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

Another error in processing job 25014
by hrbeller＠lbl.gov 01 Jun '11

01 Jun '11

Hello. I believe you tried to re-upload metagenome BioMeta3_gt800 (job 25014). There was a different error this time (dereplication). 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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Dereplication error during initial processing
by nikole kimes 01 Jun '11

01 Jun '11

Do you have any recommendations as to what I might be doing wrong. I have uploaded three metagenomes (sff files), and all three seem to be stuck at the first phase of processing. Thank you kindly, Nikole Your Data (In Progress)back to all metagenomes[?]<http://blog.metagenomics.anl.gov/howto/the-metagenome-browser/> *current filter* » all data[?]<http://blog.metagenomics.anl.gov/howto/using-collections> personal collection- project86 Moving pictures of the human microbiome (1965) turnbaugh_twins_moafts_v2 (265) jones_fleas (251) costello_whole_body_sites (214) costello_snakes (109) Global Ocean Sampling Expedition (88) fierer_undergraduate_palms (82) dominguez_bello_babies (80) lauber_88_soils (76) keonig_infant_time_series (56) [ + ] view all (76 more) chu_arctic_soils (52) eilers_soils (45) muegge_mammals_paper_mammal_samples_MG (39) crawford_mice (38) muegge_mammals_paper_mammal_samples_16S (38) nemergut_costa_rica_soils (27) Chula Vista, CA Solar Saltern Study (24) rousk_ph_gradient (23) NIH Protist cDNA Survey (21) Diel Metatranscriptomes at Western Channel Observatory (19) mladenov_bangladesh_arsenic (18) muegge_mammals_paper_human_samples_16S (18) muegge_mammals_paper_human_samples_MG (18) Twin Gut Microflora Study (18) Microbial Community Genomics at the HOT/ALOHA (14) Stressed Coral Holobionts (13) Human Faeces - Kurokawa (13) iCOMM (Western English Channel PML samples) (12) ramirez_voc (12) iCOMM Resampled (Western English Channel PML samples) (12) Surface Water Marine Microbial Community Gene Expression (12) Ocean Viruses (10) Aquacultured Fish (Kent State) (10) Guerrero Negro Metagenomes (10) Metagenomic Analysis of Kimchi (10) not specified (9) bowers_storm_peak_air (9) Freshwater Fish from Aquaculture Facility Metagenomes - Viral an (9) Mussel Transcripts Metagenomes (Varying body locations) (9) Antarctica Aquatic Microbial Metagenome (9) Northern Line Islands (8) cDNA - Plymouth Marine Lab Coastal Waters project (8) Sapelo Island Bacterioplankton Vanillate/DSMP Study (8) Marine Metagenome from Coastal Waters project at Plymouth Marine (8) Sapelo Island Bacterioplankton Metagenome (8) Biodiversity of Viruses in Wild Plants (8) Marine Bacterioplankton Metagenomes (7) Microbialites (6) Monterey Bay Microbial Study (6) Yellowstone National Park Octopus/Mushroom Hot Springs Metagenom (6) Laboratory Mosquitoes Metagenome (5) Peru Margin Subseafloor Biosphere (5) Human Lung Healthy vs Cystic Fibrosis Metagenome (5) Botany Bay Metagenomes (5) Marine Phages (4) Chicken Cecum Microbiome (4) Cow Rumen (4) Metagenomic Analysis of the North Atlantic Spring Bloom (4) Canine Intestinal Microbiome (4) "Whale Fall" Bone Metagenome (3) Salton Sea (3) Viral Metagenome from Terrestrial Hot Springs (3) Mosquito Metagenome (3) Populus Microbiome (3) Soudan Mine Metagenome (2) Alvinella Pompejana Epibiont Metagenome (2) Oxygen Minimum Zone (2) Mediterranean Bathypelagic Habitat (2) Marine NaCl-Saturated Brine Metagenome (2) Human Faeces - Turnbaugh (2) Marine Synechococcus Metagenome (2) Sargasso Sea Bacterioplankton Community (2) Human Oropharyngeal Metagenome (2) Acid Mine Drainage Metagenome (2) Tampa Bay Viral Metagenome (1) Skan Bay, Alaska Ocean Viruses (1) Chesapeake Bay Virioplankton (1) Gut Microbiome of Termites (1) Oral Metagenome - Human (1) Deep Sea Microorganisms (1) Rain Forest Soil Microbial Communities (1) Human Gut Microbial Metagenome (1) Filtered Microorganisms in Mariana Trough Hydrothermal Fluid (1) Waseca County Farm Soil Metagenome (1) Phosphorus Removing (EBPR) Sludge Community (1) Mediterranean Gutless Worm Metagenome (1) [ - ] view less PI51 not specified (3128) Jones (251) Venter (88) Gilbert (59) Ley (56) Rodriguez-Brito (33) Katz (21) Gordon (20) Moran (18) DeLong (15) [ + ] view all (41 more) Rohwer (14) Vega Thurber (13) hattori (13) Angly (12) Hewson (12) Dinsdale (11) Hugenholtz (10) Jeon (10) Craft (9) Hoffman (9) White (8) Roossinck (8) Willner (7) Karl (7) Breitbart (6) Delong (6) Bhaya (6) Bishop-Lilly (5) Biddle (5) Thomas (5) Rubin (4) Giovannoni (4) Fahey Jr. (4) Valentine (3) Schoenfeld (3) Schadt (3) Edwards (2) Cary (2) Rodríguez-Valera (2) Rodriguez-Valera (2) Palenik (2) Naganuma (2) Banfield (2) McDaniel (1) Kendall (1) Wommack (1) Leadbetter (1) Lazarevic (1) Hazen (1) Wang (1) Dubilier (1) [ - ] view less biome23 not specified (2979) animal-associated habitat (531) marine habitat (253) soil (55) saltern (21) freshwater (15) microbial mat (11) food (10) plant associated (8) sediment (6) [ + ] view all (13 more) hot spring ; microbial mat (6) extreme habitat ; hypersaline (5) mine drainage (3) hydrothermal vent (3) hot spring (3) plant-associated habitat (3) fossil (2) freshwater habitat (1) microbial mat ; fossil (1) extreme habitat (1) human-associated habitat (1) sludge (1) mine drainage ; microbial mat (1) [ - ] view less altitude19 not specified (3448) 1655 ; Meter (359) 277 ; Meter (43) na (11) 310 (10) 965-970 ; Meter (8) -69.1896 (8) 600 (8) -152 ; Meter (5) 79 (4) [ + ] view all (9 more) ~2438 (3) 12.19200 (2) 3100 (2) -731 ; Meter (1) 1 (1) na ; Meter (1) 5 ; Meter (1) 250 (1) 323 (1) [ - ] view less depth89 not specified (3612) .05 ; Meter (44) 2 (30) surface (25) 5 (21) 1 (13) 1.8 (11) 1.5 (9) ~10 (9) na (7) [ + ] view all (79 more) 1.7 (6) 5 ; Meter (6) .001 (6) 1.9 (4) 0-0.005 ; Meter (4) 0-0.002 ; Meter (4) 2.1 (4) 14 (4) 10 (4) 1.4 (3) 2.2 (3) 200 (3) 9 (3) 714 (2) 12 (2) 2500 (2) 1674 (2) 80 (2) 1-120 m (2) surface - 5 (2) 2850 ; Meter (2) 3101 (2) 130 (2) 4000 (2) 500 (2) 70 (2) 770 (2) 1 ; Meter (2) .05 (2) 30 (1) western GOM = surface to 164, Eastern GOM =3 to 90, Northeastern GOM = 1 to 120, Texas Coast = 1 to 120 (1) 13.2 m (1) 2 m (1) 4.2 (1) 1.6 (1) 1.1 (1) 19 (1) surface to 245 (1) .1 (1) 0.2 m (1) .3 (1) 560 (1) 2-968 m (1) 10 to 3246 (1) 0 - 245 (1) 3-90 (1) 0-164 (1) 2 to 968 (1) 32 ; Meter (1) 50 ; Meter (1) 731 ; Meter (1) 90 (1) 65 (1) na ; Meter (1) 18 (1) 12.7 (1) 11.5 (1) 23 (1) 0.15 ; Meter (1) 1.82926829268293 ; Meter (1) 2 ; Meter (1) 2,850 (1) 0-.1 (1) 0-.001 (1) .001-.002 (1) .002-.003 (1) .003-.004 (1) .004-.005 (1) .005-.006 (1) .006-.010 (1) .010-.022 (1) .022-.034 (1) .034-.049 (1) 16 ; Meter (1) 0 (1) 0-.1 ; Meter (1) 1.2 (1) 2.07 (1) 2.8 (1) [ - ] view less location150 not specified (3014) Boulder County (251) Boulder, CO (110) Cedar Creek Natural History Area in Minnesota (44) St Louis Zoo (44) L4 sampling site, Western Channel Obersvatory (42) Amherst, Massachusetts (21) St. Louis, MO (18) Chula Vista, CA (17) coastal waters of a fjord close to Bergen, Norway (16) [ + ] view all (140 more) Sapelo Island, GA (16) HOT station ALOHA (14) San Diego University, San Diego, California (12) Hawaii Institute of Marine Biology (12) Sargasso Sea (10) Exportadora de Sal saltworks, Guerrero Negro, Baja California Sur, Mexico(10) Seoul (10) Indian Ocean (9) Mercury, Navada (8) Area de Conservación Guanacaste (8) Tropical South Pacific (6) Tilapia Channel (FW1) at Kent SeaTech, Salton Sea, CA (6) Yellowstone