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Welcome to the MG-RAST google group!

This forum is intended as a platform for users of MG-RAST its API and the R client to discuss all matters concerning our services and web-sites.

Please NOTE: This is not the MG-RAST help-desk.

MG-RAST for the impatient is a good starting point. For further reading we recommend the MG-RAST handbook. The MG-RAST team will attempt to capture content from this group and integrate in the manual and/or the FAQ where possible.

We recommend reading Metagenomics-a guide from sampling to data analysis (PMID 22587947) in Microbial Informatics and Experimentation, 2012 for best practices.

Please feel free to create Questions or discussion topics.

Please NOTE: This is not the MG-RAST help-desk.

0 selected

Rakeshkumar Yadav, Meagan Maxwell2

8/27/20

linking microbial taxonomy to functional entities

I experienced a similar issue when attempting to make connections between the RefSeq taxonomic and

unread,

general-discussion

linking microbial taxonomy to functional entities

I experienced a similar issue when attempting to make connections between the RefSeq taxonomic and

8/27/20

Miriam Gonçalves de Chaves

3/15/20

Doubt about databases use in MGRast

I used the databases "Subsystem and Refseq" in MG-RAST but, I d' like to kown when this

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general-discussion

Doubt about databases use in MGRast

I used the databases "Subsystem and Refseq" in MG-RAST but, I d' like to kown when this

3/15/20

N. Gilbert, MG-RAST2

3/23/20

How to download .fna file output from the gene-calling step?

I note that this is not the help desk. Certain files are not stored to limit the storage requirements

unread,

general-discussion

How to download .fna file output from the gene-calling step?

I note that this is not the help desk. Certain files are not stored to limit the storage requirements

3/23/20

William Patton, Folker Meyer2

1/30/20

How to remove DNA from metagenomic FASTQ file using a reference genome?

in MG-RAST you'd have to send us pointer to a genome sequence for lichen so that we can set up

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general-discussion

How to remove DNA from metagenomic FASTQ file using a reference genome?

in MG-RAST you'd have to send us pointer to a genome sequence for lichen so that we can set up

1/30/20

Josias Rodrigues

12/2/19

Dear all I uploaded some files on Saturday in the MGR server, but till now it is not yet stats

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general-discussion

Dear all I uploaded some files on Saturday in the MGR server, but till now it is not yet stats

12/2/19

Rakeshkumar Yadav, Folker Meyer2

11/26/19

Processing of the data

Can I suggest you contact the help desk? On Wednesday, May 29, 2019 at 12:18:02 AM UTC-5, Rakeshkumar

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general-discussion

Processing of the data

Can I suggest you contact the help desk? On Wednesday, May 29, 2019 at 12:18:02 AM UTC-5, Rakeshkumar

11/26/19

jigyasa arora, Folker Meyer2

4/29/19

difference between Carbohydrate Metabolism and carbohydrate metabolism in KEGG groups level2?

Hi, this probably should have gone to the help desk. In any case, this is a curation artifact. AFAIK

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general-discussion

difference between Carbohydrate Metabolism and carbohydrate metabolism in KEGG groups level2?

Hi, this probably should have gone to the help desk. In any case, this is a curation artifact. AFAIK

4/29/19

jigyasa arora, Folker Meyer2

4/29/19

.gtf file after gene calling with FragGeneScan

Hi we do not provide a GTF file at this time. best, Folker On Thursday, March 28, 2019 at 10:22:24 PM

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general-discussion

.gtf file after gene calling with FragGeneScan

Hi we do not provide a GTF file at this time. best, Folker On Thursday, March 28, 2019 at 10:22:24 PM

4/29/19

Helen Dukes, Folker Meyer2

3/7/19

MG-RAST data no longer on profile??

Hi Helen, this is really a matter for the help desk. We do not delete collections or collection

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general-discussion

MG-RAST data no longer on profile??

Hi Helen, this is really a matter for the help desk. We do not delete collections or collection

3/7/19

Maraike Probst, Folker Meyer2

1/4/19

Associated publication

Hi Maraike, [ Please note: this is not the help desk ;-) ] However if the authors have included that

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general-discussion

Associated publication

Hi Maraike, [ Please note: this is not the help desk ;-) ] However if the authors have included that

1/4/19

Dietrich Epp Schmidt, Folker Meyer2

11/12/18

MG-Rast ID Shifts

Hi Dietrich, the idea is that the IDs you are seeing are temporary. We HAD to do that since folks

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general-discussion

MG-Rast ID Shifts

Hi Dietrich, the idea is that the IDs you are seeing are temporary. We HAD to do that since folks

11/12/18

Dr. Mohamed Moselhy Zein ElDin, Folker Meyer2

11/12/18

phylogentic tree

Since we do not support whole genome data analysis, you cannot export a tree from that. On Thursday,

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general-discussion

phylogentic tree

Since we do not support whole genome data analysis, you cannot export a tree from that. On Thursday,

11/12/18

Bobbie Shaban, Folker Meyer3

10/10/18

Apologies. I saw the other threads and they looked like help related topics. I'll email help desk

unread,

general-discussion

Apologies. I saw the other threads and they looked like help related topics. I'll email help desk

