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

Re: [mg-rast] 9 metagenomes uploaded yesterday and today not on the in progress list?
by Mark D'Souza 02 Jun '11

02 Jun '11

Hi, Sorry about that, the processing of the jobs was completed and the database was not updated to reflect the changed status correctly. We should be able to clean things up on our end, I will get back to you when this is done. 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 2, 2011, at 1:11 PM, Humphrey, Sam wrote: > Hi, > > I uploaded 9 metagenome files and they were on the in progress list yesterday but today they are no longer there. Do I need to resubmit or are they still in progress? > > Thank you, > > Sam Humphrey > Microbiologist > National Animal Disease Center > Agriculture Research Service-USDA > Ames, IA 50010 > > Samuel.Humphrey(a)ars.usda.gov > (515) 337-7495 > (515) 337-7428 > >

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9 metagenomes uploaded yesterday and today not on the in progress list?
by Humphrey, Sam 02 Jun '11

02 Jun '11

Hi, I uploaded 9 metagenome files and they were on the in progress list yesterday but today they are no longer there. Do I need to resubmit or are they still in progress? Thank you, Sam Humphrey Microbiologist National Animal Disease Center Agriculture Research Service-USDA Ames, IA 50010 Samuel.Humphrey(a)ars.usda.gov (515) 337-7495 (515) 337-7428

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Re: [mg-rast] How to Delete Data?
by Mark D'Souza 02 Jun '11

02 Jun '11

Hi, We will add a delete capability to the website soon, till then if you let me know your user login and the MGRAST ID for the dataset to be deleted 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 2, 2011, at 9:20 AM, Cleo HC Ho wrote: > Hi, > > I have uploaded the same data twice, so I'm wondering if there's a way to delete the extra metagenome?. > > Regards, > Cleo

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Re: [mg-rast] Problem - uploading Metagenomes
by Mark D'Souza 02 Jun '11

02 Jun '11

Hi Pedro, Sorry about that, the two jobs had a problem which was delaying the computation. I think it would be best to re-upload these two datasets, they are pretty small and will go through quickly. Please use the mg-rast(a)mcs.anl.gov address for future email, if I am on vacation another member of the team will help 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 On Jun 2, 2011, at 10:11 AM, Pedro Meirelles wrote: > Dear Mark, > I Uploaded 3 metagenomes in May 26th, only one has been completed (CVT2009_Coral3 (4465363.3)), the other 2 are "in progress": > > 4465361.3 – CVT2009_Coral1 > > 4465362.3 – CVT2009_Coral2 > > I have to re-upload them? > > Thank you very much > > Best regards > > Pedro

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How to Delete Data?
by Cleo HC Ho 02 Jun '11

02 Jun '11

Hi, I have uploaded the same data twice, so I'm wondering if there's a way to delete the extra metagenome?. Regards, Cleo

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Re: [mg-rast] Data analysis
by Tobias Paczian 02 Jun '11

02 Jun '11

Hm, I used the exact metagenomes the user did and was still unable to reproduce the problem. One thing to note is that in the example she used there are only two metagenomes. This will result in all p-values being 0, since there must be at least two groups and at least two metagenomes in at least one of the groups (making it a minimum of three mgs for a useful analysis). She is also apparently using a different browser, looking at her buttons. That should not cause a problem like this though. Although, I believe there is a safari bug that stores image maps in the cache. If the browser cached the image-map at the time when this was still broken, that might cause the problem. Cheers Tobi On Jun 1, 2011, at 10:58 AM, Mark DSouza wrote: > Hi Tobi, this may help, I have not tested the selections used to > get to the stage shown in the PDF. > Mark > > ----- Forwarded Message ----- >> From: "Torey Looft" <tlooft(a)iastate.edu> >> To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> >> Sent: Wednesday, June 1, 2011 10:42:39 AM >> Subject: Re: [mg-rast] Data analysis >> Thanks, >> >> After reproducing your steps I still have the same problem. Below >> is a >> screen shot of my analysis after selecting the "other sequences" >> category. As you can see, bacteria is expanded below. I am using >> Firefox v 3.6.11. Can you think of any reason it would work for you >> and not me? Thanks! >> >> Best, >> Torey >> >> On Wed, Jun 1, 2011 at 10:20 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> >> wrote: >>> Hi, >>> >>> I am still not able to reproduce this problem, I used your account >>> and datasets but the correct category gets displayed -- I clicked on >>> 'unclassified' for the image below. >>> >>> The steps I am taking are: >>> go to analysis page for a dataset, >>> select some additional metagenomes to add in the analysis, >>> select PCA and generate, >>> select metagenomes into two groups, >>> click on 'store grouping', >>> select barchart option and generate, >>> select 'calculate p-values' and draw >>> >>> Are we doing anything different? >>> >>> Thanks, >>> Mark >>> >>> >>> >>> >>> >>> On Jun 1, 2011, at 9:15 AM, Torey Looft wrote: >>> >>>> Hello Mark, >>>> >>>> I am still having the problem, it is how the categories are sorted >>>> with the p-values being displayed. >>>> What I did was: >>>> Picked a couple of my metagenomes and had MGRAST create a PCA plot >>>> (taxonomic catagories), I indicate 2 groups for my metagenomes, I >>>> go >>>> to the barchart and plot with p-values. The catagories are now >>>> sorted >>>> by p-value correct? When I click on a catagory like "bacteria", >>>> "bacteria" isn't what expands below, "unclassified" is what is >>>> shown. >>>> I believe the catagories that expand below reflect the non-sorted >>>> (non-p-value) positioned catagories. >>>> Example: the non-sorted categories would have "bacteria" on top, >>>> but >>>> when p-value is used, an "unclassified" category is shown. If I >>>> click >>>> on the "unclassified" category, "bacteria" is what is expanded >>>> below. >>>> This sorting problem continues with each taxonomic or functional >>>> level. >>>> I hope this explains it better. Thanks! >>>> >>>> Best, >>>> Torey >>>> >>>> On Tue, May 31, 2011 at 4:12 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> >>>> wrote: >>>>> Hi, >>>>> >>>>> No problem, we do want to get all the bugs fixed and everything >>>>> working the way it should. >>>>> >>>>> We did look into this and found a bug in the way the categories >>>>> were sorted which messed up the display. I believe it was fixed at >>>>> that time (2nd May) and I am not able to reproduce the error on >>>>> the website right now. The tools are getting more complex and it >>>>> is entirely possible that I am talking about a slightly different >>>>> bug which got fixed, please check and let us know if you can still >>>>> reproduce it and let us know, including additional details so we >>>>> can pinpoint the bug. >>>>> >>>>> Thanks, >>>>> Mark >>>>> >>>>> >>>>> >>>>> On May 31, 2011, at 3:34 PM, Torey Looft wrote: >>>>> >>>>>> Hello, >>>>>> >>>>>> Back in April I noticed the below problem and emailed MGRAST help >>>>>> and >>>>>> got a response. Sorry if I'm bugging, but I'm excited to compare >>>>>> some >>>>>> sample with your p-value tool and thought I would see if a fix is >>>>>> in >>>>>> the near future. Thanks a lot!! >>>>>> >>>>>> Best, >>>>>> Torey >>>>>> >>>>>> I think I have noticed a problem with the barchart section of >>>>>> your >>>>>> organism and functional classification analysis. When I use the >>>>>> p-value option, and I click on the categories (at each level >>>>>> distribution) the category that is expanded below isn't the one I >>>>>> clicked on. For example, if I click on nitrogen metabolism on >>>>>> level >>>>>> one, level two shows Clustering-based subsystem rather than the >>>>>> expanded nitrogen metabolism. I think I only noticed this with >>>>>> the >>>>>> p-vale option being used, but I what to use it for comparing >>>>>> groups. >>>>>> Thanks for your time! >>>>> >>>>> >>> >>> >>> >>> <mg rast.pdf>

