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

Re: [mg-rast] processing error in pipeline
by Mark DSouza 21 Jul '11

21 Jul '11

Hi, The jobs look OK and are queued for computation, the error status should clear, you do not need to resubmit. The queue is rather long right now, so you may have to wait a few days to see progress, if there is none in, say, two days please let us know and we will check once again. -- 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: "Sheri Simmons" <ssimmons(a)mbl.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Thursday, July 21, 2011 11:09:31 AM > Subject: [mg-rast] processing error in pipeline > Hi > I have 31 metagenomes currently in the processing pipeline at various > stages. All but 7 of them currently show a red square and a message of > "Sequence Screening: Error" in the "In Progress" screen. The error has > been present for a couple days now. Do I need to resubmit these files, > or will the error eventually clear and processing resume? > > (The progress table showing job IDs is below). > > Thanks > Sheri > > > 28194 4468597.3 203_Macros_RNA_lane3_complete_NoDeRep > Upload : completed > 28193 4468596.3 CTS_Plot_301_Complete > Sequence Screening : error > 28192 4468595.3 CTS_Plot_201_Complete > Sequence Screening : error > 28189 4468592.3 NTS_Plot_101_Complete > Sequence Screening : error > 28073 4468476.3 102_MIM_RNA_lane3_Complete_NoDeRep > Sequence Screening : error > 28072 4468475.3 102_FreeMicros_RNA_lane3_Complete_NoDeRep > Sequence Screening : error > 28071 4468474.3 102_Macros_RNA_Lane3_Complete_NoDeRep > Sequence Screening : error > 28046 4468449.3 NTS_Plot_204_Complete > Sequence Screening : error > 28045 4468448.3 NTS_Plot_304_Complete > Sequence Screening : error > 28044 4468447.3 303_MiM_RNA_complete_NoDeRep > Sequence Screening : error > 28043 4468446.3 Lane3_not_in_pool > Sequence Screening : error > 28042 4468445.3 203_MiM_RNA_lane3_complete_NoDeRep > Sequence Screening : error > 28041 4468444.3 203_Macros_RNA_lane2_complete_NoDeRep > Sequence Screening : error > 28040 4468443.3 CTG_Plot_302_complete > Sequence Screening : error > 28038 4468441.3 CTG_Plot_202_complete > Sequence Screening : error > 28037 4468440.3 102_MIM_RNA_lane2_complete_NoDeRep > Sequence Screening : error > 28036 4468439.3 NTG_Plot_303_complete > Sequence Screening : error > 28035 4468438.3 102_FreeMicros_RNA_lane2_complete_NoDeRep > Sequence Screening : error > 28033 4468436.3 203_MiM_RNA_lane2_complete_NoDeRep > Sequence Screening : error > 28030 4468433.3 102_Macros_RNA_Lane2_Complete_NoDeRep > Sequence Screening : error > 28025 4468428.3 NTG_Plot_203_complete > Sequence Screening : error > 28024 4468427.3 203_MiM_RNA_lane2_complete > Sequence Screening : error > 28023 4468426.3 Lane2_Not_in_Pool > Sequence Screening : error > 28022 4468425.3 CTG_Plot_104_complete > Sequence Screening : error > 28021 4468424.3 NTG_Plot_102_complete > Sequence Screening : error > 27272 4467675.3 203_Macros_RNA_lane2 > Finalizing Data : error > 27271 4467674.3 203_Macros_RNA_lane3 > Finalizing Data : error > 27268 4467671.3 102_MIM_RNA_lane3 > Finalizing Data : error > 27261 4467664.3 102_MIM_RNA_lane2 > Finalizing Data : error > 27259 4467662.3 102_FreeMicros_RNA_lane3 > Loading Database : completed > 27258 4467661.3 102_FreeMicros_RNA_lane2 > > > -- > Sheri Simmons > Assistant Scientist, Bay Paul Center | Marine Biological Laboratory > Woods Hole, MA 02543 > (508) 289-7177 > http://www.simmonslab.org

