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

Re: [mg-rast] Failure in uploading data.
by Mark D'Souza 07 Feb '11

07 Feb '11

Hi, We do not limit the number of data sets you upload and we do not limit the size within reasonable limits, the 240M file should not be a problem, though the processing may take longer than usual. I can not find any trace of the failed uploads, please retry the uploads completing all three steps for each data set and let us know at which point you have a problem. ----- Original Message ----- > From: "yf3" <yf3(a)qibebt.ac.cn> > To: "mg-rast" <mg-rast(a)mcs.anl.gov> > Sent: Monday, February 7, 2011 5:07:58 AM > Subject: [mg-rast] Failure in uploading data. > Hello, > > I have 4 samples for metagenomic analysis in MG-RAST. Now the first > sample data has been uploaded and being analysed. Could I upload the > second in the meantime? As I found it always failed in uploading the > second data. Is it the reason? Furthermore, my data is from solexa GA > sequencing and so is very large. For example, the largest data is > about 240M after compression. Is this out of the limit in your website > that lead to upload failure? Could you kind please help me check for > the reason? > Looking forward for your reply! > Thanks very much! > > > 2011-02-07 > > yf3 -- 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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Re: [mg-rast] Question
by Mark D'Souza 07 Feb '11

07 Feb '11

Hi, There is no problem with the job, it is queued for similarity computation. The volume of new data sets on the MG-RAST system has been high recently at the same time we have had a shortage of compute cycles, resulting in longer than usual processing time. We are working to rectify this. ----- Original Message ----- > From: "Scott Weese" <jsweese(a)uoguelph.ca> > To: mg-rast(a)mcs.anl.gov > Sent: Sunday, February 6, 2011 2:00:47 PM > Subject: [mg-rast] Question > I'm using MG-RAST for the first time so this question may just relate > to my inexperience. I uploaded a job (#14077) on Thursday and it > progressed through the first 3 stages quickly, but has been a > "Similarity final check has not yet started" for a few days. I'm just > wondering whether this is normal and if it's still in a queue,or > whether there's a problem with the job. Any information you can > provide would be appreciated. > > Thanks. > > Scott > > J Scott Weese DVM DVSc DipACVIM > Dept of Pathobiology > Ontario Veterinary College > University of Guelph > Guelph, Ontario > > http://www.wormsandgermsblog.com > http://www.equidblog.com -- 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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Re: [mg-rast] MG-RAST website
by Mark D'Souza 07 Feb '11

07 Feb '11

Hi, The machine had dropped off the network, it is now back. Thanks again for letting us know. Mark ----- Original Message ----- > From: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > To: "yf3" <yf3(a)qibebt.ac.cn> > Cc: "mg-rast" <mg-rast(a)mcs.anl.gov> > Sent: Monday, February 7, 2011 8:37:10 AM > Subject: Re: [mg-rast] MG-RAST website > Thanks, it is not responding, we will look into this. > > ----- Original Message ----- > > From: "yf3" <yf3(a)qibebt.ac.cn> > > To: "mg-rast" <mg-rast(a)mcs.anl.gov> > > Sent: Monday, February 7, 2011 8:16:33 AM > > Subject: [mg-rast] MG-RAST website > > Hello, > > > > Is there anything wrong with the MG-RAST website. I can't reach it. > > > > Would you mind checking for that? > > > > Thanks very much! > > > > > > 2011-02-07 > > > > yf3 > > -- > 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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Re: [mg-rast] MG-RAST website
by Mark D'Souza 07 Feb '11

07 Feb '11

Thanks, it is not responding, we will look into this. ----- Original Message ----- > From: "yf3" <yf3(a)qibebt.ac.cn> > To: "mg-rast" <mg-rast(a)mcs.anl.gov> > Sent: Monday, February 7, 2011 8:16:33 AM > Subject: [mg-rast] MG-RAST website > Hello, > > Is there anything wrong with the MG-RAST website. I can't reach it. > > Would you mind checking for that? > > Thanks very much! > > > 2011-02-07 > > yf3 -- 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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MG-RAST website
by yf3 07 Feb '11

07 Feb '11

Hello, Is there anything wrong with the MG-RAST website. I can't reach it. Would you mind checking for that? Thanks very much! 2011-02-07 yf3

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Failure in uploading data.
by yf3 07 Feb '11

07 Feb '11

Hello, I have 4 samples for metagenomic analysis in MG-RAST. Now the first sample data has been uploaded and being analysed. Could I upload the second in the meantime? As I found it always failed in uploading the second data. Is it the reason? Furthermore, my data is from solexa GA sequencing and so is very large. For example, the largest data is about 240M after compression. Is this out of the limit in your website that lead to upload failure? Could you kind please help me check for the reason? Looking forward for your reply! Thanks very much! 2011-02-07 yf3

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Question
by Scott Weese 06 Feb '11

06 Feb '11

I'm using MG-RAST for the first time so this question may just relate to my inexperience. I uploaded a job (#14077) on Thursday and it progressed through the first 3 stages quickly, but has been a "Similarity final check has not yet started" for a few days. I'm just wondering whether this is normal and if it's still in a queue,or whether there's a problem with the job. Any information you can provide would be appreciated. Thanks. Scott J Scott Weese DVM DVSc DipACVIM Dept of Pathobiology Ontario Veterinary College University of Guelph Guelph, Ontario http://www.wormsandgermsblog.com http://www.equidblog.com

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Your MG-RAST jobs (14056, 14079)
by Mark D'Souza 04 Feb '11

04 Feb '11

Hi, The jobs you submitted to MG-RAST (14056, 14079) have failed and can not be restarted as the sequence files contain alignment information in the form of the '-' characters which are not accepted by the system. Please edit your sequence files to remove these characters 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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Your MG-RAST job (14085, D13A)
by Mark D'Souza 04 Feb '11

04 Feb '11

Hi, The job you submitted to MG-RAST (14085, D13A) has failed and can not be restarted as the sequence file contains alignment information in the form of the '-' characters which are not accepted by the system. Please edit your sequence file to remove these characters and resubmit this job 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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Re: [mg-rast] Your MG-RAST jobs (13945, 13946, 13947)
by Mark D'Souza 04 Feb '11

04 Feb '11

Hi, The problem is with the uncompressed fasta file, the ^Z end of file character needs to be removed as it is being treated as part of the last sequence. Mark ----- Original Message ----- > From: "Xiangzhen Li" <lixz(a)illinois.edu> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Friday, February 4, 2011 4:10:11 PM > Subject: Re: Your MG-RAST jobs (13945, 13946, 13947) > Dear Mark > I submited our files (Job 14093-14095) several times in different > formates, including .tgz formate, but it is not successful. Is it size > too big? But I submitted even bigger file before. Would you please > give me suggestions how to solve the problems? > Thanks. > Xiangzhen > > > > On Thu, Feb 3, 2011 at 12:26 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> > wrote: > > Hi, > > > > The jobs you submitted to MG-RAST have failed as the sequence files > > contain a non-ASCII character which shows up as '^Z' at the end of > > the file. This is probably the end-of-file character used by some > > software, the MG-RAST code treats it as part of the previous > > sequence and fails. Please check that your sequence file has not > > been corrupted and remove this character before resubmitting 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 > > > > > > -- > Xiangzhen Li > Department of Civil and Environmental Engineering > University of Illinois at Urbana-Champaign > 205 N. Mathews > Urbana, IL 61802

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