April 2009 - Mg-rast - mailman3.cels.anl.gov

Re: [mg-rast] Slow progress? (fwd)
by Mark D'Souza 27 Apr '09

27 Apr '09

Read the email just below this. His job was completed an hour after I emailed him. Mark ---------- Forwarded message ---------- Date: Mon, 27 Apr 2009 07:14:08 -0400 From: David J. Schneider <Dave.Schneider(a)ars.usda.gov> To: Mark D'Souza <dsouza(a)mcs.anl.gov> Subject: Re: [mg-rast] Slow progress? Mark, Thanks for the information. I suspected that the system was heavily loaded. A lot of groups (like mine) have shut down their internal machine annotation efforts because what is produced by the RAST/MG-RAST system is superior to what we can do ourselves. Great work. Dave On 4/26/09 1:21 PM, "Mark D'Souza" <dsouza(a)mcs.anl.gov> wrote: > Hi Dave, > > Your job is progressing, similarities are being computed right now. There > are over 3Gbp of sequence data in the system with similarities to be > computed so things are moving a little sluggishly right now. The system > =is= supposed to send the little jobs through past the bigger ones, but > for some reason this is not happening. I can shepherd them through > manually until this gets fixed, I expect your job should be done within a > day. > > Regards, > Mark D'Souza > -- for the MG-RAST team > > mg-rast(a)mcs.anl.gov > http://metagenomics.nmpdr.org/ > > > On Sun, 26 Apr 2009, David J. Schneider wrote: > >> Hello, >> >> The job I submitted the other day (no. 2832) has not making progress since >> Friday evening. Is the system unusually busy? Thanks for your help. >> >> Dave >> >>

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Re: [mg-rast] Approximated Time of Completion?
by Mark D'Souza 27 Apr '09

27 Apr '09

Hi Lars, I would estimate your metagenome will take a couple of days to complete. The processing time depends on the size of the metagenome and the status of the queue. Large jobs of 100s of Mbp may take upto a couple of weeks, and there is over 3Gbp of sequence data in the queue, but we try to slip the smaller jobs through past the large ones. Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/ On Mon, 27 Apr 2009, Lars Schreiber wrote: > Hello, > > My name is Lars Schreiber and I am currently working at the Max-Planck > Insitute for Marine Microbiology in Bremen, Germany. > > I just uploaded one of my metagenomes to your server (job number 3272). Since > I would like to use the annotation data for a student project, I would like > to know if you could > tell me the approximate time when the annotation is completed or what's my > current position in the queue. > > Thanks a lot and best regards from Bremen, > > Lars Schreiber > > -- > Lars Schreiber > Max Planck Institute for Marine Microbiology > PhD Student / Department for Molecular Ecology > Celsiusstr.1 > 28359 Bremen > Germany > ------------------------------------------------------------------ > Phone: ++49-(0)-421-2028-941 > ------------------------------------------------------------------ > Email: lschreib(a)mpi-bremen.de > > >

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Approximated Time of Completion?
by Lars Schreiber 27 Apr '09

27 Apr '09

Hello, My name is Lars Schreiber and I am currently working at the Max-Planck Insitute for Marine Microbiology in Bremen, Germany. I just uploaded one of my metagenomes to your server (job number 3272). Since I would like to use the annotation data for a student project, I would like to know if you could tell me the approximate time when the annotation is completed or what's my current position in the queue. Thanks a lot and best regards from Bremen, Lars Schreiber -- Lars Schreiber Max Planck Institute for Marine Microbiology PhD Student / Department for Molecular Ecology Celsiusstr.1 28359 Bremen Germany ------------------------------------------------------------------ Phone: ++49-(0)-421-2028-941 ------------------------------------------------------------------ Email: lschreib(a)mpi-bremen.de

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Re: [mg-rast] sge priorities
by Mark D'Souza 26 Apr '09