1 0

Re: [mg-rast] Fwd: Re: Analysis question
by Mark DSouza 21 Jul '11

21 Jul '11

Hi, It does look like the steps which had to be rerun have completed, I am verifying this with a colleague and will get back to you as soon as I have confirmation. Regards, Mark ----- Original Message ----- > From: legatzki(a)email.arizona.edu > To: mg-rast(a)mcs.anl.gov > Cc: dsouza(a)mcs.anl.gov > Sent: Thursday, July 21, 2011 10:45:09 AM > Subject: Re: [mg-rast] Fwd: Re: Analysis question > Hi Analysis team, > please see below. I wanted to ask what the status of this is. > I checked my data set and it seems that you solved the problem since > the numbers > for Speleothem B went down. But I wanted to confirm with you. > > Thanks, > Antje > > > Quoting Mark D'Souza <dsouza(a)mcs.anl.gov>: > > > Hi, > > > > Your explanation was clear, I had mis-read your earlier email. > > > > The numbers for SpeleothemB do seem unusual, we are rerunning one of > > the pipeline stages which may be responsible, I will get back to you > > when this is done. > > > > Regards, > > Mark > > > > > > > > On Jul 11, 2011, at 11:34 AM, legatzki(a)email.arizona.edu wrote: > > > >> Hi Analysis team, > >> thanks for your fast response. > >> The MG-Rast ID's for the three samples are: > >> 4466357.3 (Speleothem A); 4466359.3 (Wet Rock); 4466556.3 > >> (Speleothem B) > >> 4466556.3 (Speleothem B) is the sample I NAMED IN MY FIRST EMAIL > >> SAMPLE A. > >> > >> The number of counts for sample A were significantly higher. > >> For example when I compared the three samples in the organisms > >> classification > >> mode using the SEED database (max. e-value cutoff: 1e-5, min. > >> identity cutoff: > >> 50%, min. alignment cutoff: 50, raw data) than I got for the > >> bacteria bar > >> (barchart graph): > >> > >> MG-RAST ID 4466556.3 - 2,454,565 counts > >> MG-RAST ID 4466359.3 - 488,597 counts > >> MG RAST ID 4466556.3 - 447,833 counts. For the other categories > >> (unassigned, > >> Archaea...) the counts of MG-RAST ID 4466556.3 were also much > >> higher > >> compared > >> to the other two samples. > >> When I chose another database to compare it looked similar. For > >> example when I > >> chose Swiss Prot (same settings like before fore SEED), than I got > >> for > >> bacteria: > >> MG-RAST ID 4466556.3 - 567,335 counts > >> MG-RAST ID 4466359.3 - 81,623 counts > >> MG-RAST ID 4466357.3 - 71,885 counts. > >> > >> Please let me know, if you have any questions regarding my > >> explanation. > >> > >> Regards, > >> > >> Antje > >> > >> -- > >> Antje Legatzki > >> Dept Soil Water and Environmental Science > >> Shantz Bldg. Rm 429 > >> University of Arizona > >> Tucson, AZ 85721 > >> 520-621-9759 > >> > >> ----- Forwarded message from dsouza(a)mcs.anl.gov ----- > >> Date: Mon, 11 Jul 2011 10:33:23 -0500 > >> From: Mark D'Souza > >> Reply-To: Mark D'Souza > >> Subject: Re: [mg-rast] Analysis question > >> To: legatzki(a)email.arizona.edu > >> > >> Hi, > >> > >> Yes, once you redraw the barchart using raw values, you will see > >> the > >> number of > >> hits in your metagenomic sample. > >> > >> Each read can have multiple hits against the database, so it is > >> possible that > >> the number of hits exceeds the number of sequences, can you send us > >> the MG-RAST > >> IDs for the samples A,B &C, we can check that this is the case and > >> look into > >> the > >> discrepancy in the counts for hits against bacteria. > >> > >> To clarify, you say "we get with this analysis about 2,450,000 > >> counts for > >> bacteria (it is similar with the other databases)" and "Sample A > >> has always > >> much more assigned sequences than sample B and C". Is the number > >> for A > >> significantly higher than B and C? > >> > >> 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 Jul 8, 2011, at 7:42 PM, legatzki(a)email.arizona.edu wrote: > >> > >>> Hi MG-RAST support team, > >>> we uploaded several metagenomic data sets to MG-RAST, I will call > >>> them here > >> A,B, > >>> and C. I have a couple of questions regarding the organisms > >>> classification of > >>> one of our data sets with the barchart option (raw data). First: > >>> Do I > >>> understand it right that if I move the cursor over the regenerated > >>> barchart, > >>> that the number in the brackets are the counts for the hits? > >>> > >>> For the second question I have to explain further: As an example I > >>> generated > >> a > >>> barchart graph using the SEED database, max. e-value 1e-5, min % > >>> identity cut > >>> off 50%, min alignment length 50. We have about 780,000 sequences > >>> after post > >> QC > >>> and we get with this analysis about 2,450,000 counts for bacteria > >>> (it is > >> similar > >>> with the other databases). These are much more hits than we have > >>> sequences. > >> Is > >>> this real? Do you have any idea how this can be? > >>> > >>> And third: We have two other metagenomic datasets (B, C) from the > >>> same > >>> environment (from other sample sites). Those gave us post QC about > >>> 750,000 > >> and > >>> 780,000 sequences, respectively. If we use the same settings like > >>> for sample > >> A > >>> for the taxonomic classification, than we got 450,000 or 490,000 > >>> assigned > >>> sequences for bacteria (bacteria are in all 3 samples the dominant > >>> group). > >>> Sample A has always much more assigned sequences than sample B and > >>> C. The > >>> sample sites are not so different that I think the difference is > >>> real. Do you > >>> have any explanation for this? If this seems not normal, do you > >>> have any > >>> suggestion what we should do (for example run the samples again > >>> through the > >>> pipeline? > >>> > >>> Thanks, > >>> > >>> Antje > >>> > >>> > >>> -- > >>> Antje Legatzki > >>> Dept Soil Water and Environmental Science > >>> Shantz Bldg. Rm 429 > >>> University of Arizona > >>> Tucson, AZ 85721 > >>> 520-621-9759 > >>> > >>> > >>> > >>> > >> > >> ----- End forwarded message ----- > >>

