Anvi'o Google Groups

1–30 of 539

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Libby Brennan, A. Murat Eren (Meren)2

11/7/23

Interpreting Anvi'o pangenome results

I think this is a good tutorial that helps people to get better insights into pangenomics is the

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Interpreting Anvi'o pangenome results

I think this is a good tutorial that helps people to get better insights into pangenomics is the

11/7/23

Jonathon Baker, … Iva Veseli9

8/31/23

anvi-get-sequences-for-hmm-hits says 16S is there but then can't find it

Funny story, I wrote a reply to this thread earlier that was rejected because my institutional email

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anvi-get-sequences-for-hmm-hits says 16S is there but then can't find it

Funny story, I wrote a reply to this thread earlier that was rejected because my institutional email

8/31/23

Daniel Han, A. Murat Eren (Meren)2

6/30/23

Config Error of anvi-display-pan

I'm not sure what is the question here :) The error message explains very clearly why anvi-

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Config Error of anvi-display-pan

I'm not sure what is the question here :) The error message explains very clearly why anvi-

6/30/23

jayos...@gmail.com, A. Murat Eren (Meren)2

6/26/23

anvi-pan-genome bad alignment with Muscle

Jey Jay, Sorry for the very late response! I was on a break, and I'm not sure if this is still a

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anvi-pan-genome bad alignment with Muscle

Jey Jay, Sorry for the very late response! I was on a break, and I'm not sure if this is still a

6/26/23

5/30/23

repeated entry in functional enrichment groups--txt file

Hi, I am using anvio-7.1. I have 20 different samples from 3 groups mapped to the same contigs

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repeated entry in functional enrichment groups--txt file

Hi, I am using anvio-7.1. I have 20 different samples from 3 groups mapped to the same contigs

5/30/23

Jelani Williams

5/10/23

Using bbduk vs bbmap for decontamination

Hello, Is there a specific reason some folks use bbmap.sh to remove human genome sequences from

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Using bbduk vs bbmap for decontamination

Hello, Is there a specific reason some folks use bbmap.sh to remove human genome sequences from

5/10/23

Vladislav Shevtsov2

1/12/23

Running Anvi'o on Windows 10 with the linux subsystem

Problem solved by using http://localhost:8080 address, instead of http://0.0.0.0:8080 :) Have a good

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Running Anvi'o on Windows 10 with the linux subsystem

Problem solved by using http://localhost:8080 address, instead of http://0.0.0.0:8080 :) Have a good

1/12/23

Iris Noordermeer

12/13/22

anvi-script-run-eggnog-mapper

Hi Anvi'o developers, I ran the latest version of emapper.py (version 2.1.9) to annotate genes in

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anvi-script-run-eggnog-mapper

Hi Anvi'o developers, I ran the latest version of emapper.py (version 2.1.9) to annotate genes in

12/13/22

Guillaume Cailleau, A. Murat Eren (Meren)3

11/23/22

Does Gene caller IDs from a GC shouldn't all have positive hits following anvi-estimate-metabolism run?

Hi Meren, Thank you for these explanations, that confirm my guessing but with more accurate wording.

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Does Gene caller IDs from a GC shouldn't all have positive hits following anvi-estimate-metabolism run?

Hi Meren, Thank you for these explanations, that confirm my guessing but with more accurate wording.

11/23/22

Emily St. John, Florian Trigodet6

7/8/22

Genes missing from pangenome analysis

Hi Emily, We have found that Diamond use a mask for low complexity sequences (including repeats) and

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Genes missing from pangenome analysis

Hi Emily, We have found that Diamond use a mask for low complexity sequences (including repeats) and

7/8/22

Emily St. John, Florian Trigodet3

6/6/22

anvi-get-sequences-for-gene-clusters

Hi Florian, Thanks so much for the clarification! Best, Emily On Mon, Jun 6, 2022 at 4:48 PM Florian

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anvi-get-sequences-for-gene-clusters

Hi Florian, Thanks so much for the clarification! Best, Emily On Mon, Jun 6, 2022 at 4:48 PM Florian

6/6/22

Andrea Cast, A. Murat Eren (Meren)2

5/4/22

Gene Caller IDs not found

Hi Andrea, Sorry for the late response! I just discovered this email in my spam folder :( Which makes

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Gene Caller IDs not found

Hi Andrea, Sorry for the late response! I just discovered this email in my spam folder :( Which makes

5/4/22

Nastassia Patin, A. Murat Eren (Meren)4

5/2/22

exported interactive interface SVG is warped

No, in Illustrator. On Mon, May 2, 2022 at 2:04 AM A. Murat Eren (Meren) <a.mura...@gmail.com

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exported interactive interface SVG is warped

No, in Illustrator. On Mon, May 2, 2022 at 2:04 AM A. Murat Eren (Meren) <a.mura...@gmail.com

5/2/22

4/19/22

gff_parser.py error

I am trying to import prokka annotations and am encountering the following error with the script

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gff_parser.py error

I am trying to import prokka annotations and am encountering the following error with the script

4/19/22

Kyle Wolf, A. Murat Eren (Meren)2

4/19/22

anvi'o installation troubleshooting, WSL

Thank you very much for reporting this, Kyle! -- A. Murat Eren (Meren) | he/him https://merenlab.org

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anvi'o installation troubleshooting, WSL

Thank you very much for reporting this, Kyle! -- A. Murat Eren (Meren) | he/him https://merenlab.org

4/19/22

Hannah Schweitzer

4/14/22

Docker error: Error response from daemon: the working directory ''pwd'' is invalid, it needs to be an absolute path.

