January 2010 - Mg-rast - mailman3.cels.anl.gov

Re: [mg-rast] HMP_lane_2
by Dionysios Antonopoulos 31 Jan '10

31 Jan '10

RDP won't recognize euks -- it's 16S based. This explains that discrepancy. Jen and I just checked and the level of euk contamination between Solexa and 454 for that particular sample is equivalent. If this is the case, then Lanes 2 and 3 will have this issue (i.e. corresponding samples on 454 exhibited high level of euk contamination). Lanes 7 and 8 minimally impacted (low level euk contamination). -- Dion On Jan 31, 2010, at 4:30 PM, Folker Meyer wrote: > Mark: > > this is a big problem. We need to find out exactly what is going on > here. Please troubleshoot this. > > > Folker > > On Jan 31, 2010, at 2:21 PM, dsouza(a)mcs.anl.gov wrote: > >> Hi, >> >> job 6138 has the HMP lane 2 results -- all sequences were run >> against RDP, only the first 1 Gbp was run against SEED protein >> database, and silva and green genes were not run. >> >> The phylogenetic profile against SEED has 80% euk -- probably >> contamination, but the RDP profile has 100% bacterial. Not sure >> what this means. >> >> I had to bypass some load steps in the pipeline, if you see >> anything extremely odd that may be the reason. >> >> Mark > ________________________________ Dionysios A. Antonopoulos, PhD Assistant Biologist, Microbial Systems Institute for Genomics & Systems Biology Biosciences Division Argonne National Laboratory 9700 S. Cass Avenue Bldg 202, Room A-249 Argonne, IL 60439 Office phone: (630) 252-3935

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Re: [mg-rast] HMP_lane_2
by Folker Meyer 31 Jan '10

31 Jan '10

Mark: this is a big problem. We need to find out exactly what is going on here. Please troubleshoot this. Folker On Jan 31, 2010, at 2:21 PM, dsouza(a)mcs.anl.gov wrote: > Hi, > > job 6138 has the HMP lane 2 results -- all sequences were run against RDP, only the first 1 Gbp was run against SEED protein database, and silva and green genes were not run. > > The phylogenetic profile against SEED has 80% euk -- probably contamination, but the RDP profile has 100% bacterial. Not sure what this means. > > I had to bypass some load steps in the pipeline, if you see anything extremely odd that may be the reason. > > Mark

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HMP_lane_2
by dsouza＠mcs.anl.gov 31 Jan '10

31 Jan '10

Hi, job 6138 has the HMP lane 2 results -- all sequences were run against RDP, only the first 1 Gbp was run against SEED protein database, and silva and green genes were not run. The phylogenetic profile against SEED has 80% euk -- probably contamination, but the RDP profile has 100% bacterial. Not sure what this means. I had to bypass some load steps in the pipeline, if you see anything extremely odd that may be the reason. Mark

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HMP mgrast runs
by dsouza＠mcs.anl.gov 30 Jan '10

30 Jan '10

Hi, The job with HMP_lane_2 is not complete -- this has the first 1 Gbp results against SEED and complete results against RDP. More later today if I can get it done. The HMP loads with euk data stripped out are at: 6153 -- HMP1 6154 -- HMP100 6155 -- HMP2 6156 -- HMP3 you should all have access. These have all hits against SEED as well as the DNA databases. The sequence file used for these jobs do not contain duplicate sequences, so the =submitted= numbers may be slightly different than before but analyzed sequence data is the same as the same as earlier (5933, 5934, 5952, 5953). Mark

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Your Mg-RAST jobs
by Mark D'Souza 29 Jan '10

29 Jan '10

Hi, Some of the jobs you submitted lately have failed -- please make sure that the sequence files you submit have an extension -- '.fasta' will do. For example, 'metagenome_sequence.fasta' and resubmit them to the MG-RAST server. Please do inform us if you continue to have problems with the upload. -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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Re: [mg-rast] checking status of job 5269
by Mark D'Souza 29 Jan '10