1 0

processing error in pipeline
by Sheri Simmons 21 Jul '11

21 Jul '11

Hi I have 31 metagenomes currently in the processing pipeline at various stages. All but 7 of them currently show a red square and a message of "Sequence Screening: Error" in the "In Progress" screen. The error has been present for a couple days now. Do I need to resubmit these files, or will the error eventually clear and processing resume? (The progress table showing job IDs is below). Thanks Sheri 28194 4468597.3 203_Macros_RNA_lane3_complete_NoDeRep Upload : completed 28193 4468596.3 CTS_Plot_301_Complete Sequence Screening : error 28192 4468595.3 CTS_Plot_201_Complete Sequence Screening : error 28189 4468592.3 NTS_Plot_101_Complete Sequence Screening : error 28073 4468476.3 102_MIM_RNA_lane3_Complete_NoDeRep Sequence Screening : error 28072 4468475.3 102_FreeMicros_RNA_lane3_Complete_NoDeRep Sequence Screening : error 28071 4468474.3 102_Macros_RNA_Lane3_Complete_NoDeRep Sequence Screening : error 28046 4468449.3 NTS_Plot_204_Complete Sequence Screening : error 28045 4468448.3 NTS_Plot_304_Complete Sequence Screening : error 28044 4468447.3 303_MiM_RNA_complete_NoDeRep Sequence Screening : error 28043 4468446.3 Lane3_not_in_pool Sequence Screening : error 28042 4468445.3 203_MiM_RNA_lane3_complete_NoDeRep Sequence Screening : error 28041 4468444.3 203_Macros_RNA_lane2_complete_NoDeRep Sequence Screening : error 28040 4468443.3 CTG_Plot_302_complete Sequence Screening : error 28038 4468441.3 CTG_Plot_202_complete Sequence Screening : error 28037 4468440.3 102_MIM_RNA_lane2_complete_NoDeRep Sequence Screening : error 28036 4468439.3 NTG_Plot_303_complete Sequence Screening : error 28035 4468438.3 102_FreeMicros_RNA_lane2_complete_NoDeRep Sequence Screening : error 28033 4468436.3 203_MiM_RNA_lane2_complete_NoDeRep Sequence Screening : error 28030 4468433.3 102_Macros_RNA_Lane2_Complete_NoDeRep Sequence Screening : error 28025 4468428.3 NTG_Plot_203_complete Sequence Screening : error 28024 4468427.3 203_MiM_RNA_lane2_complete Sequence Screening : error 28023 4468426.3 Lane2_Not_in_Pool Sequence Screening : error 28022 4468425.3 CTG_Plot_104_complete Sequence Screening : error 28021 4468424.3 NTG_Plot_102_complete Sequence Screening : error 27272 4467675.3 203_Macros_RNA_lane2 Finalizing Data : error 27271 4467674.3 203_Macros_RNA_lane3 Finalizing Data : error 27268 4467671.3 102_MIM_RNA_lane3 Finalizing Data : error 27261 4467664.3 102_MIM_RNA_lane2 Finalizing Data : error 27259 4467662.3 102_FreeMicros_RNA_lane3 Loading Database : completed 27258 4467661.3 102_FreeMicros_RNA_lane2 -- Sheri Simmons Assistant Scientist, Bay Paul Center | Marine Biological Laboratory Woods Hole, MA 02543 (508) 289-7177 /http://www.simmonslab.org/

