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

Re: [mg-rast] Error in running file through Rast Server
by Mark DSouza 28 Jun '11

28 Jun '11

Hi, Sorry for the delay, the job has been restarted and is running through, we had a load spike last week and jobs are taking longer than usual to complete. Regards, Mark ----- Original Message ----- > From: "Jesse Port" <jport(a)u.washington.edu> > To: mg-rast(a)mcs.anl.gov > Cc: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Monday, June 27, 2011 3:59:03 PM > Subject: Re: [mg-rast] Error in running file through Rast Server > Hi, > > Just wanted to check in regarding the status of a file that has been > running through your Rast server but hasn't completed. I sent an email > last week and was told someone would look into it. The email read: > > "I uploaded a file to be run through your Rast server about a week and > a half ago and it appears to still be running through the pipeline. > The status bar reads "Loading Database: error". Does this mean that it > failed to make it through the pipeline, and if so why? The ID is > 4466192.3." > > Thanks, Jesse Port > > > > On Thu, Jun 23, 2011 at 8:49 AM, Mark D'Souza < dsouza(a)mcs.anl.gov > > wrote: > > > Hi, > > We will take a look, it probably got stuck at some stage. > > 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 23, 2011, at 10:35 AM, Jesse Port wrote: > > > Hi there, > > > > I uploaded a file to be run through your Rast server about a week > > and a half ago and it appears to still be running through the > > pipeline. The status bar reads "Loading Database: error". Does this > > mean that it failed to make it through the pipeline, and if so why? > > The ID is 4466192.3. > > > > Thanks, Jesse Port

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Re: [mg-rast] Error in running file through Rast Server
by Jesse Port 27 Jun '11

27 Jun '11

Hi, Just wanted to check in regarding the status of a file that has been running through your Rast server but hasn't completed. I sent an email last week and was told someone would look into it. The email read: "I uploaded a file to be run through your Rast server about a week and a half ago and it appears to still be running through the pipeline. The status bar reads "Loading Database: error". Does this mean that it failed to make it through the pipeline, and if so why? The ID is 4466192.3." Thanks, Jesse Port On Thu, Jun 23, 2011 at 8:49 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > Hi, > > We will take a look, it probably got stuck at some stage. > > 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 23, 2011, at 10:35 AM, Jesse Port wrote: > > > Hi there, > > > > I uploaded a file to be run through your Rast server about a week and a > half ago and it appears to still be running through the pipeline. The status > bar reads "Loading Database: error". Does this mean that it failed to make > it through the pipeline, and if so why? The ID is 4466192.3. > > > > Thanks, Jesse Port > >

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Re: [mg-rast] Error: Edit Metadata
by Mark DSouza 27 Jun '11

27 Jun '11

No problem Steve, The jobs all had the error at the 'Loading Database' stage which indicates a possible transitory database issue as the cause. Drop us an email if you ever see this again and we will take care of it. Regards, Mark ----- Original Message ----- > From: "Steve Essinger" <sessinger(a)gmail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Monday, June 27, 2011 3:00:58 PM > Subject: Re: [mg-rast] Error: Edit Metadata > Thanks you, Mark. Do you know what the issue was so that I can avoid > the errors in the future? > > > Thanks, > Steve > > > On Mon, Jun 27, 2011 at 2:16 PM, Mark D'Souza < dsouza(a)mcs.anl.gov > > wrote: > > > Hi, > > These jobs have completed. > > Regards, > Mark > > > > > > > On Jun 23, 2011, at 4:52 PM, Mark DSouza wrote: > > > Hi, > > > > We will take a look at the 4 datasets and find out what has gone > > wrong and get back to you. > > > > Regards, > > Mark > > > > ----- Original Message ----- > >> From: "Steve Essinger" < sessinger(a)gmail.com > > >> To: "Mark DSouza" < dsouza(a)mcs.anl.gov > > >> Cc: mg-rast(a)mcs.anl.gov > >> Sent: Thursday, June 23, 2011 3:48:10 PM > >> Subject: Re: [mg-rast] Error: Edit Metadata > >> Mark, > >> > >> > >> Thank you so much for your quick response. It appears to be working > >> correctly on my end now as well. > >> > >> > >> One more issue: I have 4 datasets in progress that indicate a > >> Loading > >> Database: Error. How do I kill these processes and restart them? I > >> do > >> not know what is causing the error. > >> > >> > >> Thanks, > >> Steve > >> > >> > >> On Thu, Jun 23, 2011 at 4:35 PM, Mark DSouza < dsouza(a)mcs.anl.gov > > >> wrote: > >> > >> > >> Hi, > >> > >> This has now been fixed, thanks for letting us know about the > >> problem. > >> > >> Regards, > >> Mark > >> > >> > >> > >> > >> ----- Original Message ----- > >>> From: "Mark DSouza" < dsouza(a)mcs.anl.gov > > >>> To: "Steve Essinger" < sessinger(a)gmail.com > > >>> Cc: mg-rast(a)mcs.anl.gov > >>> Sent: Thursday, June 23, 2011 2:39:14 PM > >>> Subject: Re: [mg-rast] Error: Edit Metadata > >>> Hi, > >>> > >>> Sorry about that, we will take a look and get it fixed. > >>> > >>> -- > >>> 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: "Steve Essinger" < sessinger(a)gmail.com > > >>>> To: mg-rast(a)mcs.anl.gov > >>>> Sent: Thursday, June 23, 2011 2:27:03 PM > >>>> Subject: [mg-rast] Error: Edit Metadata > >>>> Hi, > >>>> > >>>> > >>>> I've uploaded a bunch of metagenomic datasets that I now wish to > >>>> edit > >>>> their metadata. When I click on the link 'Edit Metadata' I get > >>>> the > >>>> following response: > >>>> > >>>> > >>>>>>> Unable to fetch attribute 'owner' of JobDB::Job id 28416 from > >>>>>>> db > >>>>>>> 'WebAppBackend' of type 'User' with id 49300. at > >>>>>>> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_1_0/common/lib/PPO/DBObject.pm > >>>>>>> line 736 > >>>> > >>>> > >>>> Any thoughts? > >>>> > >>>> > >>>> Thanks, > >>>> Steve