Natl Park Hot Springs, Moran, WY (6) Ocean Drilling Program leg 201, site 1229 (5) San Diego Zoo (5) Port Quin, Cornwall (5) Adult cystic fibrosis Clinic at the University of California San Diego Medical Center (5) Ace Lake Vestfold Hills, Antarctica (5) Botany Bay near Bare Island, Sydney, Australia (5) Naval Medical Research Center, Silver Spring, Maryland (4) Urbana, IL (4) Bloomington, IL (4) Firth of Clyde (4) Small Animal Clinic of the University of Illinois, College of Veterinary Medicine, Urbana, IL (4) Indian Ocean - Coccos Keeling, Inside Lagoon (3) water hole (3) Salton Sea, California (3) Yellowstone Natl Park (3) Caney Fork River, TN (3) Indian Ocean - International waters between Madagascar and South Africa (2) Polynesia Archipelagos - Moorea, Cooks Bay (2) Indian Ocean - St. Anne Island, Seychelles (2) Indian Ocean - International Water Outside of Reunion Island (2) Outside Halifax, Nova Scotia (2) Northern Gulf of Maine (2) Fanning (Tabuaeran) Atoll (2) Soudan Underground Mine, on the south shore of Lake Vermilion, MN (2) Chesapeake Bay, MD (2) Upwelling, Fernandina Island (2) Indian Ocean - International water between Madagascar and South Africa (2) Black smoker chimneys on East Pacific Rise (2) Pacific Ocean, Santa Cruz Basin (2) Northeastern Gulf of Mexico (2) Texas Coast, Gulf of Mexico (2) Iquique, Chile (2) Colorado (2) Pozas Azules II (2) Rio Mesquites (2) Highborne Cay Island (2) Ionian Km3 station (2) crystallizer pond CR30 in the multi-pond saltern "Bras del Port" located in Santa Pola (2) prebead pond at Kent SeaTech, Salton Sea, CA (2) Washington University, St. Louis, MI (2) South Pacific Subtropical Gyre (2) Pacific North Equatorial (2) Scripps Institution of Oceanography, La Jolla, CA (2) Bermuda Atlantic Time-series Study (BATS) station (2) SJ0609.03 Station (2) SJ0609.12 Station (2) KM0703.04 Station (2) KM0703.24 Station (2) Kingman Atoll (2) Mariana Trough (2) Christmas (Kiritimati) Atoll (2) Palmyra Atoll (2) Richmond Mine, Iron Mountain, CA (2) Block Island, NY (1) Cape May, NJ (1) Equatorial Pacific TAO Buoy (1) Tropical South Pacific - 201 miles from F. Polynesia (1) Outside Seychelles, Indian Ocean (1) Tampa Bay, CA (1) Gulf of Maine (1) Browns Bank, Gulf of Maine (1) Bedford Basin, Nova Scotia (1) Bay of Fundy, Nova Scotia (1) Gulf of Mexico (1) Newport Harbor, RI (1) Delaware Bay, NJ (1) Off Nags Head, NC (1) North American East Coast, South of Charleston, SC (1) Caribbean Sea, Off Key West, FL (1) Caribbean Sea, Gulf of Mexico (1) Yucatan Channel (1) Caribbean Sea, Rosario Bank (1) Caribbean Sea, Northeast of Colon (1) Lake Gatun, Panama (1) Eastern Tropical Pacific, Gulf of Panama (1) Eastern Tropical Pacific, 250 miles from Panama City (1) Eastern Tropical Pacific, 30 miles from Cocos Island (1) Eastern Tropical Pacific, Dirty Rock, Cocos Island (1) Open Ocean, 134 miles NE of Galapagos (1) Galapagos Islands, Devil (1) Galapagos Islands, Coastal Floreana (1) Galapagos Islands - North James Bay, Santigo Island (1) Galapagos Islands - Warm seep, Roca Redonda (1) Strait of Georgia and adjacent inlets, Barclay Sound (1) Galapagos Islands - Mangrove on Isabella Island (1) Punta Cormorant, Hypersaline Lagoon, Floreana Island (1) Galapagos Islands - North Seamore Island (1) Galapagos Islands - Wolf Island (1) Cabo Marshall, Isabella Island (1) Polynesia Archipelagos - Moorea, Outside Cooks (1) Polynesia Archipelagos - Rangirora Atoll (1) Indian Ocean - 500 Miles west of the Seychelles in the Indian Ocean (1) Indian Ocean - East coast Zanzibar (Tanzania), offshore Paje lagoon (1) Indian Ocean - West coast Zanzibar (Tanzania), harbour region (1) Southern Ocean off the west Antarctic Peninsula shelf (1) Canadian Arctic (1) Arctic