1 0

Fwd: Fwd: Re: Analysis question
by Mark DSouza 21 Jul '11

21 Jul '11

Travis, You had rerun some pipeline stages for this job 26153, but I don't know which and can't tell if they all completed. The stats files at /mcs/bio/mg-rast/jobsv3/26153/analysis/ have changed, but none of the big files. Could you take a look and let me know if the job is fixed? Thanks, Mark ----- Forwarded Message ----- > From: legatzki(a)email.arizona.edu > To: mg-rast(a)mcs.anl.gov > Cc: dsouza(a)mcs.anl.gov > Sent: Thursday, July 21, 2011 10:45:09 AM > Subject: Re: [mg-rast] Fwd: Re: Analysis question > Hi Analysis team, > please see below. I wanted to ask what the status of this is. > I checked my data set and it seems that you solved the problem since > the numbers > for Speleothem B went down. But I wanted to confirm with you. > > Thanks, > Antje > > > Quoting Mark D'Souza <dsouza(a)mcs.anl.gov>: > > > Hi, > > > > Your explanation was clear, I had mis-read your earlier email. > > > > The numbers for SpeleothemB do seem unusual, we are rerunning one of > > the pipeline stages which may be responsible, I will get back to you > > when this is done. > > > > Regards, > > Mark > > > > > > > > On Jul 11, 2011, at 11:34 AM, legatzki(a)email.arizona.edu wrote: > > > >> Hi Analysis team, > >> thanks for your fast response. > >> The MG-Rast ID's for the three samples are: > >> 4466357.3 (Speleothem A); 4466359.3 (Wet Rock); 4466556.3 > >> (Speleothem B) > >> 4466556.3 (Speleothem B) is the sample I NAMED IN MY FIRST EMAIL > >> SAMPLE A. > >> > >> The number of counts for sample A were significantly higher. > >> For example when I compared the three samples in the organisms > >> classification > >> mode using the SEED database (max. e-value cutoff: 1e-5, min. > >> identity cutoff: > >> 50%, min. alignment cutoff: 50, raw data) than I got for the > >> bacteria bar > >> (barchart graph): > >> > >> MG-RAST ID 4466556.3 - 2,454,565 counts > >> MG-RAST ID 4466359.3 - 488,597 counts > >> MG RAST ID 4466556.3 - 447,833 counts. For the other categories > >> (unassigned, > >> Archaea...) the counts of MG-RAST ID 4466556.3 were also much > >> higher > >> compared > >> to the other two samples. > >> When I chose another database to compare it looked similar. For > >> example when I > >> chose Swiss Prot (same settings like before fore SEED), than I got > >> for > >> bacteria: > >> MG-RAST ID 4466556.3 - 567,335 counts > >> MG-RAST ID 4466359.3 - 81,623 counts > >> MG-RAST ID 4466357.3 - 71,885 counts. > >> > >> Please let me know, if you have any questions regarding my > >> explanation. > >> > >> Regards, > >> > >> Antje > >> > >> -- > >> Antje Legatzki > >> Dept Soil Water and Environmental Science > >> Shantz Bldg. Rm 429 > >> University of Arizona > >> Tucson, AZ 85721 > >> 520-621-9759 > >> > >> ----- Forwarded message from dsouza(a)mcs.anl.gov ----- > >> Date: Mon, 11 Jul 2011 10:33:23 -0500 > >> From: Mark D'Souza > >> Reply-To: Mark D'Souza > >> Subject: Re: [mg-rast] Analysis question > >> To: legatzki(a)email.arizona.edu > >> > >> Hi, > >> > >> Yes, once you redraw the barchart using raw values, you will see > >> the > >> number of > >> hits in your metagenomic sample. > >> > >> Each read can have multiple hits against the database, so it is > >> possible that > >> the number of hits exceeds the number of sequences, can you send us > >> the MG-RAST > >> IDs for the samples A,B &C, we can check that this is the case and > >> look into > >> the > >> discrepancy in the counts for hits against bacteria. > >> > >> To clarify, you say "we get with this analysis about 2,450,000 > >> counts for > >> bacteria (it is similar with the other databases)" and "Sample A > >> has always > >> much more assigned sequences than sample B and C". Is the number > >> for A > >> significantly higher than B and C? > >> > >> 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 Jul 8, 2011, at 7:42 PM, legatzki(a)email.arizona.edu wrote: > >> > >>> Hi MG-RAST support team, > >>> we uploaded several metagenomic data sets to MG-RAST, I will call > >>> them here > >> A,B, > >>> and C. I have a couple of questions regarding the organisms > >>> classification of > >>> one of our data sets with the barchart option (raw data). First: > >>> Do I > >>> understand it right that if I move the cursor over the regenerated > >>> barchart, > >>> that the number in the brackets are the counts for the hits? > >>> > >>> For the second question I have to explain further: As an example I > >>> generated > >> a > >>> barchart graph using the SEED database, max. e-value 1e-5, min % > >>> identity cut > >>> off 50%, min alignment length 50. We have about 780,000 sequences > >>> after post > >> QC > >>> and we get with this analysis about 2,450,000 counts for bacteria > >>> (it is > >> similar > >>> with the other databases). These are much more hits than we have > >>> sequences. > >> Is > >>> this real? Do you have any idea how this can be? > >>> > >>> And third: We have two other metagenomic datasets (B, C) from the > >>> same > >>> environment (from other sample sites). Those gave us post QC about > >>> 750,000 > >> and > >>> 780,000 sequences, respectively. If we use the same settings like > >>> for sample > >> A > >>> for the taxonomic classification, than we got 450,000 or 490,000 > >>> assigned > >>> sequences for bacteria (bacteria are in all 3 samples the dominant > >>> group). > >>> Sample A has always much more assigned sequences than sample B and > >>> C. The > >>> sample sites are not so different that I think the difference is > >>> real. Do you > >>> have any explanation for this? If this seems not normal, do you > >>> have any > >>> suggestion what we should do (for example run the samples again > >>> through the > >>> pipeline? > >>> > >>> Thanks, > >>> > >>> Antje > >>> > >>> > >>> -- > >>> Antje Legatzki > >>> Dept Soil Water and Environmental Science > >>> Shantz Bldg. Rm 429 > >>> University of Arizona > >>> Tucson, AZ 85721 > >>> 520-621-9759 > >>> > >>> > >>> > >>> > >> > >> ----- End forwarded message ----- > >>

