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

Re: [mg-rast] For MGRAST pipeline processing time
by Shangang Jia 06 Jun '11

06 Jun '11

Dear sir, I am sorry for my stuck jobs, job number: 23787, 23788, 23789. These three jobs have been in the status of Caculating Sims: In progress, for almost 21 days. Yet they have not been finished. Could you help me with them and get them running through all the pipile in MG-RAST? Thank you! Should I resubmit my data into MG-RAST? Sincerely, Shangang Jia 2011-06-06 Shangang Jia 发件人： Mark D'Souza 发送时间： 2011-05-26 02:50:52 收件人： jsg200830 抄送： mg-rast 主题： Re: [mg-rast] For MGRAST pipeline processing time Hi, It is not clear why the last set (23786-23789) did not complete, I restarted them and they should go through OK. Regards, Mark On May 25, 2011, at 11:37 AM, Mark D'Souza wrote: > Hi, > > I restarted the two (23967, 23970) jobs and the set I started earlier (23962-23965) have completed. That leaves 23786-23789, I will see what needs to be done with them. > > Regards, > Mark > > > > On May 24, 2011, at 12:30 PM, Shangang Jia wrote: > >> Hi, >> Thank you for the reply and help. I am sorry that there are still two jobs suspended, job numbers:23967, 23970. In the last email, I have missed these two jobs, and all of my 8 job numbers are: >> 23970 (suspended right now) >> 23967 (suspended right now) >> 23965 (now in progress, suspended before in the status of "upload: completed" ) >> 23962 (now in progress, suspended before in the status of "upload: completed" ) >> 23789 (before in the status of Calculating Sims: In Progress, and still the same right now) >> 23788 (before in the status of Calculating Sims: In Progress, and still the same right now) >> 23787 (before in the status of Calculating Sims: In Progress, and still the same right now) >> 23786 (before in the status of Calculating Sims: In Progress, and still the same right now) >> >> Could you start the stuck jobs? Thanks a lot! >> >> Sincerely, >> >> Shangang Jia >> >> 2011-05-25 >> Shangang Jia >> 发件人： Mark DSouza >> 发送时间： 2011-05-25 01:06:43 >> 收件人： jsg200830 >> 抄送： mg-rast >> 主题： Re: [mg-rast] For MGRAST pipeline processing time >> Hi, >> Sorry about that, the four jobs at the 'upload completed stage' had failed and I restarted them. The other four got through most of the analysis pipeline without a problem before getting stuck, I will find out what happened to them and get them moving, for now there is nothing you need to do. >> -- >> 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: "Shangang Jia" <jsg200830(a)163.com> >>> To: "mg-rast" <mg-rast(a)mcs.anl.gov> >>> Sent: Friday, May 20, 2011 4:55:28 AM >>> Subject: [mg-rast] For MGRAST pipeline processing time >>> Dear sir, >>> >>> I am a user for MGRAST, and have submitted totally 8 jobs. However, >>> about 6 days have passed, and none of them have been finished. Four of >>> them (job number: 23786-23789) are in the status of Calculating Sims: >>> In Progress, and the other four ones (job number: 23962-23965) are in >>> the status of "upload: completed". My question is whether the server >>> has been over loaded, whether my jobs has been suspended, how long it >>> will take to finish all my jobs, and what I should do right now (just >>> waiting, resubmitting all my jobs or anything else?). Thank you! >>> >>> Sincerely, >>> >>> Shangang Jia >>> >>> 2011-05-20 >>> >>> Shangang Jia >

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Re: [mg-rast] Sample input
by Michael Maguire 06 Jun '11

06 Jun '11

Hello I am having a few difficulties with the new MG-RAST. Firstly two of my older metagenomes have not tranfered correctly to the new version and seem to have stopped progressing through the analysis, the job numbers are 10994 and 10995. Secondly when I was inputing a new metagenome last week I kept receiving an error message in uploader. When it finally did work I noticed that I had 3 jobs in progress (all the same metagenome) none of which have progressed since. These jobs are 24993, 24994 and 24995. Is there any way of deleting jobs which are still in progress? Regards Michael Maguire Michael Maguire School of Civil Engineering and Geosciences 3rd Floor Devonshire Building Newcastle University Newcastle upon Tyne NE1 7RU * m.j.maguire(a)ncl.ac.uk<mailto:[email protected]> * 0191 246 4874

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(Job 12679 , ID 4453083.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 05 Jun '11

05 Jun '11

Renee Smith (WebServerBackend::User=HASH(0x1a96ccc8)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4453083.3.

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Re: [mg-rast] Fwd: Analysis data-Reg
by Mark D'Souza 04 Jun '11

04 Jun '11

Hi, Sorry about that, the version2 jobs are not being displayed after some files containing some sequence metadata were moved. The data for the jobs is intact and we are working on restoring the visibility. Regards, Mark On Jun 4, 2011, at 12:50 AM, suchitra sena <dssena26(a)gmail.com> wrote: > > Respected Sir, > Kindly make my metagenome data available on MG-RAST version 2.0 also as I am in the final stage of preparation of an article. > Waiting for an earliest reply in this regard. > Anticipatory thanks for the needful to be done > Thanking you, > Yours faithfully > D. Suchitra Sena, > Senior Scientist (VMD) > ---------- Forwarded message ---------- > From: suchitra sena <dssena26(a)gmail.com> > Date: Fri, Jun 3, 2011 at 7:58 AM > Subject: Analysis data-Reg > To: mg-rast(a)mcs.anl.gov > Cc: Mark D'Souza <dsouza(a)mcs.anl.gov> > > > Sir, > It is to kindly mention that I am unable to view the private metagenomes once I login to my account. In vers 3.0 I am able to view them. But I am writing the paper as per analysis 2.0 where the sequences are available. So I sincerely request you to kindly make the data available on both version 2.0 and 3.0 for 2 more months so that I can write the articles and later publicise that metagenome. M job Ids are 13802 and 13803. > Waiting for an earliest reply in this regard. > Anticipatory thanks for the needful to be done. > Regards > D. Suchitra Sena >