Chukchi (1) Bay of British Columbia (1) Eastern Gulf of Mexico (1) Western Gulf of Mexico (1) the Arctic Ocean, the Strait of Georgia, (1) Water hole (1) Mid-Atlantic Ridge (1) Bocas del Toro (1) Sargasso Sea, Hydrostation S (1) Skan Bay, Alaska (1) Chesapeake Bay (1) the secondary forest of Bosque Lluvioso, an INBio private reserve near the town of Guápiles, Costa Rica (1) Organic Lake (1) Newcomb Bay, Antarctica (1) Antarctic Territory Claimed by Australia (1) Pacific Equatorial Divergence Province (1) Pacific North Equatorial Countercurrent (1) North Pacific Tropical Gyre (1) SJ0609.07 Station (1) SJ0609.07 Station (1) Station SJ0609.09 (1) SJ0609.09 Station (1) Geneva (1) subtropical lower montane wet forest in the Luquillo Experimental Forest (1) Farm in Waseca County, Minnesota. (1) Nine Springs Wastwater Treatment Plant, Madison, WI (1) Polynesia Archipelagos - Tikehau Lagoon (1) Tropical South Pacific - 600 miles from F. Polynesia (1) Tropical South Pacific - 400 miles from F. Polynesia (1) Tropical South Pacific - 300 miles from F. Polynesia (1) Indian Ocean - Madagascar Waters (1) [ - ] view less ph17 not specified (3830) 7 ; pH (44) 8.1 (10) 6-9 (10) 8.05 (5) 7.7 ; pH (2) 7.9 ; pH (2) 7.4 ; pH (2) 5.33-6.40 (2) 8.14 (2) [ + ] view all (7 more) 6.7 (2) 8.0 ; pH (1) 6.70 (1) 5.5 (1) 7.34 (1) .83 (1) 1.1 (1) [ - ] view less country30 not specified (3043) United States of America (669) United Kingdom (50) Norway (16) Mexico (15) Japan (14) Ecuador (12) Costa Rica (11) Bermuda (9) Korea (South) (9) [ + ] view all (20 more) 0 (8) Canada (8) Australia (7) French Polynesia (6) Antarctica (6) Panama (5) Peru (5) Namibia (4) Seychelles (3) Tanzania (2) Chile (2) Bahamas (2) Italy (2) Spain (2) Argentina (2) Honduras (1) Portugal (1) Switzerland (1) Puerto Rico (1) Madagascar (1) [ - ] view less temperature122 not specified (3661) 20 (13) 15 (11) 30 ; Celsius (8) 15 ; Celsius (5) 17.1-18.3 (5) 26.4 (4) 26 ; Celsius (4) 10.3 (4) 13.9 (4) [ + ] view all (112 more) 15.5 (4) 15.9 (4) 27.6 (4) 25.8 (4) 27-30 (4) 30 (4) 15.8 (4) 28.6 (3) 28 (3) 22.9 (3) 18.6 (3) 27 (3) 27.8 (3) 30-34 (3) 10.01 (3) 4 ; Celsius (3) 20.2 (2) 11 (2) 28.9 (2) 26.6 (2) 26.2 (2) 26.5 (2) 23.8 (2) 17.3 (2) 17.9 (2) 10.1 (2) 11.8 (2) 12.4 (2) 15.2 (2) 15.4 (2) 20.5 (2) 19.8 (2) 25 (2) 28.7 (2) 28.3 (2) 27.5 (2) 20-80 (2) 18.7-30 (2) 14.7 - 30.5 (2) 13.93 (2) 22.19 (2) 18.53 (2) 1.46 (2) 7.25 (2) 24.93 (2) 4.78 (2) 93 (2) 10.05 (2) 9.7 (2) 9.6 (2) 15.7 (2) 27.64 ; Celsius (2) 17.8 (2) 21.2 (2) 28.4537 (2) 25.1453 (2) 26.8523 (2) 26.3084 (2) 29.1718 (2) 28.7966 (2) 60 (2) 65 (2) 58-67 (2) 12 (1) 27.2 (1) 27.9 (1) 18.2 (1) 11.7 (1) 11.2 (1) western GOM = 20.2 to 30.5, Eastern GOM =21.6 to 30.0, Northeastern GOM = 18.7 to 30.0, Texas Coast = 14.7 to 30.5 (1) 9.4 (1) 1 (1) 9.3 (1) 27.4 (1) 27.7 (1) 29.3 (1) 25.5 (1) 26.9 (1) 7.0 to 22.6 (1) 25.4 (1) 37.6 (1) 21.8 (1) 28.8 (1) 27.3 (1) 27.0 (1) 28.2 (1) 23.1 (1) 20.4 (1) -1.5-1.5 C (1) -1.4-5.4 (1) 7.0 - 22.6 (1) 21.6 - 30.0 (1) 20.2 - 30.5 (1) -1.5 to 1.5 (1) 20-70 ; Celsius (1) 1-6 (1) -0.5 ; Celsius (1) -0.16 ; Celsius (1) 29.08 ; Celsius (1) 30.07 ; Celsius (1) 27.4 ; Celsius (1) 2.747 ; Celsius (1) 28.18 ; Celsius (1) 106 (1) 106 ; Celsius (1) 74 (1) 20-24 (1) 42 (1) 41 (1) 28.4 (1) 15.02 (1) 22.5 (1) [ - ] view less sequencing method6 not specified (3001) 454 (741) other (138) sanger (33) unknown (2) illumina (2) Metagenome nameProgressStatus GoM Deep Sea Sediment 315 Dereplication: Error GoM Deep Sea Sediment 278 Dereplication: Error GoM Deep Sea Sediment 023 Dereplication: ErrorJobs Details #25088 - Metagenome ID - Name4465491.3 - GoM Deep Sea Sediment 315 - Job25088 - Userbuckole - Date2011-06-01 10:07:32 - Number of uploaded sequences144700