1 0

Re: [mg-rast] Fwd: Re: Analysis question
by legatzki＠email.arizona.edu 21 Jul '11

21 Jul '11

Hi Analysis team, please see below. I wanted to ask what the status of this is. I checked my data set and it seems that you solved the problem since the numbers for Speleothem B went down. But I wanted to confirm with you. Thanks, Antje Quoting Mark D'Souza <dsouza(a)mcs.anl.gov>: > Hi, > > Your explanation was clear, I had mis-read your earlier email. > > The numbers for SpeleothemB do seem unusual, we are rerunning one of > the pipeline stages which may be responsible, I will get back to you > when this is done. > > Regards, > Mark > > > > On Jul 11, 2011, at 11:34 AM, legatzki(a)email.arizona.edu wrote: > >> Hi Analysis team, >> thanks for your fast response. >> The MG-Rast ID's for the three samples are: >> 4466357.3 (Speleothem A); 4466359.3 (Wet Rock); 4466556.3 (Speleothem B) >> 4466556.3 (Speleothem B) is the sample I NAMED IN MY FIRST EMAIL SAMPLE A. >> >> The number of counts for sample A were significantly higher. >> For example when I compared the three samples in the organisms >> classification >> mode using the SEED database (max. e-value cutoff: 1e-5, min. >> identity cutoff: >> 50%, min. alignment cutoff: 50, raw data) than I got for the bacteria bar >> (barchart graph): >> >> MG-RAST ID 4466556.3 - 2,454,565 counts >> MG-RAST ID 4466359.3 - 488,597 counts >> MG RAST ID 4466556.3 - 447,833 counts. For the other categories (unassigned, >> Archaea...) the counts of MG-RAST ID 4466556.3 were also much higher >> compared >> to the other two samples. >> When I chose another database to compare it looked similar. For >> example when I >> chose Swiss Prot (same settings like before fore SEED), than I got for >> bacteria: >> MG-RAST ID 4466556.3 - 567,335 counts >> MG-RAST ID 4466359.3 - 81,623 counts >> MG-RAST ID 4466357.3 - 71,885 counts. >> >> Please let me know, if you have any questions regarding my explanation. >> >> Regards, >> >> Antje >> >> -- >> Antje Legatzki >> Dept Soil Water and Environmental Science >> Shantz Bldg. Rm 429 >> University of Arizona >> Tucson, AZ 85721 >> 520-621-9759 >> >> ----- Forwarded message from dsouza(a)mcs.anl.gov ----- >> Date: Mon, 11 Jul 2011 10:33:23 -0500 >> From: Mark D'Souza >> Reply-To: Mark D'Souza >> Subject: Re: [mg-rast] Analysis question >> To: legatzki(a)email.arizona.edu >> >> Hi, >> >> Yes, once you redraw the barchart using raw values, you will see the >> number of >> hits in your metagenomic sample. >> >> Each read can have multiple hits against the database, so it is >> possible that >> the number of hits exceeds the number of sequences, can you send us >> the MG-RAST >> IDs for the samples A,B &C, we can check that this is the case and look into >> the >> discrepancy in the counts for hits against bacteria. >> >> To clarify, you say "we get with this analysis about 2,450,000 counts for >> bacteria (it is similar with the other databases)" and "Sample A has always >> much more assigned sequences than sample B and C". Is the number for A >> significantly higher than B and C? >> >> 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 Jul 8, 2011, at 7:42 PM, legatzki(a)email.arizona.edu wrote: >> >>> Hi MG-RAST support team, >>> we uploaded several metagenomic data sets to MG-RAST, I will call them here >> A,B, >>> and C. I have a couple of questions regarding the organisms >>> classification of >>> one of our data sets with the barchart option (raw data). First: Do I >>> understand it right that if I move the cursor over the regenerated >>> barchart, >>> that the number in the brackets are the counts for the hits? >>> >>> For the second question I have to explain further: As an example I >>> generated >> a >>> barchart graph using the SEED database, max. e-value 1e-5, min % >>> identity cut >>> off 50%, min alignment length 50. We have about 780,000 sequences >>> after post >> QC >>> and we get with this analysis about 2,450,000 counts for bacteria (it is >> similar >>> with the other databases). These are much more hits than we have sequences. >> Is >>> this real? Do you have any idea how this can be? >>> >>> And third: We have two other metagenomic datasets (B, C) from the same >>> environment (from other sample sites). Those gave us post QC about 750,000 >> and >>> 780,000 sequences, respectively. If we use the same settings like >>> for sample >> A >>> for the taxonomic classification, than we got 450,000 or 490,000 assigned >>> sequences for bacteria (bacteria are in all 3 samples the dominant group). >>> Sample A has always much more assigned sequences than sample B and C. The >>> sample sites are not so different that I think the difference is >>> real. Do you >>> have any explanation for this? If this seems not normal, do you have any >>> suggestion what we should do (for example run the samples again through the >>> pipeline? >>> >>> Thanks, >>> >>> Antje >>> >>> >>> -- >>> Antje Legatzki >>> Dept Soil Water and Environmental Science >>> Shantz Bldg. Rm 429 >>> University of Arizona >>> Tucson, AZ 85721 >>> 520-621-9759 >>> >>> >>> >>> >> >> ----- End forwarded message ----- >>

1 0

groups on MG-RAST
by Tracy Teal 21 Jul '11

21 Jul '11

Hi, I'm sure I'm missing something obvious in the documentation, but I was wondering how to create membership groups and if we can use those groups to share metagenomes? We have several metagenomes that we want to share with multiple people in the lab, and it would be easiest to provide group access and then add memebers to that group, rather than having to individually add a new person to each metagenome. Thanks so much for your help. -Tracy --- Tracy K. Teal Postdoctoral researcher T. Schmidt laboratory Michigan State University tkteal(a)msu.edu