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Re: [mg-rast] Fwd: Comment on MG-RAST
by Mark DSouza 27 Jun '11

27 Jun '11

Hi, The only absolutely certain indication that a job is stuck is if it has an error status. However, if the status has not changed for a couple of days or if the processing has not completed within a week there is a chance that the job got stuck somewhere in the processing pipeline. In any of these cases, please let us know and we will investigate and take action if necessary to move it along. Your job 26601 is queued and appears to be progressing OK, the RNA computation completed yesterday. We had a load spike last week and this job is unfortunately towards the tail end of the spike so it may take a little longer than usual to complete. I'm afraid I can not answer your RAST/FIG questions, you can address them to the RAST folks at rast(a)mcs.anl.gov -- 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 ----- > Begin forwarded message: > > > From: Aaron Darling <aarondarling(a)ucdavis.edu> > > Date: June 27, 2011 2:16:40 PM CDT > > To: Folker Meyer <folker(a)anl.gov> > > Cc: "Gordon D. Pusch" <gdpusch(a)xnet.com> > > Subject: Re: Comment on MG-RAST > > > > That's good news Folker, thanks. I look forward to using the new > > speedier MG-RAST. How can I tell if a job is stuck or just > > proceeding > > slowly? For example my current job 26601 has a status of "Sequence > > Screening: completed" for a day now and I'm not sure when I should > > get > > worried that it might be stuck. > > > > While I have you on the line, I've been meaning to ask what the > > status > > of standalone RAST/FIG tools is. We have some potentially sensitive > > datasets coming and may be restricted to analyzing them in-house. > > Are > > there any (serviceable) options for using your tools? I'm not afraid > > to > > use VMs/clouds or get down & dirty with perl & SGE. I found a source > > code package online but can't tell how recent it is and didn't find > > much > > in the way of documentation. > > > > > > On Mon, 2011-06-27 at 14:04 -0500, Folker Meyer wrote: > >> Hi Aaron: > >> > >> while it is true that MG-RAST was BLAST based that is no longer > >> true. > >> > >> We typically process several tens of gigabases per day. However > >> sometimes jobs fail and need to be restarted. If there are jobs of > >> yours that are stuck let us know. > >> > >> Current turn around time is significantly lower than one week. > >> (Actually less than 2 days for most jobs), > >> > >> Best, > >> Folker (for the MG-RAST team) > > > >

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Fwd: Comment on MG-RAST
by Folker Meyer 27 Jun '11