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Fwd: Analysis data-Reg
by suchitra sena 04 Jun '11

04 Jun '11

Respected Sir, Kindly make my metagenome data available on MG-RAST version 2.0 also as I am in the final stage of preparation of an article. Waiting for an earliest reply in this regard. Anticipatory thanks for the needful to be done Thanking you, Yours faithfully D. Suchitra Sena, Senior Scientist (VMD) ---------- Forwarded message ---------- From: suchitra sena <dssena26(a)gmail.com> Date: Fri, Jun 3, 2011 at 7:58 AM Subject: Analysis data-Reg To: mg-rast(a)mcs.anl.gov Cc: Mark D'Souza <dsouza(a)mcs.anl.gov> Sir, It is to kindly mention that I am unable to view the private metagenomes once I login to my account. In vers 3.0 I am able to view them. But I am writing the paper as per analysis 2.0 where the sequences are available. So I sincerely request you to kindly make the data available on both version 2.0 and 3.0 for 2 more months so that I can write the articles and later publicise that metagenome. M job Ids are 13802 and 13803. Waiting for an earliest reply in this regard. Anticipatory thanks for the needful to be done. Regards D. Suchitra Sena

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Re: [mg-rast] Uploading file problem to MG-Rast server
by Mark DSouza 03 Jun '11

03 Jun '11

Hi, I do not see anything wrong with the file and will have to investigate further, I will get back to you when this is fixed. ----- Original Message ----- > From: "Jesse Port" <jport(a)u.washington.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Friday, June 3, 2011 1:46:33 PM > Subject: [mg-rast] Uploading file problem to MG-Rast server > Hi there, > > I am trying to upload a metagenome to your Rast Server but for some > reason it is stuck in the "processing uploaded file" step. The file > was 550 Mbp, which I first attempted to upload on June 1, and because > it was not getting past that step, I compressed it to 150 Mbp but am > still having the same problem. The file extension is .fa (fasta). I > haven't had any problems uploading in the past, so not sure why now. > The file name meets your criteria. If you could provide any assistance > I'd appreciate it. > > Thanks much, > > Jesse Port -- 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

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Uploading file problem to MG-Rast server
by Jesse Port 03 Jun '11

03 Jun '11

Hi there, I am trying to upload a metagenome to your Rast Server but for some reason it is stuck in the "processing uploaded file" step. The file was 550 Mbp, which I first attempted to upload on June 1, and because it was not getting past that step, I compressed it to 150 Mbp but am still having the same problem. The file extension is .fa (fasta). I haven't had any problems uploading in the past, so not sure why now. The file name meets your criteria. If you could provide any assistance I'd appreciate it. Thanks much, Jesse Port

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Your MG-RAST job (25097, 4465500.3, TNPo3)
by Mark DSouza 03 Jun '11

03 Jun '11

Hi, The job you submitted to MG-RAST has failed as the sequence identifiers are not unique, there are 7991 sequences and 4549 unique sequence IDs. Please edit your sequence file to remove this redundancy and resubmit to the MG-RAST server. -- 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

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Fwd: Metagenome processing
by Mark D'Souza 03 Jun '11

03 Jun '11

Hi Travis, Please check these two jobs -- 25039 25048 Thanks, Mark Begin forwarded message: > From: Louisi Oliveira <louisioliveira(a)gmail.com> > Date: June 3, 2011 8:26:45 AM CDT > To: mg-rast(a)mcs.anl.gov > Subject: [mg-rast] Metagenome processing > > Dear MG-RAST team, > > I submitted 10 metagenomes to MG-RAST last Tuesday (may-31) and 8 of them were available for analysis on Wednesday afternoon. However the other 2 are still at the same step of process up to now (Calculating Sims: In Progress). Is there any problem with these data? > > User account: louisioliveira > > Thank you in advance! > Louisi > -- > Louisi Souza de Oliveira (PhD student) > > Universidade Federal Fluminense - UFF > Outeiro de São João Batista, s/n, > Campus do Valonguinho,Centro, Niterói, RJ > CEP: 24020-140

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Re: [mg-rast] Metagenome processing
by Mark D'Souza 03 Jun '11

03 Jun '11

Hi, There does not appear to be any problem with the data, we will investigate and get the jobs restarted. 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 3, 2011, at 8:26 AM, Louisi Oliveira wrote: > Dear MG-RAST team, > > I submitted 10 metagenomes to MG-RAST last Tuesday (may-31) and 8 of them were available for analysis on Wednesday afternoon. However the other 2 are still at the same step of process up to now (Calculating Sims: In Progress). Is there any problem with these data? > > User account: louisioliveira > > Thank you in advance! > Louisi > -- > Louisi Souza de Oliveira (PhD student) > > Universidade Federal Fluminense - UFF > Outeiro de São João Batista, s/n, > Campus do Valonguinho,Centro, Niterói, RJ > CEP: 24020-140

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