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

Re: [mg-rast] MGRAST - account request approved
by raw937＠gmail.com 27 Jun '11

27 Jun '11

Thank you Mark! I have some general questions: Blast/blat are used how many sequences have no hits? Also for the recruitment plot How do you read this correctly? Can you obtain n50 values or percent coverage? Thanks Rick Sent from my “contract free” BlackBerry® smartphone on the WIND network. -----Original Message----- From: Mark D'Souza <dsouza(a)mcs.anl.gov> Date: Mon, 27 Jun 2011 13:02:20 To: Rick White<raw937(a)gmail.com> Cc: <mg-rast(a)mcs.anl.gov> Subject: Re: [mg-rast] MGRAST - account request approved Hi Rick, We restarted 26428, the others are queued and should move along the pipeline as resources become available. Regards, Mark On Jun 27, 2011, at 12:21 PM, Rick White wrote: > Hello Mark, > Most went through over the weekend. > This job: > 26428 4466831.3 45M_VC had an error with loading the database > The rest are not moving forward. > > What should we do? > > Thanks > Rick > > > > > > > > > On Fri, Jun 24, 2011 at 1:18 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > Hi, > > We had a load spike that is probably causing the delay, let us know if they do not go through over the weekend. > > Regards, > Mark > > > > On Jun 24, 2011, at 2:40 PM, Rick White wrote: > > > Hello Mark, > > Most of these samples have few reads and look to be stuck in Dereplication. > > Runs 26413 - 26421 and the rest of my stuff? > > > > It ran some fast the last time, I am worried that its stuck.. > > > > Sorry to bother... > > > > Thanks > > Rick > > > > On Fri, Jun 24, 2011 at 1:22 AM, Rick White <raw937(a)gmail.com> wrote: > > Hello again > > This sample in analysis > > 26349 4466752.3 SB_Mic_Filtered_PS_true > > Finalizing Data : completed > > > > Looks stuck > > > > Rest loaded are stuck in Dereplication.. > > > > Let me know? > > > > Thanks > > Rick > > > > > > On Thu, Jun 23, 2011 at 6:47 PM, Rick White <raw937(a)gmail.com> wrote: > > Hello again, > > The analysis is running very slow is their a reason for it? > > > > Also, one states completed in analysis but looks stuck? > > > > Whats up with that? > > > > YOUR #1 FAN > > Rick > > > > On Thu, Jun 23, 2011 at 10:30 AM, <raw937(a)gmail.com> wrote: > > Thanks buddy! > > Sent from my “contract free” BlackBerry® smartphone on the WIND network. > > > > -----Original Message----- > > From: Mark D'Souza <dsouza(a)mcs.anl.gov> > > Date: Thu, 23 Jun 2011 12:10:11 > > To: Rick White<raw937(a)gmail.com> > > Cc: <mg-rast(a)mcs.anl.gov> > > Subject: Re: [mg-rast] MGRAST - account request approved > > > > Hi Rick, > > > > Sorry about that, I reset the upload and it should work fine now. > > > > 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 22, 2011, at 11:49 PM, Rick White wrote: > > > > > Hello again, > > > I cant upload any more files... > > > > > > uploaded a RMStromCCMexMic20050722.fa.gz file and its stuck... > > > > > > I can't upload any more? > > > > > > Please help! > > > > > > Thanks > > > rick > > > > > > On Tue, Jun 21, 2011 at 2:16 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > > > Hi, > > > > > > Give us the metagenome IDs and queries the next time you get an undefined tree, we will check into it. We have seen this happen before, querying the database for huge amounts of data is the problem and we are working on fixing this. > > > > > > What are the parameters you are using for the sequence trimming? > > > > > > Regards, > > > Mark > > > > > > > > > > > > On Jun 21, 2011, at 11:50 AM, Rick White wrote: > > > > > > > I have noticed a bug with the tree output it keeps stating undefined? Is this a bug or something else? > > > > > > > > Yes, I will let you know the asap the renaming & deletion. > > > > > > > > Also, when I put in my amplicons & use the trimmer it takes the mean 400 bp down to 205 bp. It would be great to reject reads that are shorter then the length you want them. > > > > > > > > ONCE AGAIN, I AM A HUGE FAN OF THE SITE! I plan on using from now on. > > > > > > > > Keep up the great work! > > > > Rick > > > > > > > > On Tue, Jun 21, 2011 at 9:32 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > > > > Hi, and thanks for the compliment, > > > > > > > > The deletion/renaming is something we are working on, if you let me know the MG-RAST IDs and changes to be made I can take care of it. > > > > > > > > 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 20, 2011, at 5:49 PM, Rick White wrote: > > > > > > > > > Mark, > > > > > MG-RAST, is the greatest thing ever!!!!!!!!! > > > > > > > > > > It has saved me so much TIME! I wished I would have known about it sooner. > > > > > > > > > > Quick question, how do I delete ones that completed analysis but I labeled wrong? > > > > > > > > > > Or how can I edit them? Just rename them it sends me a wierd error message. I would like to input pH etc or rename them! > > > > > > > > > > Thanks > > > > > Rick > > > > > > > > > > On Thu, Jun 9, 2011 at 11:59 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > > > > > Hi, > > > > > > > > > > Can you tell us what you see when you login and the browser you are using? You will need to set the preferences for your browser to accept cookies (required for login) and we test on FireFox. The URL in the notification email you