29 Jan '10

Bob, The Kegg page is now working for 5269, sorry about the delay. Mark ----- "Robert T. Deboy" <RDeboy(a)jcvi.org> wrote: > From: "Robert T. Deboy" <RDeboy(a)jcvi.org> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Thursday, January 28, 2010 12:57:04 PM GMT -06:00 US/Canada Central > Subject: RE: [mg-rast] checking status of job 5269 > > Hi Mark, > > This problem doesn't seem to be fixed. Is this something you can do > soon? > > Thanks, > Bob > > -----Original Message----- > From: Mark D'Souza [mailto:[email protected]] > Sent: Monday, January 11, 2010 11:35 AM > To: Deboy, Robert T. > Subject: Re: [mg-rast] checking status of job 5269 > > Hi Bob, > > I figured out what went wrong, fixing it should take a few days. > > Mark > > > ----- "Robert T. Deboy" <RDeboy(a)jcvi.org> wrote: > > > From: "Robert T. Deboy" <RDeboy(a)jcvi.org> > > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > > Sent: Monday, January 11, 2010 9:02:58 AM GMT -06:00 US/Canada > Central > > Subject: RE: [mg-rast] checking status of job 5269 > > > > Hi Mark, > > > > Any progress on the missing EC numbers? > > > > Thanks, > > Bob > > > > -----Original Message----- > > From: Mark D'Souza [mailto:[email protected]] > > Sent: Friday, December 18, 2009 12:46 PM > > To: Deboy, Robert T. > > Cc: MG-RAST > > Subject: Re: [mg-rast] checking status of job 5269 > > > > Hi Bob, > > > > Thanks for letting us know about this, we are looking into it and > will > > get back to you. > > > > Regards. > > Mark > > > > ----- "Robert T. Deboy" <RDeboy(a)jcvi.org> wrote: > > > > > From: "Robert T. Deboy" <RDeboy(a)jcvi.org> > > > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > > > Sent: Friday, December 18, 2009 8:44:02 AM GMT -06:00 US/Canada > > Central > > > Subject: RE: [mg-rast] checking status of job 5269 > > > > > > Hi Mark, > > > > > > This job finished about a week ago. However, there are no ec > > numbers > > > in the metabolic profile/kegg comparison. The older metagenome > jobs > > > look fine. It's just this new one. Can you please take a look to > > see > > > why ec numbers are missing? > > > > > > Thanks, > > > Bob DeBoy > > > > > > -----Original Message----- > > > From: Mark D'Souza [mailto:[email protected]] > > > Sent: Tuesday, November 17, 2009 12:38 AM > > > To: Deboy, Robert T. > > > Cc: mg-rast(a)mcs.anl.gov > > > Subject: Re: [mg-rast] checking status of job 5269 > > > > > > Hi, > > > > > > A very rough estimate would be between one and two weeks. > > > > > > ----- "Robert T. Deboy" <RDeboy(a)jcvi.org> wrote: > > > > > > > From: "Robert T. Deboy" <RDeboy(a)jcvi.org> > > > > To: mg-rast(a)mcs.anl.gov > > > > Sent: Friday, November 13, 2009 11:33:26 AM GMT -06:00 > US/Canada > > > Central > > > > Subject: [mg-rast] checking status of job 5269 > > > > > > > > Hello, > > > > > > > > > > > > > > > > I started job 5269 on Monday. Can you please give me an > estimate > > > for > > > > when it will finish going through the pipeline? > > > > > > > > > > > > > > > > Thanks, > > > > > > > > Bob DeBoy > > > > > > -- > > > Regards, > > > Mark D'Souza > > > -- for the MG-RAST team > > > > > > mg-rast(a)mcs.anl.gov > > > http://metagenomics.nmpdr.org/

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Re: [mg-rast] need some jobs to be done as soon as possible
by dsouza＠mcs.anl.gov 29 Jan '10

29 Jan '10

Huma, I should be able to have these three jobs done within a day or two -- I have been sending them through one at a time as the DNA BLAST takes an extremely long time. ----- "Huma Siddiqui" <huma.siddiqui(a)bio.uio.no> wrote: > From: "Huma Siddiqui" <huma.siddiqui(a)bio.uio.no> > To: mg-rast(a)mcs.anl.gov > Sent: Friday, January 29, 2010 4:05:17 AM GMT -06:00 US/Canada Central > Subject: [mg-rast] need some jobs to be done as soon as possible > > Hi . > I have been using you web-tool for a time now, and Iam satisfied with > > it, but lately there has been much waiting and I saw your mail about > it > explaining your problem. > > Anyway , there is 3 jobs that I really need at the earliest , they > have > already been processed half way, but is there any possibilty for you > to > get them done before next week. > > The jobs number are : 5839, 58443 and 5846. > > I am supposed to make a presentation for a meeting early next week, > and > I am confused about what to do. I really need the data analysed before > that. > > My username is: humas > > Hope that you can help me out in this. > > Regards > Huma Siddiqui > > > -- > Huma Siddiqui > PhD student > University of Oslo > Dept. of Biology > Center for Ecological and Evolutionary Synthesis (CEES) > P.O. Box 1066 Blindern > 0316 Oslo, Norway > Ph. +47-22844132 > Fax. +47-22854001 > e-mail: huma.siddiqui(a)bio.uio.no -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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Re: [mg-rast] MG-RAST job (4444724.3)
by dsouza＠mcs.anl.gov 29 Jan '10

