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

M5NR
by sophie.davidson＠dpi.vic.gov.au 23 Jun '11

23 Jun '11

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

23 Jun '11

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] Downloading a LARGE batch of 16S metagenomes
by Jack Gilbert 23 Jun '11

23 Jun '11

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

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Re: [mg-rast] Error: Edit Metadata
by Mark DSouza 23 Jun '11

23 Jun '11

Hi, We will take a look at the 4 datasets and find out what has gone wrong and get back to you. Regards, Mark ----- Original Message ----- > From: "Steve Essinger" <sessinger(a)gmail.com> > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > Cc: mg-rast(a)mcs.anl.gov > Sent: Thursday, June 23, 2011 3:48:10 PM > Subject: Re: [mg-rast] Error: Edit Metadata > Mark, > > > Thank you so much for your quick response. It appears to be working > correctly on my end now as well. > > > One more issue: I have 4 datasets in progress that indicate a Loading > Database: Error. How do I kill these processes and restart them? I do > not know what is causing the error. > > > Thanks, > Steve > > > On Thu, Jun 23, 2011 at 4:35 PM, Mark DSouza < dsouza(a)mcs.anl.gov > > wrote: > > > Hi, > > This has now been fixed, thanks for letting us know about the problem. > > Regards, > Mark > > > > > ----- Original Message ----- > > From: "Mark DSouza" < dsouza(a)mcs.anl.gov > > > To: "Steve Essinger" < sessinger(a)gmail.com > > > Cc: mg-rast(a)mcs.anl.gov > > Sent: Thursday, June 23, 2011 2:39:14 PM > > Subject: Re: [mg-rast] Error: Edit Metadata > > Hi, > > > > Sorry about that, we will take a look and get it fixed. > > > > -- > > 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: "Steve Essinger" < sessinger(a)gmail.com > > > > To: mg-rast(a)mcs.anl.gov > > > Sent: Thursday, June 23, 2011 2:27:03 PM > > > Subject: [mg-rast] Error: Edit Metadata > > > Hi, > > > > > > > > > I've uploaded a bunch of metagenomic datasets that I now wish to > > > edit > > > their metadata. When I click on the link 'Edit Metadata' I get the > > > following response: > > > > > > > > > >>> Unable to fetch attribute 'owner' of JobDB::Job id 28416 from > > > >>> db > > > >>> 'WebAppBackend' of type 'User' with id 49300. at > > > >>> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_1_0/common/lib/PPO/DBObject.pm > > > >>> line 736 > > > > > > > > > Any thoughts? > > > > > > > > > Thanks, > > > Steve

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Re: [mg-rast] New file for transfer to my account
by Mark DSouza 23 Jun '11

23 Jun '11

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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Your MG-RAST jobs (24943, 24944, 1215_sample1, GSR2NIA01.sff)
by Mark DSouza 23 Jun '11

23 Jun '11

Hi, I am sorry but the jobs you submitted to MG-RAST have failed and will need to be resubmitted. The data files used to create the jobs were lost due to a hardware problem and we are not able to restart the jobs. Once again, I apologize for the inconvenience and delay before you can get the results. -- 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] Error: Edit Metadata
by Steve Essinger 23 Jun '11

23 Jun '11

Mark, Thank you so much for your quick response. It appears to be working correctly on my end now as well. One more issue: I have 4 datasets in progress that indicate a Loading Database: Error. How do I kill these processes and restart them? I do not know what is causing the error. Thanks, Steve On Thu, Jun 23, 2011 at 4:35 PM, Mark DSouza <dsouza(a)mcs.anl.gov> wrote: > Hi, > > This has now been fixed, thanks for letting us know about the problem. > > Regards, > Mark > > ----- Original Message ----- > > From: "Mark DSouza" <dsouza(a)mcs.anl.gov> > > To: "Steve Essinger" <sessinger(a)gmail.com> > > Cc: mg-rast(a)mcs.anl.gov > > Sent: Thursday, June 23, 2011 2:39:14 PM > > Subject: Re: [mg-rast] Error: Edit Metadata > > Hi, > > > > Sorry about that, we will take a look and get it fixed. > > > > -- > > 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: "Steve Essinger" <sessinger(a)gmail.com> > > > To: mg-rast(a)mcs.anl.gov > > > Sent: Thursday, June 23, 2011 2:27:03 PM > > > Subject: [mg-rast] Error: Edit Metadata > > > Hi, > > > > > > > > > I've uploaded a bunch of metagenomic datasets that I now wish to > > > edit > > > their metadata. When I click on the link 'Edit Metadata' I get the > > > following response: > > > > > > > > > >>> Unable to fetch attribute 'owner' of JobDB::Job id 28416 from db > > > >>> 'WebAppBackend' of type 'User' with id 49300. at > > > >>> > /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_1_0/common/lib/PPO/DBObject.pm > > > >>> line 736 > > > > > > > > > Any thoughts? > > > > > > > > > Thanks, > > > Steve >