received (http://metagenomics.anl.gov/) points to the V3.1 site. > > > > > > > > > > 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 9, 2011, at 12:46 PM, Rick White wrote: > > > > > > > > > > > Is verison 3 avaliable? > > > > > > > > > > > > I can't login or upload my data on using ubuntu?? > > > > > > > > > > > > On Thu, Jun 9, 2011 at 10:27 AM, <mg-rast(a)mcs.anl.gov> wrote: > > > > > > Dear RIck White, > > > > > > > > > > > > your account request for access to our web service MGRAST has been accepted. > > > > > > > > > > > > Your login is: raw937 > > > > > > Your password is: v307SsCD > > > > > > > > > > > > We recommend to change the password immediately. To do so please go to our web service http://metagenomics.anl.gov/ and change your password from the account management. > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > This email was automatically generated by the MGRAST web service. Do not reply. > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > Richard Allen White III M.S. > > > > > > PhD Student - Suttle Lab > > > > > > Department of Microbiology & Immunology > > > > > > The University of British Columbia > > > > > > Vancouver, BC, Canada > > > > > > V6T 1Z4 > > > > > > ph.(604) 827-5715 > > > > > > cell. ***My new number is 604-440-5150*** > > > > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > > > > > > > For Shipping: > > > > > > Richard Allen White III & Amy Chan > > > > > > Suttle Lab > > > > > > UBC-Botany/zoology/micro > > > > > > 1316-6270 University Blvd. > > > > > > Vancouver, BC > > > > > > V6T 1Z4 > > > > > > 1.604.827.5715 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Richard Allen White III M.S. > > > > > PhD Student - Suttle Lab > > > > > Department of Microbiology & Immunology > > > > > The University of British Columbia > > > > > Vancouver, BC, Canada > > > > > V6T 1Z4 > > > > > ph.(604) 827-5715 > > > > > cell. ***My new number is 604-440-5150*** > > > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > > > > > For Shipping: > > > > > Richard Allen White III & Amy Chan > > > > > Suttle Lab > > > > > UBC-Botany/zoology/micro > > > > > 1316-6270 University Blvd. > > > > > Vancouver, BC > > > > > V6T 1Z4 > > > > > 1.604.827.5715 > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > Richard Allen White III M.S. > > > > PhD Student - Suttle Lab > > > > Department of Microbiology & Immunology > > > > The University of British Columbia > > > > Vancouver, BC, Canada > > > > V6T 1Z4 > > > > ph.(604) 827-5715 > > > > cell. ***My new number is 604-440-5150*** > > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > > > For Shipping: > > > > Richard Allen White III & Amy Chan > > > > Suttle Lab > > > > UBC-Botany/zoology/micro > > > > 1316-6270 University Blvd. > > > > Vancouver, BC > > > > V6T 1Z4 > > > > 1.604.827.5715 > > > > > > > > > > > > > > > > > > > -- > > > Richard Allen White III M.S. > > > PhD Student - Suttle Lab > > > Department of Microbiology & Immunology > > > The University of British Columbia > > > Vancouver, BC, Canada > > > V6T 1Z4 > > > ph.(604) 827-5715 > > > cell. ***My new number is 604-440-5150*** > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > For Shipping: > > > Richard Allen White III & Amy Chan > > > Suttle Lab > > > UBC-Botany/zoology/micro > > > 1316-6270 University Blvd. > > > Vancouver, BC > > > V6T 1Z4 > > > 1.604.827.5715 > > > > > > > > > > > > > -- > > Richard Allen White III M.S. > > PhD Student - Suttle Lab > > Department of Microbiology & Immunology > > The University of British Columbia > > Vancouver, BC, Canada > > V6T 1Z4 > > ph.(604) 827-5715 > > cell. ***My new number is 604-440-5150*** > > http://www.ocgy.ubc.ca/~suttle/ > > > > For Shipping: > > Richard Allen White III & Amy Chan > > Suttle Lab > > UBC-Botany/zoology/micro > > 1316-6270 University Blvd. > > Vancouver, BC > > V6T 1Z4 > > 1.604.827.5715 > > > > > > > > > > -- > > Richard Allen White III M.S. > > PhD Student - Suttle Lab > > Department of Microbiology & Immunology > > The University of British Columbia > > Vancouver, BC, Canada > > V6T 1Z4 > > ph.(604) 827-5715 > > cell. ***My new number is 604-440-5150*** > > http://www.ocgy.ubc.ca/~suttle/ > > > > For Shipping: > > Richard Allen White III & Amy Chan > > Suttle Lab > > UBC-Botany/zoology/micro > > 1316-6270 University Blvd. > > Vancouver, BC > > V6T 1Z4 > > 1.604.827.5715 > > > > > > > > > > -- > > Richard Allen White III M.S. > > PhD Student - Suttle Lab > > Department of Microbiology & Immunology > > The University of British Columbia > > Vancouver, BC, Canada > > V6T 1Z4 > > ph.(604) 827-5715 > > cell. ***My new number is 604-440-5150*** > > http://www.ocgy.ubc.ca/~suttle/ > > > > For Shipping: > > Richard Allen White III & Amy Chan > > Suttle Lab > > UBC-Botany/zoology/micro > > 1316-6270 University Blvd. > > Vancouver, BC > > V6T 1Z4 > > 1.604.827.5715 > > > > > > > -- > Richard Allen White III M.S. > PhD Student - Suttle Lab > Department of Microbiology & Immunology > The University of British Columbia > Vancouver, BC, Canada > V6T 1Z4 > ph.(604) 827-5715 > cell. ***My new number is 604-440-5150*** > http://www.ocgy.ubc.ca/~suttle/ > > For Shipping: > Richard Allen White III & Amy Chan > Suttle Lab > UBC-Botany/zoology/micro > 1316-6270 University Blvd. > Vancouver, BC > V6T 1Z4 > 1.604.827.5715 >