10/10/18

7/27/18

Discrepancy interpretation in hits number according to certain databases

Hi all I am working with 20 metagenomes and I have found a significant difference in one of my

unread,

general-discussion

Discrepancy interpretation in hits number according to certain databases

Hi all I am working with 20 metagenomes and I have found a significant difference in one of my

7/27/18

Kayo Bianco, MG-RAST2

7/10/18

Database for analysis

Hi Kayo, good question. We are actively working on adding new databases. CARD was on the list as well

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general-discussion

Database for analysis

Hi Kayo, good question. We are actively working on adding new databases. CARD was on the list as well

7/10/18

osama ali, Andreas4

12/25/18

generating new webkey

Please Help The following quote was extracted from Mg-Rast API overview page : "You can create a

unread,

general-discussion

generating new webkey

Please Help The following quote was extracted from Mg-Rast API overview page : "You can create a

12/25/18

Steve Baeyen, Folker Meyer2

5/7/18

API uploads failing

Hi Steve, this is not the help desk. we do not have the resouces to monitor this group routinely.

unread,

general-discussion

API uploads failing

Hi Steve, this is not the help desk. we do not have the resouces to monitor this group routinely.

5/7/18

5/4/18

API upload fails

Dear Mrs., Mr., When I want to use the the API to upload files, I get this error: curl: (56) Recv

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general-discussion

API upload fails

Dear Mrs., Mr., When I want to use the the API to upload files, I get this error: curl: (56) Recv

5/4/18

4/27/18

MG-RAST API throttled after several _accidental_ denial of service attacks

We experienced several denial of service attacks (DOS), which we believe to be accidents, not

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general-discussion

MG-RAST API throttled after several _accidental_ denial of service attacks

We experienced several denial of service attacks (DOS), which we believe to be accidents, not

4/27/18

faizan saleem, Folker Meyer2

4/27/18

Problem with project submission.

as stated in several places, this is not the help desk. please use the help desk email address. An

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general-discussion

Problem with project submission.

as stated in several places, this is not the help desk. please use the help desk email address. An

4/27/18

Lourdes Ortiz Alvarez, … Folker Meyer4

4/10/18

SERVIDOR VERY SLOW

Update: we are now testing a throttling solution that will limit the number of requests per second

unread,

general-discussion

SERVIDOR VERY SLOW

Update: we are now testing a throttling solution that will limit the number of requests per second

4/10/18

osama ali, MG-RAST2

3/12/18

Creating new web-key for my private study

Webkeys get refreshed / renewed upon logging out and back in to MG-RAST. To view your current webkey

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general-discussion

Creating new web-key for my private study

Webkeys get refreshed / renewed upon logging out and back in to MG-RAST. To view your current webkey

3/12/18

Garima Suneja, Folker Meyer2

2/14/18

Error: environmental package sheet "microbial mat|biofilm" referenced but not filled out in row 1

Hi Garima, I hope you are aware that this is not the help desk? My advice is to check a working

unread,

general-discussion

Error: environmental package sheet "microbial mat|biofilm" referenced but not filled out in row 1

Hi Garima, I hope you are aware that this is not the help desk? My advice is to check a working

2/14/18

DCCC, Folker Meyer2

1/2/18

Hi DCCC? the easiest path forward might likely be to debug your web browser problem. The "crash

unread,

general-discussion

Hi DCCC? the easiest path forward might likely be to debug your web browser problem. The "crash

1/2/18

DCCC, Folker Meyer2

12/31/17

Please update data in the most raw format you can provide. The system will remove adapters etc. On

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general-discussion

Please update data in the most raw format you can provide. The system will remove adapters etc. On

12/31/17

9/27/17

A question about the update of M5NR database

Hi, I'd like to get information on the update of M5NR database. When was M5NR database updated

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general-discussion

A question about the update of M5NR database

Hi, I'd like to get information on the update of M5NR database. When was M5NR database updated

9/27/17

PAULA GARCÍA FRAILE, … MG-RAST5

1/11/18

Problem to select a sequence file in the "submit" section

Hovering over the entry will show why it is not selectable. Either the maximum sequence length of

unread,

general-discussion

Problem to select a sequence file in the "submit" section

Hovering over the entry will show why it is not selectable. Either the maximum sequence length of

1/11/18

Angel Martín Ortiz Estrada

8/21/17

A Doubt about krona files

I new in this group. I have tried to download the Krona files of my data with the option Snapshot;

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general-discussion

A Doubt about krona files

I new in this group. I have tried to download the Krona files of my data with the option Snapshot;

8/21/17

Jose's lair, Jonathan Greenberg2

9/5/17

where to find singleton's number per sample in MG-RAST

I did this manually with Excel after downloading the CSVs for each of my samples. Don't think

unread,

general-discussion

where to find singleton's number per sample in MG-RAST

I did this manually with Excel after downloading the CSVs for each of my samples. Don't think

9/5/17

Laetitia Georgina Elisabeth Wilkins, Folker Meyer2

7/30/17

metagenomic contig data is treated like amplicon data

this is a case for the help desk. Make sure to provide identifiers. On Tuesday, July 18, 2017 at 8:23

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general-discussion

metagenomic contig data is treated like amplicon data

this is a case for the help desk. Make sure to provide identifiers. On Tuesday, July 18, 2017 at 8:23

7/30/17

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