27 Jun '11

FYI: Mark please handle from now on Begin forwarded message: > From: Aaron Darling <aarondarling(a)ucdavis.edu> > Date: June 27, 2011 2:16:40 PM CDT > To: Folker Meyer <folker(a)anl.gov> > Cc: "Gordon D. Pusch" <gdpusch(a)xnet.com> > Subject: Re: Comment on MG-RAST > > That's good news Folker, thanks. I look forward to using the new > speedier MG-RAST. How can I tell if a job is stuck or just proceeding > slowly? For example my current job 26601 has a status of "Sequence > Screening: completed" for a day now and I'm not sure when I should get > worried that it might be stuck. > > While I have you on the line, I've been meaning to ask what the status > of standalone RAST/FIG tools is. We have some potentially sensitive > datasets coming and may be restricted to analyzing them in-house. Are > there any (serviceable) options for using your tools? I'm not afraid to > use VMs/clouds or get down & dirty with perl & SGE. I found a source > code package online but can't tell how recent it is and didn't find much > in the way of documentation. > > > On Mon, 2011-06-27 at 14:04 -0500, Folker Meyer wrote: >> Hi Aaron: >> >> while it is true that MG-RAST was BLAST based that is no longer true. >> >> We typically process several tens of gigabases per day. However sometimes jobs fail and need to be restarted. If there are jobs of yours that are stuck let us know. >> >> Current turn around time is significantly lower than one week. (Actually less than 2 days for most jobs), >> >> Best, >> Folker (for the MG-RAST team) > >

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Re: [mg-rast] question about sequence hits
by William Trimble 27 Jun '11

27 Jun '11

There was a problem this morning that caused some reads to be double counted in the table. This has now been fixed; the abundance numbers for this dataset now match the number of sequences they represent. Thank you for alerting us to the problem. William Trimble for the MG-RAST team On Mon, Jun 27, 2011 at 10:45 AM, Mirjam Perner <mirjam.perner(a)uni-hamburg.de> wrote: > Am 27.06.2011 17:39, schrieb William Trimble: > > Thanks for using MG-RAST. > > Which MG-RAST dataset numbers are you looking at? > > MG-RAST 4460162.2 > Metagenome Name SP_metgen_consens_98perc > MG-RAST Job Number 19759 > > Upload sequence counts: 147,867, but when analyzing the dataset "organism > classification"; M5NR, max evalue cutoff 1e-3 the numbers for abundance of > bacteria, archaea, eukaryota, viruses, otra sequences, unassigned and > unclassified sequences add up to >>147,867 > mirjam > > William Trimble > for the MG-RAST team > > > On Mon, Jun 27, 2011 at 8:51 AM, Mirjam Perner > <mirjam.perner(a)uni-hamburg.de> wrote: > > Dear madame, > dear sir, > just a very brief question: > I have uploaded 147,867 sequences (sequence count) with roughly 400 bp, but > when comparing these sequences with the M5NR databse I get a total of > 188,640 number of reads hit. how can I have more hits than uploaded > sequences? The other databases, Genbank etc dont have this problem > Thanks, for your time > Mirjam > > -- > > > (jun.) Prof. Dr. Mirjam Perner > Microbiology & Biotechnology > University of Hamburg > room 3155/3156 > > Ohnhorststr. 18 > 22609 Hamburg > Germany > > Tel.: ++49(0) 40 42816 444 (Monday-Thursday) > Tel.: ++49(0) 40 42838 6006 (fridays) > Fax: ++49(0) 40 42816 459 > Email: mirjam.perner(a)uni-hamburg.de > > http://www.genmibio.de/html/ag_perner.html > http://www.chemie.uni-hamburg.de/lexi/gsc1chem/Principal_Investigators_Proj… > > > -- > > > (jun.) Prof. Dr. Mirjam Perner > Microbiology & Biotechnology > University of Hamburg > room 3155/3156 > > Ohnhorststr. 18 > 22609 Hamburg > Germany > > Tel.: ++49(0) 40 42816 444 (Monday-Thursday) > Tel.: ++49(0) 40 42838 6006 (fridays) > Fax: ++49(0) 40 42816 459 > Email: mirjam.perner(a)uni-hamburg.de > > http://www.genmibio.de/html/ag_perner.html > http://www.chemie.uni-hamburg.de/lexi/gsc1chem/Principal_Investigators_Proj…

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Re: [mg-rast] I think I have 19 jobs stalled
by Robert J Boissy 27 Jun '11

27 Jun '11

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Re: [mg-rast] Duration of progress
by Mark D'Souza 27 Jun '11

27 Jun '11

Hi, These jobs have completed, sorry for the delay. Regards, Mark On Jun 23, 2011, at 10:18 AM, Mark D'Souza wrote: > Hi, > > Sorry for the delay, we will check what happened 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 Jun 23, 2011, at 7:44 AM, Will, Christiane wrote: > >> Dear MG-Rast-Team, >> >> I am writing to you in relation to our data with the Job# 24921-24941 and >> 24945-24955 which my colleague and I uploaded one month ago. We wonder why >> the progress takes so long this time: there is still only 1 of 9 segments in >> the progress bar green for each of the 32 samples. We remember that it always >> took a couple of weeks to upload data last year with the old system. But this >> time our datasets are much smaller, however there is no progress visible up >> to now. Can you make any prediction on how long it is going to take until the >> progressing is completed? You will probably understand that we cannot wait >> another 7-8 months until the progresses are completed before we can even >> start to analyze our data. >> >> Regards, >> Christiane Will >> >> ----------------------------------------------- >> Dr. Christiane Will >> Georg-August-University Göttingen >> Institute of Microbiology and Genetics >> Department of Genomic and Applied Microbiology >> Grisebachstr. 8 >> 37077 Göttingen >> Germany >> Phone: +49 (0)551 394897 >> Mail: cwill2(a)gwdg.de >> >