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Re: [mg-rast] MGRAST - account request approved
by Mark D'Souza 27 Jun '11

27 Jun '11

Hi Rick, We restarted 26428, the others are queued and should move along the pipeline as resources become available. Regards, Mark On Jun 27, 2011, at 12:21 PM, Rick White wrote: > Hello Mark, > Most went through over the weekend. > This job: > 26428 4466831.3 45M_VC had an error with loading the database > The rest are not moving forward. > > What should we do? > > Thanks > Rick > > > > > > > > > On Fri, Jun 24, 2011 at 1:18 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > Hi, > > We had a load spike that is probably causing the delay, let us know if they do not go through over the weekend. > > Regards, > Mark > > > > On Jun 24, 2011, at 2:40 PM, Rick White wrote: > > > Hello Mark, > > Most of these samples have few reads and look to be stuck in Dereplication. > > Runs 26413 - 26421 and the rest of my stuff? > > > > It ran some fast the last time, I am worried that its stuck.. > > > > Sorry to bother... > > > > Thanks > > Rick > > > > On Fri, Jun 24, 2011 at 1:22 AM, Rick White <raw937(a)gmail.com> wrote: > > Hello again > > This sample in analysis > > 26349 4466752.3 SB_Mic_Filtered_PS_true > > Finalizing Data : completed > > > > Looks stuck > > > > Rest loaded are stuck in Dereplication.. > > > > Let me know? > > > > Thanks > > Rick > > > > > > On Thu, Jun 23, 2011 at 6:47 PM, Rick White <raw937(a)gmail.com> wrote: > > Hello again, > > The analysis is running very slow is their a reason for it? > > > > Also, one states completed in analysis but looks stuck? > > > > Whats up with that? > > > > YOUR #1 FAN > > Rick > > > > On Thu, Jun 23, 2011 at 10:30 AM, <raw937(a)gmail.com> wrote: > > Thanks buddy! > > Sent from my “contract free” BlackBerry® smartphone on the WIND network. > > > > -----Original Message----- > > From: Mark D'Souza <dsouza(a)mcs.anl.gov> > > Date: Thu, 23 Jun 2011 12:10:11 > > To: Rick White<raw937(a)gmail.com> > > Cc: <mg-rast(a)mcs.anl.gov> > > Subject: Re: [mg-rast] MGRAST - account request approved > > > > Hi Rick, > > > > Sorry about that, I reset the upload and it should work fine now. > > > > 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 22, 2011, at 11:49 PM, Rick White wrote: > > > > > Hello again, > > > I cant upload any more files... > > > > > > uploaded a RMStromCCMexMic20050722.fa.gz file and its stuck... > > > > > > I can't upload any more? > > > > > > Please help! > > > > > > Thanks > > > rick > > > > > > On Tue, Jun 21, 2011 at 2:16 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > > > Hi, > > > > > > Give us the metagenome IDs and queries the next time you get an undefined tree, we will check into it. We have seen this happen before, querying the database for huge amounts of data is the problem and we are working on fixing this. > > > > > > What are the parameters you are using for the sequence trimming? > > > > > > Regards, > > > Mark > > > > > > > > > > > > On Jun 21, 2011, at 11:50 AM, Rick White wrote: > > > > > > > I have noticed a bug with the tree output it keeps stating undefined? Is this a bug or something else? > > > > > > > > Yes, I will let you know the asap the renaming & deletion. > > > > > > > > Also, when I put in my amplicons & use the trimmer it takes the mean 400 bp down to 205 bp. It would be great to reject reads that are shorter then the length you want them. > > > > > > > > ONCE AGAIN, I AM A HUGE FAN OF THE SITE! I plan on using from now on. > > > > > > > > Keep up the great work! > > > > Rick > > > > > > > > On Tue, Jun 21, 2011 at 9:32 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > > > > Hi, and thanks for the compliment, > > > > > > > > The deletion/renaming is something we are working on, if you let me know the MG-RAST IDs and changes to be made I can take care of it. > > > > > > > > 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 20, 2011, at 5:49 PM, Rick White wrote: > > > > > > > > > Mark, > > > > > MG-RAST, is the greatest thing ever!!!!!!!!! > > > > > > > > > > It has saved me so much TIME! I wished I would have known about it sooner. > > > > > > > > > > Quick question, how do I delete ones that completed analysis but I labeled wrong? > > > > > > > > > > Or how can I edit them? Just rename them it sends me a wierd error message. I would like to input pH etc or rename them! > > > > > > > > > > Thanks > > > > > Rick > > > > > > > > > > On Thu, Jun 9, 2011 at 11:59 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > > > > > Hi, > > > > > > > > > > Can you tell us what you see when you login and the browser you are using? You will need to set the preferences for your browser to accept cookies (required for login) and we test on FireFox. The URL in the notification email you received (http://metagenomics.anl.gov/) points to the V3.1 site. > > > > > > > > > > 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 9, 2011, at 12:46 PM, Rick White wrote: > > > > > > > > > > > Is verison 3 avaliable? > > > > > > > > > > > > I can't login