29 Jan '10

Hi Pengfei, Go to: http://metagenomics.nmpdr.org/metagenomics.cgi?page=MetagenomeSubsetDownloa… This should download the file 'sequence_subset.txt' which is 22553841 bytes large, with all the 245943 results. The table does load now, but the download using the 'export table' button will give you only the first 10000 results -- as displayed in the table. Sorry about the ad hoc nature of this solution, we will make it easily accessible soon, let me know how it works for you. Regards, Mark ----- "Pengfei Song" <psong(a)oeb.harvard.edu> wrote: > From: "Pengfei Song" <psong(a)oeb.harvard.edu> > To: dsouza(a)mcs.anl.gov, mg-rast(a)mcs.anl.gov > Sent: Wednesday, January 27, 2010 4:35:11 PM GMT -06:00 US/Canada Central > Subject: Re: MG-RAST job (4444724.3) > > Thanks, Mark, > > I'm looking forward to it. I'll check again on Friday! If it can not > be solved anytime sooner though (may god forbidden), can you please > update my data to a server? > > Best, > Pengfei > > On 1/27/2010 5:33 PM, dsouza(a)mcs.anl.gov wrote: > > Hi, > > I took a look into this, and the problem is with the data acquisition > from the database. We are digging deeper into this and hope to have a > solution for you in a few days. Sorry for the delay. > > > > ----- "Pengfei Song" <psong(a)oeb.harvard.edu> wrote: > > From: "Pengfei Song" <psong(a)oeb.harvard.edu> To: mg-rast(a)mcs.anl.gov > Cc: dsouza(a)mcs.anl.gov Sent: Wednesday, January 27, 2010 9:42:01 AM > GMT -06:00 US/Canada Central > Subject: MG-RAST job (4444724.3) > > Hello again! > > Happy New Year. > > I'm still trying (I've been trying since last December) to download > the SEED bacteria blast data for my job ID 4444724.3, but I guess > since the dataset is too big, the webpage kept crashing on me (I've > tried many times on many days). Do you mind sending me the data via > Email or giving me some suggestions on how to download this? I need > the E value to be 1E-2. > > Many many thanks!! > Pengfei Song, Ph.D > Harvard University

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need some jobs to be done as soon as possible
by Huma Siddiqui 29 Jan '10

29 Jan '10

Hi . I have been using you web-tool for a time now, and Iam satisfied with it, but lately there has been much waiting and I saw your mail about it explaining your problem. Anyway , there is 3 jobs that I really need at the earliest , they have already been processed half way, but is there any possibilty for you to get them done before next week. The jobs number are : 5839, 58443 and 5846. I am supposed to make a presentation for a meeting early next week, and I am confused about what to do. I really need the data analysed before that. My username is: humas Hope that you can help me out in this. Regards Huma Siddiqui -- Huma Siddiqui PhD student University of Oslo Dept. of Biology Center for Ecological and Evolutionary Synthesis (CEES) P.O. Box 1066 Blindern 0316 Oslo, Norway Ph. +47-22844132 Fax. +47-22854001 e-mail: huma.siddiqui(a)bio.uio.no

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Re: [mg-rast] mg-rast KEGG question
by Antonia Mayer 28 Jan '10

28 Jan '10

Hi - I'm forwarding the response of my colleague who is doing most of the biological interpreting. Thank you, Antonia ------- The path is private metagenomes/ Metagenome Morges2007/ Metabolic analysis/ KEGG Map Page displays zeros as below and such is the outcome for any of our three metagenomes: 4445679.3 4445601.3 4445757.3 ----- > Antonia, > > I was under the assumption it was working again. PLease send details > of what is not working for which data set. > > Best, > Folker > >>> On Jan 4, 2010, at 9:47 AM, Antonia Mayer <antonia.mayer(a)unil.ch> >>> wrote: >>> >>>> Folker, hi - >>>> Thanks a lot for your last response. >>>> >>>> One of the samples I have uploaded has completed (job #5512) or nearly >>>> so ("Exportable data creation has not yet started" remains.) but KEGG >>>> map results are 0. Is there anything I have to do to allow mapping >>>> onto KEGG? >>>> >>>> All the best and a good new year to you, >>>> Antonia

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