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

Re: [mg-rast] A Question
by Mark D'Souza 31 May '11

31 May '11

OK, Will just pointed me at the '&sims=1' trick to get the extended download page. Is this feature going to be released to our users in 3.1? Mark On May 31, 2011, at 4:41 PM, Mark D'Souza wrote: > Hi Travis, (or anyone else familiar with this operation) > > Is it possible to get all read annotations for a job through the 3.1 workbench? > > Thanks, > Mark > > > > On May 31, 2011, at 2:36 PM, Aaron Garoutte wrote: > >> Hello MG-RAST Team >> >> >> I put some assemblies through your pipeline. Now that I have the contigs annotated I would like to go back and map my raw reads to the contigs to get a better measure of abundance. To do this I need to know how each contig has been annotated. I found (under metagenome downloads) the gene clustering file. This lists the contigs that cluster together and has, what I assume is a group name like aa90_105. So my question is, this there a file I can download that links the clustered contigs (via the cluster name) to the subsystem annotation? >> >> >> As always thanks for your help >> >> >> Aaron >> >

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Re: [mg-rast] A Question
by Mark D'Souza 31 May '11

31 May '11

Hi, We have made a number of changes to the website which have not been put in place on the production and I believe one of the changes made will allow this download. I will check 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 On May 31, 2011, at 2:36 PM, Aaron Garoutte wrote: > Hello MG-RAST Team > > > I put some assemblies through your pipeline. Now that I have the contigs annotated I would like to go back and map my raw reads to the contigs to get a better measure of abundance. To do this I need to know how each contig has been annotated. I found (under metagenome downloads) the gene clustering file. This lists the contigs that cluster together and has, what I assume is a group name like aa90_105. So my question is, this there a file I can download that links the clustered contigs (via the cluster name) to the subsystem annotation? > > > As always thanks for your help > > > Aaron >

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Re: [mg-rast] A Question
by Mark D'Souza 31 May '11

31 May '11

Hi Travis, (or anyone else familiar with this operation) Is it possible to get all read annotations for a job through the 3.1 workbench? Thanks, Mark On May 31, 2011, at 2:36 PM, Aaron Garoutte wrote: > Hello MG-RAST Team > > > I put some assemblies through your pipeline. Now that I have the contigs annotated I would like to go back and map my raw reads to the contigs to get a better measure of abundance. To do this I need to know how each contig has been annotated. I found (under metagenome downloads) the gene clustering file. This lists the contigs that cluster together and has, what I assume is a group name like aa90_105. So my question is, this there a file I can download that links the clustered contigs (via the cluster name) to the subsystem annotation? > > > As always thanks for your help > > > Aaron >

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Re: [mg-rast] Data analysis
by Mark D'Souza 31 May '11

31 May '11

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!

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Data analysis
by Torey Looft 31 May '11

31 May '11

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!

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A Question
by Aaron Garoutte 31 May '11

31 May '11

Hello MG-RAST Team I put some assemblies through your pipeline. Now that I have the contigs annotated I would like to go back and map my raw reads to the contigs to get a better measure of abundance. To do this I need to know how each contig has been annotated. I found (under metagenome downloads) the gene clustering file. This lists the contigs that cluster together and has, what I assume is a group name like aa90_105. So my question is, this there a file I can download that links the clustered contigs (via the cluster name) to the subsystem annotation? As always thanks for your help Aaron

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Re: [mg-rast] Fwd: error in processing job 25014
by Travis Harrison 31 May '11

31 May '11

Problem is that memcache gets wiped clean when the server goes down. I will reload memcache for pipline, this is a good time to switch to kursk-1. - Travis On Tue, May 31, 2011 at 12:22 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > Hi Travis, > > Can you check/restart this job: > > 25014 > Job: > created_on 2011-05-30 20:54:12 > file_size_raw 73594012 > job_id 25014 > metagenome_id 4465417.3 > name BioMeta3_gt800 > owner 15232 > public > viewable > PipelineStage: > upload completed 2011-05-30 20:54:13 > preprocess completed 2011-05-30 20:54:18 > dereplication completed 2011-05-30 20:54:24 > usearch completed 2011-05-30 20:56:40 > screen completed 2011-05-30 20:54:26 > genecalling completed 2011-05-30 20:55:47 > cluster_aa90 completed 2011-05-30 20:56:03 > loadAWE error 2011-05-30 20:56:06 > cluster_rna97 completed 2011-05-30 21:41:58 > rna error 2011-05-30 21:42:15 > > seems to have failed while processing RNA sims: > /mcs/bio/mg-rast/jobsv3/25014$ cat proc/450.rna/process_sims.out > Sorting using no threades ... Done > Running in rna sim mode. > Running in lca mode. > Loading memcache ach data for mapping ... > > Thanks, > Mark > > > > Begin forwarded message: > > > From: hrbeller(a)lbl.gov > > Date: May 31, 2011 10:59:31 AM CDT > > To: MG- Rast <mg-rast(a)mcs.anl.gov> > > Subject: Re: [mg-rast] error in processing job 25014 > > > > Dear Folker, > > > > Thanks for your reply. The job number is in the title (25014). The name > is BioMeta3_gt800. > > > > Thanks, > > Harry > > > >> Dear Harry, > >> > >> please send us the metagenome ID (and Job number) if possible. > >> > >> Best, > >> Folker > >> > >> > >> On May 31, 2011, at 5:32 AM, hrbeller(a)lbl.gov wrote: > >> > >>> Hello. I uploaded a metagenome fasta file and saw that there was an > error in "calculating sims". What do I need to do at this point? > >>> > >>> Thanks, > >>> Harry > >> > -- > > > > -- > > ********************************************** > > Harry Beller, Ph.D. > > Staff Scientist > > Lawrence Berkeley National Laboratory > > 1 Cyclotron Rd., Mail Stop 70A-3317 > > Berkeley, CA 94720 > > > > Ph: 510-486-7321 > > HRBeller(a)lbl.gov > > ********************************************** > >

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Re: [mg-rast] Forward of moderated message
by Mark DSouza 31 May '11

31 May '11

This got handled through the mg-rast-users rejection message. mark > From: mg-rast-users-bounces(a)lists.mcs.anl.gov > To: mg-rast(a)mcs.anl.gov > Sent: Tuesday, May 31, 2011 12:33:12 PM > Subject: [mg-rast] Forward of moderated message

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Forward of moderated message
by mg-rast-users-bounces＠lists.mcs.anl.gov 31 May '11

31 May '11

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Re: [mg-rast] MG Rast pipeline queries
by Mark D'Souza 31 May '11

31 May '11

Hi, We will investigate and get back to you, sorry about the delay. 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 May 31, 2011, at 3:17 AM, baldrian(a)biomed.cas.cz wrote: > Dear MG Rast team, > > I have uploaded some jobs that do not seem to progress (their status is for several months > the same), is it possible to remove these. In my case, the run numbers are: > > 7801, 7918 and 12669 > > Some recent runs uploaded but do not continue in the process, this applies to runs: > > 24980-24992 > > For runs 25015-25018, there is a message "Calculating Sims: Error" - I would be happy to > know if these runs will be continued and if not what was the matter. > > Thank you for your help, > > Petr Baldrian > >

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