or upload my data on using ubuntu?? > > > > > > > > > > > > On Thu, Jun 9, 2011 at 10:27 AM, <mg-rast(a)mcs.anl.gov> wrote: > > > > > > Dear RIck White, > > > > > > > > > > > > your account request for access to our web service MGRAST has been accepted. > > > > > > > > > > > > Your login is: raw937 > > > > > > Your password is: v307SsCD > > > > > > > > > > > > We recommend to change the password immediately. To do so please go to our web service http://metagenomics.anl.gov/ and change your password from the account management. > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > This email was automatically generated by the MGRAST web service. Do not reply. > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > Richard Allen White III M.S. > > > > > > PhD Student - Suttle Lab > > > > > > Department of Microbiology & Immunology > > > > > > The University of British Columbia > > > > > > Vancouver, BC, Canada > > > > > > V6T 1Z4 > > > > > > ph.(604) 827-5715 > > > > > > cell. ***My new number is 604-440-5150*** > > > > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > > > > > > > For Shipping: > > > > > > Richard Allen White III & Amy Chan > > > > > > Suttle Lab > > > > > > UBC-Botany/zoology/micro > > > > > > 1316-6270 University Blvd. > > > > > > Vancouver, BC > > > > > > V6T 1Z4 > > > > > > 1.604.827.5715 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Richard Allen White III M.S. > > > > > PhD Student - Suttle Lab > > > > > Department of Microbiology & Immunology > > > > > The University of British Columbia > > > > > Vancouver, BC, Canada > > > > > V6T 1Z4 > > > > > ph.(604) 827-5715 > > > > > cell. ***My new number is 604-440-5150*** > > > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > > > > > For Shipping: > > > > > Richard Allen White III & Amy Chan > > > > > Suttle Lab > > > > > UBC-Botany/zoology/micro > > > > > 1316-6270 University Blvd. > > > > > Vancouver, BC > > > > > V6T 1Z4 > > > > > 1.604.827.5715 > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > Richard Allen White III M.S. > > > > PhD Student - Suttle Lab > > > > Department of Microbiology & Immunology > > > > The University of British Columbia > > > > Vancouver, BC, Canada > > > > V6T 1Z4 > > > > ph.(604) 827-5715 > > > > cell. ***My new number is 604-440-5150*** > > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > > > For Shipping: > > > > Richard Allen White III & Amy Chan > > > > Suttle Lab > > > > UBC-Botany/zoology/micro > > > > 1316-6270 University Blvd. > > > > Vancouver, BC > > > > V6T 1Z4 > > > > 1.604.827.5715 > > > > > > > > > > > > > > > > > > > -- > > > Richard Allen White III M.S. > > > PhD Student - Suttle Lab > > > Department of Microbiology & Immunology > > > The University of British Columbia > > > Vancouver, BC, Canada > > > V6T 1Z4 > > > ph.(604) 827-5715 > > > cell. ***My new number is 604-440-5150*** > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > For Shipping: > > > Richard Allen White III & Amy Chan > > > Suttle Lab > > > UBC-Botany/zoology/micro > > > 1316-6270 University Blvd. > > > Vancouver, BC > > > V6T 1Z4 > > > 1.604.827.5715 > > > > > > > > > > > > > -- > > Richard Allen White III M.S. > > PhD Student - Suttle Lab > > Department of Microbiology & Immunology > > The University of British Columbia > > Vancouver, BC, Canada > > V6T 1Z4 > > ph.(604) 827-5715 > > cell. ***My new number is 604-440-5150*** > > http://www.ocgy.ubc.ca/~suttle/ > > > > For Shipping: > > Richard Allen White III & Amy Chan > > Suttle Lab > > UBC-Botany/zoology/micro > > 1316-6270 University Blvd. > > Vancouver, BC > > V6T 1Z4 > > 1.604.827.5715 > > > > > > > > > > -- > > Richard Allen White III M.S. > > PhD Student - Suttle Lab > > Department of Microbiology & Immunology > > The University of British Columbia > > Vancouver, BC, Canada > > V6T 1Z4 > > ph.(604) 827-5715 > > cell. ***My new number is 604-440-5150*** > > http://www.ocgy.ubc.ca/~suttle/ > > > > For Shipping: > > Richard Allen White III & Amy Chan > > Suttle Lab > > UBC-Botany/zoology/micro > > 1316-6270 University Blvd. > > Vancouver, BC > > V6T 1Z4 > > 1.604.827.5715 > > > > > > > > > > -- > > Richard Allen White III M.S. > > PhD Student - Suttle Lab > > Department of Microbiology & Immunology > > The University of British Columbia > > Vancouver, BC, Canada > > V6T 1Z4 > > ph.(604) 827-5715 > > cell. ***My new number is 604-440-5150*** > > http://www.ocgy.ubc.ca/~suttle/ > > > > For Shipping: > > Richard Allen White III & Amy Chan > > Suttle Lab > > UBC-Botany/zoology/micro > > 1316-6270 University Blvd. > > Vancouver, BC > > V6T 1Z4 > > 1.604.827.5715 > > > > > > > -- > Richard Allen White III M.S. > PhD Student - Suttle Lab > Department of Microbiology & Immunology > The University of British Columbia > Vancouver, BC, Canada > V6T 1Z4 > ph.(604) 827-5715 > cell. ***My new number is 604-440-5150*** > http://www.ocgy.ubc.ca/~suttle/ > > For Shipping: > Richard Allen White III & Amy Chan > Suttle Lab > UBC-Botany/zoology/micro > 1316-6270 University Blvd. > Vancouver, BC > V6T 1Z4 > 1.604.827.5715 >