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Re: [mg-rast] MG-RAST comment
by Mark DSouza 23 Jun '11

23 Jun '11

This got resolved mark ----- Original Message ----- > From: "Adina Chuang Howe" <adina.chuang(a)gmail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Cc: mg-rast(a)mcs.anl.gov > Sent: Thursday, June 23, 2011 12:17:34 PM > Subject: Re: [mg-rast] MG-RAST comment > see screen shots...its just flipped - nbd. > > -a > > > On Thu, Jun 23, 2011 at 1:13 PM, Mark D'Souza < dsouza(a)mcs.anl.gov > > wrote: > > > Hi, > > I took a look but did not find this, can you please let us know the > steps you took and possibly a screenshot? > > Thanks, > 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 5:00 PM, Adina Chuang Howe wrote: > > > Not that it bothers me at all but just fyi... > > > > functional annotation and functional classification headings on tabs > > are swapped on the newest version. > > > > Still looks great! > > -adina > >

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Re: [mg-rast] Error: Edit Metadata
by Mark DSouza 23 Jun '11

23 Jun '11

Hi, This has now been fixed, thanks for letting us know about the problem. Regards, Mark ----- Original Message ----- > From: "Mark DSouza" <dsouza(a)mcs.anl.gov> > To: "Steve Essinger" <sessinger(a)gmail.com> > Cc: mg-rast(a)mcs.anl.gov > Sent: Thursday, June 23, 2011 2:39:14 PM > Subject: Re: [mg-rast] Error: Edit Metadata > Hi, > > Sorry about that, we will take a look and get it fixed. > > -- > 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: "Steve Essinger" <sessinger(a)gmail.com> > > To: mg-rast(a)mcs.anl.gov > > Sent: Thursday, June 23, 2011 2:27:03 PM > > Subject: [mg-rast] Error: Edit Metadata > > Hi, > > > > > > I've uploaded a bunch of metagenomic datasets that I now wish to > > edit > > their metadata. When I click on the link 'Edit Metadata' I get the > > following response: > > > > > > >>> Unable to fetch attribute 'owner' of JobDB::Job id 28416 from db > > >>> 'WebAppBackend' of type 'User' with id 49300. at > > >>> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_1_0/common/lib/PPO/DBObject.pm > > >>> line 736 > > > > > > Any thoughts? > > > > > > Thanks, > > Steve

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Re: [mg-rast] Error: Edit Metadata
by Mark DSouza 23 Jun '11

23 Jun '11

Andi, Could you take a look. I checked his jobs and was able to recreate the error, but we don't have a job 28416 in JobDB http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeOverview&metage… gets >>> Unable to fetch attribute 'owner' of JobDB::Job id 28612 from db 'WebAppBackend' of type 'User' with id 49300. at /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_1_0/common/lib/PPO/DBObject.pm line 736 Mark ----- Original Message ----- > From: "Steve Essinger" <sessinger(a)gmail.com> > To: mg-rast(a)mcs.anl.gov > Sent: Thursday, June 23, 2011 2:27:03 PM > Subject: [mg-rast] Error: Edit Metadata > Hi, > > > I've uploaded a bunch of metagenomic datasets that I now wish to edit > their metadata. When I click on the link 'Edit Metadata' I get the > following response: > > > >>> Unable to fetch attribute 'owner' of JobDB::Job id 28416 from db > >>> 'WebAppBackend' of type 'User' with id 49300. at > >>> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_1_0/common/lib/PPO/DBObject.pm > >>> line 736 > > > Any thoughts? > > > Thanks, > Steve

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