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

Fwd: Metagenomic sets
by Mark DSouza 01 Jun '11

01 Jun '11

Travis, Can you take a look and restart these (4452069.3 and 4452072.3)? Thanks, Mark ----- Forwarded Message ----- > From: "Panos Ioannidis" <panos.ioannidis(a)gmail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Cc: mg-rast(a)mcs.anl.gov > Sent: Wednesday, June 1, 2011 11:44:37 AM > Subject: Re: [mg-rast] Metagenomic sets > Hello, > > > Thanks for the quick reply! > > > I guess I'm using v3 (the one with the nice black background!). The > IDs are 4452069.3 and 4452072.3. > > > > Panos Ioannidis > > > On Wed, Jun 1, 2011 at 12:34 PM, Mark D'Souza < dsouza(a)mcs.anl.gov > > wrote: > > > Hi, > > Are you using version 2 or 3? Also, could you let us know the > metagenome IDs for the datasets that have this problem? > > We have been getting things back to normal after the power outage last > weekend, maybe we missed something. > > 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 1, 2011, at 11:07 AM, Panos Ioannidis wrote: > > > Hello, > > > > I logged in today (after a long time) and can't see my metagenomic > > data that I had uploaded almost a year ago. I can only see the > > accession numbers but can't see anything else (eg taxonomic or > > metabolic reconstruction) and in the home page of each of > > metagenomic set it says that the number of uploaded sequences is > > zero. > > > > Is this expected (eg due to maintenance on your website) and will > > come back to normal at some point? > > > > Thank you in advance, > > Panos Ioannidis

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Data analysis
by Eidy de Oliveira Santos 01 Jun '11

01 Jun '11

Dear, My data were submited to MG-RAST for more than 15 days. I wonder if there is any problem in the analysis. Regards, -- Eidy de Oliveira Santos PhD in Genetics (Biological Sciences) Pos doc Position Microbiology Lab Institute of Biology Federal University of Rio de Janeiro-UFRJ Brazil Contact: 51 21 25626567

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Re: [mg-rast] Metagenomic sets
by Panos Ioannidis 01 Jun '11

01 Jun '11

Hello, Thanks for the quick reply! I guess I'm using v3 (the one with the nice black background!). The IDs are 4452069.3 and 4452072.3. Panos Ioannidis On Wed, Jun 1, 2011 at 12:34 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > Hi, > > Are you using version 2 or 3? Also, could you let us know the metagenome > IDs for the datasets that have this problem? > > We have been getting things back to normal after the power outage last > weekend, maybe we missed something. > > 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 1, 2011, at 11:07 AM, Panos Ioannidis wrote: > > > Hello, > > > > I logged in today (after a long time) and can't see my metagenomic data > that I had uploaded almost a year ago. I can only see the accession numbers > but can't see anything else (eg taxonomic or metabolic reconstruction) and > in the home page of each of metagenomic set it says that the number of > uploaded sequences is zero. > > > > Is this expected (eg due to maintenance on your website) and will come > back to normal at some point? > > > > Thank you in advance, > > Panos Ioannidis > >

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Re: [mg-rast] Metagenomic sets
by Mark D'Souza 01 Jun '11

01 Jun '11

Hi, Are you using version 2 or 3? Also, could you let us know the metagenome IDs for the datasets that have this problem? We have been getting things back to normal after the power outage last weekend, maybe we missed something. 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 1, 2011, at 11:07 AM, Panos Ioannidis wrote: > Hello, > > I logged in today (after a long time) and can't see my metagenomic data that I had uploaded almost a year ago. I can only see the accession numbers but can't see anything else (eg taxonomic or metabolic reconstruction) and in the home page of each of metagenomic set it says that the number of uploaded sequences is zero. > > Is this expected (eg due to maintenance on your website) and will come back to normal at some point? > > Thank you in advance, > Panos Ioannidis

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Re: [mg-rast] Fwd: error in processing job 25014
by Andreas Wilke 01 Jun '11

01 Jun '11

We need a procedure to rebuild the memchache structures when they are not present. On May 31, 2011, at 12:43 PM, Travis Harrison wrote: > 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 > > ********************************************** > > 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] Dereplication error
by Mark D'Souza 01 Jun '11

01 Jun '11

Hi, This was due to a problem we had with the processing pipeline after the power outage over the weekend. It has now been fixed and your jobs are progressing, 3 have completed and 4 are at the similarity computation stage. Regards, Mark On Jun 1, 2011, at 11:05 AM, Mark D'Souza wrote: > Hi, > > Sorry about that, we will investigate 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 7:46 PM, Gustavo B. Gregoracci wrote: > >> Hello there, >> >> I've submitted 7 metagenomes for processing earlier today and it seems there is a problem. When I checked the status a dereplication error is showing in each metagenome. Can I do something about it or is it a MG-Rast error? Can you check this for me? My username is montedeletras ... >> >> Thanks in advance for the help, >> Best regards, >> Gustavo >> >> Gustavo Bueno Gregoracci >> -- >> MSc., Dr. in Microbiology (Genetics and Molecular Biology) >> Email: gustavo_biomed(a)yahoo.com >> -- >> Pos doc Student >> Laboratório de Microbiologia (Prof. Fabiano Thompson) >> Centro de Ciências de Saúde - Instituto de Biologia - UFRJ >> Tel: +55 (21) 2562-6567 >