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Re: [mg-rast] Hits and minimum length
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 8:39 AM, Peter Ahrens <PAE(a)ssi.dk> wrote: > The dataset is my own 22-hel (4466709.3 if you have access to that) and the "abundance number is the sum of the abundance of all the species and the unassigned. > I just wondered whether more hits than sequences could indicate that some of the sequences hit more than one species? > And if so, would a chimera give rise to more hits when using short alignement length but only one (or zero) when using a longer alignment length? > > Peter > > -----Oprindelig meddelelse----- > Fra: William Trimble [mailto:[email protected]] > Sendt: 27. juni 2011 15:02 > Til: mg-rast(a)mcs.anl.gov; Peter Ahrens > Emne: Re: [mg-rast] Hits and minimum length > > Thanks for using MG-RAST. > > The similarity searching step in MG-RAST isn't specifically designed to identify chimeras. It performs a similarity search and allows you to filter the results of the search. It could be chimerism, but it could just be that the best database hits don't align particularly well. > > On the face of it, it makes sense that more stringent filters will yield fewer species and fewer hits. > > I haven't been able to reproduce the numbers you report below -- which dataset are you using, and which annotation source (RDP, greengenes, or SSU)? Where are you taking the "abundance" number from? > > William Trimble > for the MG-RAST team > > > On Mon, Jun 27, 2011 at 2:00 AM, Peter Ahrens <PAE(a)ssi.dk> wrote: >> >> >> I am examining a sample of 8150 16S sequences to the species level. >> When I change the minimum alignment length cut off, the results >> changes >> dramatically: >> >> LENGTH / SPECIES / TOTAL NUMBER OF HITS >> >> 150 / 23 / 13576 >> >> 200 / 21 / 13537 >> >> 250 / 19 / 11907 >> >> 275 / 14 / 6245 >> >> 300 / 14 / 5097 >> >> >> The average length of my sequences is approximately 400 bases. >> >> Does the high number of hits with the 150 setting indicate chimeras? >> Or why will 8150 sequences give a total of 13576 hits? >> >> >> >> >> >> Thanks in advance >> >> >> >> Peter >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ***************** >> >> Peter Ahrens >> >> STI Research >> >> AMOF >> >> Build. 43/405A >> >> Statens Serum Institut >> >> Ørestads Boulevard 5 >> >> DK-2300 >> >> Copenhagen >> >> Denmark >> >> ***************** >> >> >> >> ________________________________ >> >> STATENS SERUM INSTITUT - 5, Orestads Boulevard - DK-2300 Copenhagen S >> >> Tel: +45 3268 3268 - Fax: +45 3268 3868 >> >> serum(a)ssi.dk www.ssi.dk >> >> ________________________________ >> >> This e-mail, inclusive of attachments, is intended for the person(s) >> or entity stated above and may contain confidential information. >> Unauthorised reading, disclosure, copying, distribution or use of this >> information may violate rights to proprietary information. If you are >> not an intended recipient, please return this e-mail to the sender and delete your copy. >> Thank you. >> >> > ________________________________ > STATENS SERUM INSTITUT - 5, Orestads Boulevard - DK-2300 Copenhagen S > Tel: +45 3268 3268 - Fax: +45 3268 3868 > serum(a)ssi.dk www.ssi.dk<http://www.ssi.dk> > ________________________________ > This e-mail, inclusive of attachments, is intended for the person(s) or entity stated above and may contain confidential information. Unauthorised reading, disclosure, copying, distribution or use of this information may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete your copy. Thank you. > >