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Re: [mg-rast] Error: Edit Metadata
by Mark D'Souza 27 Jun '11

27 Jun '11

Hi, These jobs have completed. Regards, Mark On Jun 23, 2011, at 4:52 PM, Mark DSouza wrote: > Hi, > > We will take a look at the 4 datasets and find out what has gone wrong and get back to you. > > Regards, > Mark > > ----- Original Message ----- >> From: "Steve Essinger" <sessinger(a)gmail.com> >> To: "Mark DSouza" <dsouza(a)mcs.anl.gov> >> Cc: mg-rast(a)mcs.anl.gov >> Sent: Thursday, June 23, 2011 3:48:10 PM >> Subject: Re: [mg-rast] Error: Edit Metadata >> Mark, >> >> >> Thank you so much for your quick response. It appears to be working >> correctly on my end now as well. >> >> >> One more issue: I have 4 datasets in progress that indicate a Loading >> Database: Error. How do I kill these processes and restart them? I do >> not know what is causing the error. >> >> >> Thanks, >> Steve >> >> >> On Thu, Jun 23, 2011 at 4:35 PM, Mark DSouza < dsouza(a)mcs.anl.gov > >> wrote: >> >> >> Hi, >> >> This has now been fixed, thanks for letting us know about the problem. >> >> Regards, >> Mark >> >> >> >> >> ----- Original Message ----- >>> From: "Mark DSouza" < dsouza(a)mcs.anl.gov > >>> To: "Steve Essinger" < sessinger(a)gmail.com > >>> Cc: mg-rast(a)mcs.anl.gov >>> Sent: Thursday, June 23, 2011 2:39:14 PM >>> Subject: Re: [mg-rast] Error: Edit Metadata >>> Hi, >>> >>> Sorry about that, we will take a look and get it fixed. >>> >>> -- >>> 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: "Steve Essinger" < sessinger(a)gmail.com > >>>> To: mg-rast(a)mcs.anl.gov >>>> Sent: Thursday, June 23, 2011 2:27:03 PM >>>> Subject: [mg-rast] Error: Edit Metadata >>>> Hi, >>>> >>>> >>>> I've uploaded a bunch of metagenomic datasets that I now wish to >>>> edit >>>> their metadata. When I click on the link 'Edit Metadata' I get the >>>> following response: >>>> >>>> >>>>>>> Unable to fetch attribute 'owner' of JobDB::Job id 28416 from >>>>>>> db >>>>>>> 'WebAppBackend' of type 'User' with id 49300. at >>>>>>> /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_1_0/common/lib/PPO/DBObject.pm >>>>>>> line 736 >>>> >>>> >>>> Any thoughts? >>>> >>>> >>>> Thanks, >>>> Steve

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Re: [mg-rast] I think I have 19 jobs stalled
by Mark D'Souza 27 Jun '11

27 Jun '11

Hi, These jobs are completed. Regards, Mark On Jun 22, 2011, at 9:51 AM, Mark DSouza wrote: > Hi, > > No bother and sorry for the delay, the jobs seem to be stuck we will give them a nudge. > > -- > 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: "Robert J Boissy" <rboissy(a)unmc.edu> >> To: mg-rast(a)mcs.anl.gov >> Sent: Tuesday, June 21, 2011 5:34:10 PM >> Subject: [mg-rast] I think I have 19 jobs stalled >> Hi, >> >> Sorry to bother you again but I think I have 19 jobs stalled. They all >> seem frozen at the same stage. They were submitted over 2 weeks ago. >> >> Thanks again for your help! >> >> Best wishes, >> >> Robert >> >> Robert Boissy, Ph.D. >> Assistant Professor, Bioinformatics and Genomics >> Department of Internal Medicine >> University of Nebraska Medical Center >> Center for Bioinformatics and Systems Biology >> Swanson Hall Room 2048 >> 984360 Nebraska Medical Center >> Omaha, NE 68198-5152 >> >> rboissy(a)unmc.edu >> 402.559.4307 office phone >> 402.559.4104 office fax >> 402.889.7544 mobile

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