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Re: [mg-rast] QC-pipeline for 454-amplicon projects
by Mark D'Souza 01 Jun '11

01 Jun '11

Hi, The demultiplexing should not take long, a couple of minutes for small files, more for large files. I will take a look and see what the problem is. There is some documentation at: http://blog.metagenomics.anl.gov/howto/ http://blog.metagenomics.anl.gov/mg-rast-v3-0-faq/ 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 9:03 AM, leo.heijnen(a)KWRWater.nl wrote: > I currently started using the MG-RAST program to process multiplexed 454-amplicon sequences. We have uploaded a 454 .sff file and we then started using the MG-RAST QC pipeline. I also tried to use the "de-multiplexing" option to separate the differentially MID-labeled amplicons. Is there any special rule for filling in the MID sequences that are used in the experiment in the corresponding field? I have just filled in the used MID sequences and separated these individual MID's by a "hard return", is that correct? After starting the uploading and processing pipeline, the following messages appear under the "current uploads" tab: Filename, Status: (Demultiplexing started), Next step: (demultiplexing completed), progress: (demultiplexing.....). The program does not seem to get any further. Am I doing something wrong, or should I be more patient? > Is there a more extensive MG-RAST manual for beginners available? > > Thank you for your help in advance. > > Kind regards, > Leo Heijnen

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Re: [mg-rast] Data analysis
by Tobias Paczian 01 Jun '11