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Fwd: question about sequence hits
by William Trimble 27 Jun '11

27 Jun '11

Essentially the same symptom as Peter Ahrens this morning, but with shotgun/protein data. w 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] MGRAST - account request approved
by Rick White 27 Jun '11

27 Jun '11

Hello Mark, Most went through over the weekend. This job: 26428 4466831.3 45M_VC had an error with loading the database The rest are not moving forward. What should we do? Thanks Rick On Fri, Jun 24, 2011 at 1:18 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > Hi, > > We had a load spike that is probably causing the delay, let us know if they > do not go through over the weekend. > > Regards, > Mark > > > > On Jun 24, 2011, at 2:40 PM, Rick White wrote: > > > Hello Mark, > > Most of these samples have few reads and look to be stuck in > Dereplication. > > Runs 26413 - 26421 and the rest of my stuff? > > > > It ran some fast the last time, I am worried that its stuck.. > > > > Sorry to bother... > > > > Thanks > > Rick > > > > On Fri, Jun 24, 2011 at 1:22 AM, Rick White <raw937(a)gmail.com> wrote: > > Hello again > > This sample in analysis > > 26349 4466752.3 SB_Mic_Filtered_PS_true > > Finalizing Data : completed > > > > Looks stuck > > > > Rest loaded are stuck in Dereplication.. > > > > Let me know? > > > > Thanks > > Rick > > > > > > On Thu, Jun 23, 2011 at 6:47 PM, Rick White <raw937(a)gmail.com> wrote: > > Hello again, > > The analysis is running very slow is their a reason for it? > > > > Also, one states completed in analysis but looks stuck? > > > > Whats up with that? > > > > YOUR #1 FAN > > Rick > > > > On Thu, Jun 23, 2011 at 10:30 AM, <raw937(a)gmail.com> wrote: > > Thanks buddy! > > Sent from my “contract free” BlackBerry® smartphone on the WIND network. > > > > -----Original Message----- > > From: Mark D'Souza <dsouza(a)mcs.anl.gov> > > Date: Thu, 23 Jun 2011 12:10:11 > > To: Rick White<raw937(a)gmail.com> > > Cc: <mg-rast(a)mcs.anl.gov> > > Subject: Re: [mg-rast] MGRAST - account request approved > > > > Hi Rick, > > > > Sorry about that, I reset the upload and it should work fine now. > > > > 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 22, 2011, at 11:49 PM, Rick White wrote: > > > > > Hello again, > > > I cant upload any more files... > > > > > > uploaded a RMStromCCMexMic20050722.fa.gz file and its stuck... > > > > > > I can't upload any more? > > > > > > Please help! > > > > > > Thanks > > > rick > > > > > > On Tue, Jun 21, 2011 at 2:16 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> > wrote: > > > Hi, > > > > > > Give us the metagenome IDs and queries the next time you get an > undefined tree, we will check into it. We have seen this happen before, > querying the database for huge amounts of data is the problem and we are > working on fixing this. > > > > > > What are the parameters you are using for the sequence trimming? > > > > > > Regards, > > > Mark > > > > > > > > > > > > On Jun 21, 2011, at 11:50 AM, Rick White wrote: > > > > > > > I have noticed a bug with the tree output it keeps stating undefined? > Is this a bug or something else? > > > > > > > > Yes, I will let you know the asap the renaming & deletion. > > > > > > > > Also, when I put in my amplicons & use the trimmer it takes the mean > 400 bp down to 205 bp. It would be great to reject reads that are shorter > then the length you want them. > > > > > > > > ONCE AGAIN, I AM A HUGE FAN OF THE SITE! I plan on using from now on. > > > > > > > > Keep up the great work! > > > > Rick > > > > > > > > On Tue, Jun 21, 2011 at 9:32 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> > wrote: > > > > Hi, and thanks for the compliment, > > > > > > > > The deletion/renaming is something we are working on, if you let me > know the MG-RAST IDs and changes to be made I can take care of it. > > > > > > > > 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 20, 2011, at 5:49 PM, Rick White wrote: > > > > > > > > > Mark, > > > > > MG-RAST, is the greatest thing ever!!!!!!!!! > > > > > > > > > > It has saved me so much TIME! I wished I would have known about it > sooner. > > > > > > > > > > Quick question, how do I delete ones that completed analysis but I > labeled wrong? > > > > > > > > > > Or how can I edit them? Just rename them it sends me a wierd error > message. I would like to input pH etc or rename them! > > > > > > > > > > Thanks > > > > > Rick > > > > > > > > > > On Thu, Jun 9, 2011 at 11:59 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> > wrote: > > > > > Hi, > > > > > > > > > > Can you tell us what you see when you login and the browser you are > using? You will need to set the preferences for your browser to accept > cookies (required for login) and we test on FireFox. The URL in the > notification email you received (http://metagenomics.anl.gov/) points to > the V3.1 site. > > > > > > > > > > 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 9, 2011, at 12:46 PM, Rick White wrote: > > > > > > > > > > > Is verison 