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Problems with upload
by sophie.davidson＠dpi.vic.gov.au 01 Jun '11

01 Jun '11

Hi, I've been trying to upload my metagenomic data sets for about a month now and without any success. I have gone through the uploading process (i.e. dragged my sff file into the box and then clicked 'upload') but then the info in the 'upload status' tab says either 'upload completed' and 'waiting for processing' or 'upload started' and 'uploading...'. They have been at these stages for about 4 weeks now. According to the instructions I don't need to initiate processing of the upload so I was hoping you could help me out Cheers, Sophie 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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Fwd: Question about data in process
by William Trimble 01 Jun '11

01 Jun '11

---------- Forwarded message ---------- From: Nicolás Rascovan <nicorascovan(a)soilgene.net> Date: 2011/6/1 Subject: Question about data in process To: William Trimble <wltrimbl(a)gmail.com>, jared.wilkening(a)gmail.com Cc: mgrast(a)mcs.anl.gov Hi, I would like to ask you about 3 projects we have in progress. We had 9 metagenomes analyzed in the previous version of MG RAST and in the new one, only 6 of them have been finished. We were waiting for a couple of month, thinking that you might have lot of data to re analyze, but we are surprised that they have been in the same step since ever, so now we are wondering if maybe something failed and they got stucked there. I send you a screenshot of the samples that are in progress... Thanks a lot for your help, Nicolas Rascovan.

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Question about data in process
by Nicolás Rascovan 01 Jun '11

01 Jun '11

Hi, I would like to ask you about 3 projects we have in progress. We had 9 metagenomes analyzed in the previous version of MG RAST and in the new one, only 6 of them have been finished. We were waiting for a couple of month, thinking that you might have lot of data to re analyze, but we are surprised that they have been in the same step since ever, so now we are wondering if maybe something failed and they got stucked there. I send you a screenshot of the samples that are in progress... Thanks a lot for your help, Nicolas Rascovan.

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Re: [mg-rast] MG-RAST access
by Mark DSouza 01 Jun '11

01 Jun '11

Hi, Wes had contacted us earlier today as he is not able to do this due to a bug in the website. We will figure out the best way to get this done 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: "Pamela J. Morris" <pjmorris(a)belle.baruch.sc.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Wednesday, June 1, 2011 3:30:06 PM > Subject: [mg-rast] MG-RAST access > Hello, > > A former postdoctoral fellow from my laboratory, Wes Johnson (he > should be registered under either johnson(a)ecosystemsolutions.org or > wesman73(a)gmail.com ) uploaded metagenomic libraries (from dolphin > blowhole/upper respiratory tracts) onto MG-RAST - and as PI of the > project, I need to be given access to these libraries (I am registered > under pjmorris(a)belle.baruch.sc.edu ). I'll also being adding two other > people to the list of folks with access to these libraries within the > next few weeks. Wes Johnson's access will also remain as well. > > If you could help me with this (tell me how I can do this) - it would > be most appreciated. > > Thanks, and best wishes, Pam > > > > -------------------- > Pamela J. Morris, Ph.D. > Belle W. Baruch Institute for Marine and Coastal Sciences > Baruch Marine Field Laboratory > University of South Carolina > PO BOX 1630 > Georgetown, SC 29442 > > BMFL Office: (843) 904-9039 > BMFL FAX: (843) 546-1632 > Cell: (843) 991-8355 > pjmorris(a)belle.baruch.sc.edu > > BMFL Shipping address: > > 2306 Crab Hall Road > Highway 17 North, Hobcaw Barony > Georgetown, SC 29440

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