01 Jun '11

I'll take a look. -- Tobi On Jun 1, 2011, at 10:27 AM, Mark D'Souza wrote: > Hi Tobi, > > This user is having a problem with the barchart category selection. > I am not able to reproduce his bug. You had fixed this bug or > something related to it around May 2nd, could you check if there is > some combination of input parameters for which it could still occur? > > Thanks, > Mark > > > > Begin forwarded message: > >> From: Mark D'Souza <dsouza(a)mcs.anl.gov> >> Date: June 1, 2011 10:20:51 AM CDT >> To: Torey Looft <tlooft(a)iastate.edu> >> Cc: mg-rast(a)mcs.anl.gov >> Subject: Re: [mg-rast] Data analysis >> >> 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 >> >> <screenshot.png> >> >> >> 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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Fwd: Data analysis
by Mark D'Souza 01 Jun '11

01 Jun '11

Hi Tobi, This user is having a problem with the barchart category selection. I am not able to reproduce his bug. You had fixed this bug or something related to it around May 2nd, could you check if there is some combination of input parameters for which it could still occur? Thanks, Mark Begin forwarded message: > From: Mark D'Souza <dsouza(a)mcs.anl.gov> > Date: June 1, 2011 10:20:51 AM CDT > To: Torey Looft <tlooft(a)iastate.edu> > Cc: mg-rast(a)mcs.anl.gov > Subject: Re: [mg-rast] Data analysis > > 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] A Question
by Andreas Wilke 01 Jun '11

01 Jun '11

Hi Aaron, we will take a look into it. If the BAM file is the right solution we will provide it to you as soon as possible. We are always glad to have some volunteers for testing :) Andreas On Jun 1, 2011, at 9:09 AM, Aaron Garoutte wrote: > Any idea when this functionality might be available? > > From: Folker Meyer [mailto:[email protected]] > Sent: Wednesday, June 01, 2011 6:30 AM > To: Andreas Wilke > Cc: Mark D'Souza; Aaron Garoutte; mg-rast(a)mcs.anl.gov > Subject: Re: [mg-rast] A Question > > we need to support creation of BAM files for mapping reads to assemblies in 3.1.x > > very simple to do > On Jun 1, 2011, at 5:05 AM, Andreas Wilke wrote: > > > no , we will put the download functionality in the overview page showing a diagram of all steps performed. > > > On May 31, 2011, at 4:50 PM, Mark D'Souza wrote: > > > 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 > > > > > 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] Data analysis
by Mark D'Souza 01 Jun '11

01 Jun '11

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] A Question
by Aaron Garoutte 01 Jun '11

01 Jun '11

Any idea when this functionality might be available? From: Folker Meyer [mailto:[email protected]] Sent: Wednesday, June 01, 2011 6:30 AM To: Andreas Wilke Cc: Mark D'Souza; Aaron Garoutte; mg-rast(a)mcs.anl.gov Subject: Re: [mg-rast] A Question we need to support creation of BAM files for mapping reads to assemblies in 3.1.x very simple to do On Jun 1, 2011, at 5:05 AM, Andreas Wilke wrote: no , we will put the download functionality in the overview page showing a diagram of all steps performed. On May 31, 2011, at 4:50 PM, Mark D'Souza wrote: 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 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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QC-pipeline for 454-amplicon projects
by leo.heijnen＠KWRWater.nl 01 Jun '11

01 Jun '11

I currently started using the MG-RAST program to process multiplexed 454-amplicon sequences. We have uploaded a 454 .sff file and we then started using the MG-RAST QC pipeline. I also tried to use the "de-multiplexing" option to separate the differentially MID-labeled amplicons. Is there any special rule for filling in the MID sequences that are used in the experiment in the corresponding field? I have just filled in the used MID sequences and separated these individual MID's by a "hard return", is that correct? After starting the uploading and processing pipeline, the following messages appear under the "current uploads" tab: Filename, Status: (Demultiplexing started), Next step: (demultiplexing completed), progress: (demultiplexing.....). The program does not seem to get any further. Am I doing something wrong, or should I be more patient? Is there a more extensive MG-RAST manual for beginners available? Thank you for your help in advance. Kind regards, Leo Heijnen

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Re: [mg-rast] A Question
by Folker Meyer 01 Jun '11

01 Jun '11

we need to support creation of BAM files for mapping reads to assemblies in 3.1.x very simple to do On Jun 1, 2011, at 5:05 AM, Andreas Wilke wrote: > no , we will put the download functionality in the overview page showing a diagram of all steps performed. > > > On May 31, 2011, at 4:50 PM, Mark D'Souza wrote: > >> 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 >>>> >>> >> > > 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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