3 avaliable? > > > > > > > > > > > > I can't login or upload my data on using ubuntu?? > > > > > > > > > > > > On Thu, Jun 9, 2011 at 10:27 AM, <mg-rast(a)mcs.anl.gov> wrote: > > > > > > Dear RIck White, > > > > > > > > > > > > your account request for access to our web service MGRAST has > been accepted. > > > > > > > > > > > > Your login is: raw937 > > > > > > Your password is: v307SsCD > > > > > > > > > > > > We recommend to change the password immediately. To do so please > go to our web service http://metagenomics.anl.gov/ and change your > password from the account management. > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > This email was automatically generated by the MGRAST web service. > Do not reply. > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > Richard Allen White III M.S. > > > > > > PhD Student - Suttle Lab > > > > > > Department of Microbiology & Immunology > > > > > > The University of British Columbia > > > > > > Vancouver, BC, Canada > > > > > > V6T 1Z4 > > > > > > ph.(604) 827-5715 > > > > > > cell. ***My new number is 604-440-5150*** > > > > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > > > > > > > For Shipping: > > > > > > Richard Allen White III & Amy Chan > > > > > > Suttle Lab > > > > > > UBC-Botany/zoology/micro > > > > > > 1316-6270 University Blvd. > > > > > > Vancouver, BC > > > > > > V6T 1Z4 > > > > > > 1.604.827.5715 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Richard Allen White III M.S. > > > > > PhD Student - Suttle Lab > > > > > Department of Microbiology & Immunology > > > > > The University of British Columbia > > > > > Vancouver, BC, Canada > > > > > V6T 1Z4 > > > > > ph.(604) 827-5715 > > > > > cell. ***My new number is 604-440-5150*** > > > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > > > > > For Shipping: > > > > > Richard Allen White III & Amy Chan > > > > > Suttle Lab > > > > > UBC-Botany/zoology/micro > > > > > 1316-6270 University Blvd. > > > > > Vancouver, BC > > > > > V6T 1Z4 > > > > > 1.604.827.5715 > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > Richard Allen White III M.S. > > > > PhD Student - Suttle Lab > > > > Department of Microbiology & Immunology > > > > The University of British Columbia > > > > Vancouver, BC, Canada > > > > V6T 1Z4 > > > > ph.(604) 827-5715 > > > > cell. ***My new number is 604-440-5150*** > > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > > > For Shipping: > > > > Richard Allen White III & Amy Chan > > > > Suttle Lab > > > > UBC-Botany/zoology/micro > > > > 1316-6270 University Blvd. > > > > Vancouver, BC > > > > V6T 1Z4 > > > > 1.604.827.5715 > > > > > > > > > > > > > > > > > > > -- > > > Richard Allen White III M.S. > > > PhD Student - Suttle Lab > > > Department of Microbiology & Immunology > > > The University of British Columbia > > > Vancouver, BC, Canada > > > V6T 1Z4 > > > ph.(604) 827-5715 > > > cell. ***My new number is 604-440-5150*** > > > http://www.ocgy.ubc.ca/~suttle/ > > > > > > For Shipping: > > > Richard Allen White III & Amy Chan > > > Suttle Lab > > > UBC-Botany/zoology/micro > > > 1316-6270 University Blvd. > > > Vancouver, BC > > > V6T 1Z4 > > > 1.604.827.5715 > > > > > > > > > > > > > -- > > Richard Allen White III M.S. > > PhD Student - Suttle Lab > > Department of Microbiology & Immunology > > The University of British Columbia > > Vancouver, BC, Canada > > V6T 1Z4 > > ph.(604) 827-5715 > > cell. ***My new number is 604-440-5150*** > > http://www.ocgy.ubc.ca/~suttle/ > > > > For Shipping: > > Richard Allen White III & Amy Chan > > Suttle Lab > > UBC-Botany/zoology/micro > > 1316-6270 University Blvd. > > Vancouver, BC > > V6T 1Z4 > > 1.604.827.5715 > > > > > > > > > > -- > > Richard Allen White III M.S. > > PhD Student - Suttle Lab > > Department of Microbiology & Immunology > > The University of British Columbia > > Vancouver, BC, Canada > > V6T 1Z4 > > ph.(604) 827-5715 > > cell. ***My new number is 604-440-5150*** > > http://www.ocgy.ubc.ca/~suttle/ > > > > For Shipping: > > Richard Allen White III & Amy Chan > > Suttle Lab > > UBC-Botany/zoology/micro > > 1316-6270 University Blvd. > > Vancouver, BC > > V6T 1Z4 > > 1.604.827.5715 > > > > > > > > > > -- > > Richard Allen White III M.S. > > PhD Student - Suttle Lab > > Department of Microbiology & Immunology > > The University of British Columbia > > Vancouver, BC, Canada > > V6T 1Z4 > > ph.(604) 827-5715 > > cell. ***My new number is 604-440-5150*** > > http://www.ocgy.ubc.ca/~suttle/ > > > > For Shipping: > > Richard Allen White III & Amy Chan > > Suttle Lab > > UBC-Botany/zoology/micro > > 1316-6270 University Blvd. > > Vancouver, BC > > V6T 1Z4 > > 1.604.827.5715 > > > > -- Richard Allen White III M.S. PhD Student - Suttle Lab Department of Microbiology & Immunology The University of British Columbia Vancouver, BC, Canada V6T 1Z4 ph.(604) 827-5715 cell. ***My new number is 604-440-5150*** http://www.ocgy.ubc.ca/~suttle/ For Shipping: Richard Allen White III & Amy Chan Suttle Lab UBC-Botany/zoology/micro 1316-6270 University Blvd. Vancouver, BC V6T 1Z4 1.604.827.5715