1 0

Re: [mg-rast] re problems uploading
by Folker Meyer 21 Jul '11

21 Jul '11

There is a lot of benefit in having MG-RAST do the de-multiplexing and also the de-replication we are about to roll out a quality assessment tool that will use replicates… Just FYI ;-) best, Folker On Jul 21, 2011, at 8:51 AM, Julian Marchesi wrote: > yes it was already down before I knew mg-rast could do it > > J > > > > Dr Julian R. Marchesi > School of Biosciences > Museum Avenue > Cardiff University > Cardiff > CF10 3AT > Telephone: +44 (0)29 208 74188 > Fax: +44 (0)29 20874305 > Mobile 07885 569144 > > The information contained in this e-mail message and any attachments is strictly confidential and is intended for the person or organisation to whom it is addressed. > If you are not the intended recipient, you must not read, use, copy or disseminate the information contained in this message and must delete it. Please advise us > immediately if you are not the named addresses or the person responsible for delivering the message to the named addressee. > > Although Cardiff University believes this e-mail and any attachments are free of any virus or defect which may affect a computer, it is the responsibility of the recipient > to ensure that it is virus free. Cardiff university will not accept any liability for any loss or damage arising in any way from its use. > > > > From: Folker Meyer <folker.meyer(a)gmail.com> > To: Julian Marchesi <MarchesiJR(a)cardiff.ac.uk> > Cc: mg-rast(a)mcs.anl.gov > Date: 21/07/2011 13:43 > Subject: Re: [mg-rast] re problems uploading > > > > Julian: > > we are working on a new uploader that is much more user friendly. Sorry for the inconvenience at this time. > > How come you have so many separate files? Did you do the de-multiplexing yourself? MG-RAST will do that happily for you. > > Best, > Folker > > On Jul 21, 2011, at 7:24 AM, Julian Marchesi wrote: > > Hi > > I've just spent the last hour uploading individual files to mg rast, because the java updloader only allows one file at a time to be uploaded and keeps forgetting which directory it was last in, to find that only 3 of the files are actually listed in my list of files being processed. > > is there a limit to how many files can be processed for an individual? > > Yours > > Julian > > Dr Julian R. Marchesi > School of Biosciences > Museum Avenue > Cardiff University > Cardiff > CF10 3AT > Telephone: +44 (0)29 208 74188 > Fax: +44 (0)29 20874305 > Mobile 07885 569144 > > The information contained in this e-mail message and any attachments is strictly confidential and is intended for the person or organisation to whom it is addressed. > If you are not the intended recipient, you must not read, use, copy or disseminate the information contained in this message and must delete it. Please advise us > immediately if you are not the named addresses or the person responsible for delivering the message to the named addressee. > > Although Cardiff University believes this e-mail and any attachments are free of any virus or defect which may affect a computer, it is the responsibility of the recipient > to ensure that it is virus free. Cardiff university will not accept any liability for any loss or damage arising in any way from its use. >