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Metagenomic sets
by Panos Ioannidis 01 Jun '11

01 Jun '11

Hello, I logged in today (after a long time) and can't see my metagenomic data that I had uploaded almost a year ago. I can only see the accession numbers but can't see anything else (eg taxonomic or metabolic reconstruction) and in the home page of each of metagenomic set it says that the number of uploaded sequences is zero. Is this expected (eg due to maintenance on your website) and will come back to normal at some point? Thank you in advance, Panos Ioannidis

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Re: [mg-rast] Dereplication error
by Mark D'Souza 01 Jun '11

01 Jun '11

Hi, Sorry about that, we will investigate 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 7:46 PM, Gustavo B. Gregoracci wrote: > Hello there, > > I've submitted 7 metagenomes for processing earlier today and it seems there is a problem. When I checked the status a dereplication error is showing in each metagenome. Can I do something about it or is it a MG-Rast error? Can you check this for me? My username is montedeletras ... > > Thanks in advance for the help, > Best regards, > Gustavo > > Gustavo Bueno Gregoracci > -- > MSc., Dr. in Microbiology (Genetics and Molecular Biology) > Email: gustavo_biomed(a)yahoo.com > -- > Pos doc Student > Laboratório de Microbiologia (Prof. Fabiano Thompson) > Centro de Ciências de Saúde - Instituto de Biologia - UFRJ > Tel: +55 (21) 2562-6567

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Fwd: Data analysis
by Mark DSouza 01 Jun '11

01 Jun '11

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! > >>> > >>> > > > > > >

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Re: [mg-rast] download
by Mark D'Souza 01 Jun '11

01 Jun '11

Hi, I did not have any problem getting the barchart information (see below) using the datasets you had selected, it gets opened in a new browser window. Some possibilities: the window got opened but was behind other windows and was not visible or maybe your browser settings do not permit new windows to be opened by a website. Also, I am using the latest version of FireFox. Let us know if this does not help and you are not able to access the barchart information. 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 Subsystems 4440281.3 4443688.3 4463913.3 4463914.3 Amino Acids and Derivatives 0.560 0.470 0.932 0.966 Carbohydrates 0.584 0.487 0.950 0.987 Cell Division and Cell Cycle 0.335 0.232 0.707 0.748 Cell Wall and Capsule 0.466 0.362 0.843 0.869 Clustering-based subsystems 0.590 0.493 0.965 1.000 Cofactors, Vitamins, Prosthetic Groups, Pigments 0.501 0.427 0.885 0.928 DNA Metabolism 0.486 0.340 0.848 0.878 Dormancy and Sporulation 0.164 0.000 0.518 0.554 Fatty Acids, Lipids, and Isoprenoids 0.430 0.384 0.800 0.844 Iron acquisition and metabolism 0.296 0.212 0.682 0.708 Membrane Transport 0.431 0.291 0.829 0.851 Metabolism of Aromatic Compounds 0.323 0.255 0.654 0.704 Miscellaneous 0.518 0.443 0.899 0.935 Motility and Chemotaxis 0.354 0.157 0.764 0.801 Nitrogen Metabolism 0.310 0.183 0.714 0.742 Nucleosides and Nucleotides 0.421 0.324 0.790 0.829 Phages, Prophages, Transposable elements, Plasmids 0.374 0.230 0.719 0.744 Phosphorus Metabolism 0.319 0.249 0.735 0.748 Photosynthesis 0.059 0.052 0.369 0.409 Potassium metabolism 0.252 0.045 0.636 0.644 Protein Metabolism 0.522 0.420 0.893 0.942 RNA Metabolism 0.479 0.397 0.867 0.908 Regulation and Cell signaling 0.351 0.208 0.736 0.755 Respiration 0.437 0.309 0.816 0.849 Secondary Metabolism 0.170 0.070 0.554 0.578 Stress Response 0.411 0.311 0.782 0.810 Sulfur Metabolism 0.301 0.185 0.653 0.693 Virulence, Disease and Defense 0.447 0.275 0.804 0.831 On Jun 1, 2011, at 3:31 AM, <Dongmei.Li(a)csiro.au> wrote: > Dear MG-RAST team, > > Thank you so much for your help. > > I have encounter another problem in download the data. In the attached fig. I tried to download in reads in “Function Distribution (Inorganic Sulfur Assimilation)” section (bottom line of Page 2), it did not work. It will be great if you can give me some advice on how to download it. Thank you in advance. > > Regards, > Dongmei > > Dr. Dongmei Li > Research Scientist| MEOR > > CSIRO Food & Nutritional Sciences > Phone: +61 2 9490 5078 | Fax: +61 2 9490 5010 > dongmei.li(a)csiro.au | www.csiro.au | www.csiro.au/CFNS > Address: 11 Julius Ave. North Ryde,NSW 2113 > > PLEASE NOTE > The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. > Please consider the environment before printing this email. > > <MG-RAST - Metagenome Analysis.pdf>

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