26 Apr '09

Odd, when all the jobs with higher priority complete, 3230 sims went back to 1.5. When I booted a job to higher priority it went back down. I first tried 'qalter -ot 100000 jobid' and that did not affect the 3230 sim jobs, had to go to 500000 before they backed down, and subsequently I used 100000 and they did not jump up again. I set a bunch of smaller jobs with high priority and cleared out some of the errored jobs. We have over 3Gbp in the queue, I am trying to keep the completion time for the smaller jobs reasonable. Mark On Sun, 26 Apr 2009, Mark D'Souza wrote: > Hi, > > Did anyone kick the priority for 3230 sim jobs higher? Earlier today it had > 1.5 priority and now it has gone down to 0.5. It is a large job, over 400 > Mbp, and had taken over the cluster. > > Mark > > >

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Re: [mg-rast] Slow progress?
by Mark D'Souza 26 Apr '09

26 Apr '09

Hi Dave, Job 2832 is now completed and available for browsing. Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/ On Sun, 26 Apr 2009, David J. Schneider wrote: > Hello, > > The job I submitted the other day (no. 2832) has not making progress since > Friday evening. Is the system unusually busy? Thanks for your help. > > Dave > >

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sge priorities
by Mark D'Souza 26 Apr '09

26 Apr '09

Hi, Did anyone kick the priority for 3230 sim jobs higher? Earlier today it had 1.5 priority and now it has gone down to 0.5. It is a large job, over 400 Mbp, and had taken over the cluster. Mark

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Re: [mg-rast] Slow progress?
by Mark D'Souza 26 Apr '09

26 Apr '09

Hi Dave, Your job is progressing, similarities are being computed right now. There are over 3Gbp of sequence data in the system with similarities to be computed so things are moving a little sluggishly right now. The system =is= supposed to send the little jobs through past the bigger ones, but for some reason this is not happening. I can shepherd them through manually until this gets fixed, I expect your job should be done within a day. Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/ On Sun, 26 Apr 2009, David J. Schneider wrote: > Hello, > > The job I submitted the other day (no. 2832) has not making progress since > Friday evening. Is the system unusually busy? Thanks for your help. > > Dave > >

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Slow progress?
by David J. Schneider 26 Apr '09

26 Apr '09

Hello, The job I submitted the other day (no. 2832) has not making progress since Friday evening. Is the system unusually busy? Thanks for your help. Dave

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Your MG-RAST jobs (3264, 3266, 3267, 3268)
by Mark D'Souza 24 Apr '09

24 Apr '09

Hi, I'm sorry, but four of the MG-RAST jobs you submitted yesterday (3264, 3266, 3267, 3268) have failed. We had disk problems yesterday and during the upload process some data required for these jobs was lost and cannot be recovered, you will need to resubmit them. 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] Problems with login?
by David J. Schneider 24 Apr '09

24 Apr '09

Mark and Folker, I restarted FireFox and everything seems to be OK. I am not sure whether that is what made a difference, or if it was the known problem mentioned in Folker's message below. Anyway, thanks for your help. Dave ========================================================================== David: we will look into this during the course of the day. Is this a very new job? The jobs in the first stage of processing have this problem :) In this case simply wait a short while and try again. The problem is not related to the password change. Best Folker On 4/24/09 12:14 PM, "Mark D'Souza" <dsouza(a)mcs.anl.gov> wrote: > Hi Dave, > > This is a bit puzzling, I was able to log on under your user name and view > the details for job 2382. Try clearing your browser cookies and logging in > again and do let us know if that does not work. > > Regards, > Mark D'Souza > -- for the MG-RAST team > > mg-rast(a)mcs.anl.gov > http://metagenomics.nmpdr.org/ > > > On Fri, 24 Apr 2009, David J. Schneider wrote: > >> Hello, >> >> I just changed my password (user name "schneid") and was able to log in, but >> I can't view the detailed report on the progress of the annotation. I tried >> logging out then back in again, but this did not fix the problem. The >> surprising thing is that the jobs do appear on the overview page. Are other >> users experiencing this problem? >> >> Thanks for your help. >> >> Dave Schneider >> >> Computational Biologist >> Plant-Microbe Interaction Research Unit >> R.W. Holley Center >> USDA Agricultural Research Service >> Ithaca, NY 14853 >> >>

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