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Fwd: Job's been running for 2 weeks+
by Mark D'Souza 27 Jun '11

27 Jun '11

Hi Travis, Please check 25131 Thanks, Mark Begin forwarded message: > From: Cleo HC Ho <cleoho175(a)gmail.com> > Date: June 27, 2011 9:12:13 AM CDT > To: mg-rast(a)mcs.anl.gov > Subject: [mg-rast] Job's been running for 2 weeks+ > > Hi, > > I uploaded a metagenome about two weeks ago, and it is still running right now. Because it usually doesn't take this long, I'm wondering if there's anything wrong with the process (or my data). The job ID is 4465534.3, and the name is "Methanogenic Benzene (phrap with debris)." Could you please let me know if anything's wrong with it, and perhaps why it is taking long? Thank you very much. > > Regards, > Cleo Ho

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Re: [mg-rast] Job's been running for 2 weeks+
by Mark D'Souza 27 Jun '11

27 Jun '11

Hi, Sorry for the delay, it looks like a load failed when we had some hardware issues near the beginning of the month, we will check and get the job moving. 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 27, 2011, at 9:12 AM, Cleo HC Ho wrote: > Hi, > > I uploaded a metagenome about two weeks ago, and it is still running right now. Because it usually doesn't take this long, I'm wondering if there's anything wrong with the process (or my data). The job ID is 4465534.3, and the name is "Methanogenic Benzene (phrap with debris)." Could you please let me know if anything's wrong with it, and perhaps why it is taking long? Thank you very much. > > Regards, > Cleo Ho

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Re: [mg-rast] UPLoads
by Mark D'Souza 27 Jun '11

27 Jun '11

Hi, I checked the upload page and it is working and other users are able to upload and when I use you account I do see the upload applet window. Which browser are you using? We recommend Firefox and if you are using it, check the information at: http://support.mozilla.com/en-US/kb/Using%20the%20Java%20plugin%20with%20Fi… If this does not help, you may be able to solve this by restarting your browser and sometimes using Safari or IE solves the problem. Let us know if you continue to have this problem. 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 27, 2011, at 10:38 AM, ian clark (RRes-Roth) wrote: > Hi. > > Can you let me know whether the Upload facility is currently working. I appear not to be getting the Upload (JumpLoader) Drop files here window. I have Java and have downloaded several data sets before, although not recently. I am using your updated MG-RAST > > Thanks > > Ian

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

27 Jun '11

Thanks for using MG-RAST. Which MG-RAST dataset numbers are you looking at? 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…

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UPLoads
by ian clark (RRes-Roth) 27 Jun '11

27 Jun '11

Hi. Can you let me know whether the Upload facility is currently working. I appear not to be getting the Upload (JumpLoader) Drop files here window. I have Java and have downloaded several data sets before, although not recently. I am using your updated MG-RAST Thanks Ian

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