1 0

Re: [mg-rast] re problems uploading
by Julian Marchesi 21 Jul '11

21 Jul '11

yes it was already down before I knew mg-rast could do it J Dr Julian R. Marchesi School of Biosciences Museum Avenue Cardiff University Cardiff CF10 3AT Telephone: +44 (0)29 208 74188 Fax: +44 (0)29 20874305 Mobile 07885 569144 The information contained in this e-mail message and any attachments is strictly confidential and is intended for the person or organisation to whom it is addressed. If you are not the intended recipient, you must not read, use, copy or disseminate the information contained in this message and must delete it. Please advise us immediately if you are not the named addresses or the person responsible for delivering the message to the named addressee. Although Cardiff University believes this e-mail and any attachments are free of any virus or defect which may affect a computer, it is the responsibility of the recipient to ensure that it is virus free. Cardiff university will not accept any liability for any loss or damage arising in any way from its use. From: Folker Meyer <folker.meyer(a)gmail.com> To: Julian Marchesi <MarchesiJR(a)cardiff.ac.uk> Cc: mg-rast(a)mcs.anl.gov Date: 21/07/2011 13:43 Subject: Re: [mg-rast] re problems uploading Julian: we are working on a new uploader that is much more user friendly. Sorry for the inconvenience at this time. How come you have so many separate files? Did you do the de-multiplexing yourself? MG-RAST will do that happily for you. Best, Folker On Jul 21, 2011, at 7:24 AM, Julian Marchesi wrote: Hi I've just spent the last hour uploading individual files to mg rast, because the java updloader only allows one file at a time to be uploaded and keeps forgetting which directory it was last in, to find that only 3 of the files are actually listed in my list of files being processed. is there a limit to how many files can be processed for an individual? Yours Julian Dr Julian R. Marchesi School of Biosciences Museum Avenue Cardiff University Cardiff CF10 3AT Telephone: +44 (0)29 208 74188 Fax: +44 (0)29 20874305 Mobile 07885 569144 The information contained in this e-mail message and any attachments is strictly confidential and is intended for the person or organisation to whom it is addressed. If you are not the intended recipient, you must not read, use, copy or disseminate the information contained in this message and must delete it. Please advise us immediately if you are not the named addresses or the person responsible for delivering the message to the named addressee. Although Cardiff University believes this e-mail and any attachments are free of any virus or defect which may affect a computer, it is the responsibility of the recipient to ensure that it is virus free. Cardiff university will not accept any liability for any loss or damage arising in any way from its use.

1 0

Re: [mg-rast] re problems uploading
by Folker Meyer 21 Jul '11

21 Jul '11

Julian: we are working on a new uploader that is much more user friendly. Sorry for the inconvenience at this time. How come you have so many separate files? Did you do the de-multiplexing yourself? MG-RAST will do that happily for you. Best, Folker On Jul 21, 2011, at 7:24 AM, Julian Marchesi wrote: > Hi > > I've just spent the last hour uploading individual files to mg rast, because the java updloader only allows one file at a time to be uploaded and keeps forgetting which directory it was last in, to find that only 3 of the files are actually listed in my list of files being processed. > > is there a limit to how many files can be processed for an individual? > > Yours > > Julian > > Dr Julian R. Marchesi > School of Biosciences > Museum Avenue > Cardiff University > Cardiff > CF10 3AT > Telephone: +44 (0)29 208 74188 > Fax: +44 (0)29 20874305 > Mobile 07885 569144 > > The information contained in this e-mail message and any attachments is strictly confidential and is intended for the person or organisation to whom it is addressed. > If you are not the intended recipient, you must not read, use, copy or disseminate the information contained in this message and must delete it. Please advise us > immediately if you are not the named addresses or the person responsible for delivering the message to the named addressee. > > Although Cardiff University believes this e-mail and any attachments are free of any virus or defect which may affect a computer, it is the responsibility of the recipient > to ensure that it is virus free. Cardiff university will not accept any liability for any loss or damage arising in any way from its use.

1 0

Re: [mg-rast] re problems uploading
by Folker Meyer 21 Jul '11

21 Jul '11

Julian: we are working on a new uploader that is much more user friendly. Sorry for the inconvenience at this time. How come you have so many separate files? Did you do the de-multiplexing yourself? MG-RAST will do that happily for you. Best, Folker On Jul 21, 2011, at 7:24 AM, Julian Marchesi wrote: > Hi > > I've just spent the last hour uploading individual files to mg rast, because the java updloader only allows one file at a time to be uploaded and keeps forgetting which directory it was last in, to find that only 3 of the files are actually listed in my list of files being processed. > > is there a limit to how many files can be processed for an individual? > > Yours > > Julian > > Dr Julian R. Marchesi > School of Biosciences > Museum Avenue > Cardiff University > Cardiff > CF10 3AT > Telephone: +44 (0)29 208 74188 > Fax: +44 (0)29 20874305 > Mobile 07885 569144 > > The information contained in this e-mail message and any attachments is strictly confidential and is intended for the person or organisation to whom it is addressed. > If you are not the intended recipient, you must not read, use, copy or disseminate the information contained in this message and must delete it. Please advise us > immediately if you are not the named addresses or the person responsible for delivering the message to the named addressee. > > Although Cardiff University believes this e-mail and any attachments are free of any virus or defect which may affect a computer, it is the responsibility of the recipient > to ensure that it is virus free. Cardiff university will not accept any liability for any loss or damage arising in any way from its use.

1 0