try generating a bar chart of any metagenomic data under the organism classification tab using this M5NR database, whether it's my own or a public dataset/s, I keep getting no bars in my graph - they are all zero! When I try selecting my group of annotation sources as all of the databases in the M5NR (i.e SwissProt, Genbank etc etc) then I get some lovely looking bars on my chart. I'm assuming this is a bug with the M5NR database since the organism classification using exactly the same databases all together result in a proper chart being generated, so I thought I'd pass this on. If it isn't a bug and I'm just not doing it properly then I apologise and look forward to getting the proper method from you guys! > > Other than this problem, so far I've found MG-RAST to be very valuable in my analysis, although it is only at the preliminary stages! So, thank you for producing such a user-friendly and robust program > > Cheers, > Sophie Davidson > > > Sophie Davidson | BioScience Researcher | BioScience Division > Department of Primary Industries | Victorian AgriBiosciences Centre | 1 Park Dr | Bundoora VIC 3083 > T: 03 9032 7111 | F: 03 9479 3618 | E: sophie.davidson(a)dpi.vic.gov.au > > > Notice: > This email and any attachments may contain information that is personal, confidential, > legally privileged and/or copyright. No part of it should be reproduced, adapted or communicated without the prior written consent of the copyright owner. > > It is the responsibility of the recipient to check for and remove viruses. > > If you have received this email in error, please notify the sender by return email, delete it from your system and destroy any copies. You are not authorised to use, communicate or rely on the information contained in this email. > > Please consider the environment before printing this email. > > > >

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