Hey Anvio Team! I have been using Anvio on our server and I have recently made 109 bins with CONCOCT.

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Docker error: Error response from daemon: the working directory ''pwd'' is invalid, it needs to be an absolute path.

Hey Anvio Team! I have been using Anvio on our server and I have recently made 109 bins with CONCOCT.

4/14/22

3/22/22

metatranscriptome issue

Dear sir/madam, Our research group is planning to do some metatranscriptome analyses using anvi'o

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metatranscriptome issue

Dear sir/madam, Our research group is planning to do some metatranscriptome analyses using anvi'o

3/22/22

Emily St. John, A. Murat Eren (Meren)3

3/11/22

noncoding genes from imported Prokka

Hi Meren, That worked perfectly. Thanks! ~Emily On Friday, March 11, 2022 at 8:55:40 AM UTC-8 Meren

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noncoding genes from imported Prokka

Hi Meren, That worked perfectly. Thanks! ~Emily On Friday, March 11, 2022 at 8:55:40 AM UTC-8 Meren

3/11/22

Emily St. John, Florian Trigodet3

3/11/22

Issue with anvi-script-process-genbank-metadata

Hi Florian, Thanks so much - I really appreciate your help! ~Emily On Wednesday, March 9, 2022 at 10:

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Issue with anvi-script-process-genbank-metadata

Hi Florian, Thanks so much - I really appreciate your help! ~Emily On Wednesday, March 9, 2022 at 10:

3/11/22

Mir Alvee Ahmed, A. Murat Eren (Meren)2

3/2/22

discrepancies in gene-luster summary from pangenome database and gene-calls from contigs database

Very interesting. This is the second time I'm hearing this today. Can you please send the exact

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discrepancies in gene-luster summary from pangenome database and gene-calls from contigs database

Very interesting. This is the second time I'm hearing this today. Can you please send the exact

3/2/22

Julius Nweze, Iva Veseli5

2/23/22

Relative abundance

I am recalculating the relative abundance of my MAGs within a sample (earlier calculated it across

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Relative abundance

I am recalculating the relative abundance of my MAGs within a sample (earlier calculated it across

2/23/22

Fulgencio Arrombado2

11/15/21

Problem with anvi-setup-ncbi-cogs

Hi, I have just tried again and anvio told me that is an issue due to internet connection. https://

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Problem with anvi-setup-ncbi-cogs

Hi, I have just tried again and anvio told me that is an issue due to internet connection. https://

11/15/21

邹仁彬, … kiefl...@gmail.com18

11/5/21

Protein structure issue

OK, thank you sir. I will tell him. 在2021年11月5日星期五 UTC+8 上午11:46:30<kiefl...@gmail.com> 写道：

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Protein structure issue

OK, thank you sir. I will tell him. 在2021年11月5日星期五 UTC+8 上午11:46:30<kiefl...@gmail.com> 写道：

11/5/21

Shashank, A. Murat Eren2

10/18/21

intallation problem

I am sorry, I can't reproduce this following the online installation tutorial. -- A. Murat Eren (

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intallation problem

I am sorry, I can't reproduce this following the online installation tutorial. -- A. Murat Eren (

10/18/21

Sirbius, … A. Murat Eren6

10/5/21

Enrichment VS singletons

OK guys, got it. Thank you very much! Silvia Il giorno martedì 5 ottobre 2021 alle 16:21:24 UTC+2

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Enrichment VS singletons

OK guys, got it. Thank you very much! Silvia Il giorno martedì 5 ottobre 2021 alle 16:21:24 UTC+2

10/5/21

Thomas Hanson, A. Murat Eren2

8/24/21

Pangenome tutorial issue

Hi Tom, Apologies for the late response. Almost the entire team has been traveling. I am sorry that

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Pangenome tutorial issue

Hi Tom, Apologies for the late response. Almost the entire team has been traveling. I am sorry that

8/24/21

8/20/21

Importing multiple samples into Anvio

Hello, I'm extremely new to metagenomics in general, so apologies in advance if I'm asking a

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Importing multiple samples into Anvio

Hello, I'm extremely new to metagenomics in general, so apologies in advance if I'm asking a

8/20/21

Débora P. de Oliveira, … Mike Lee6

8/17/21

Hey Mike, Thank you SO much. I tried it in several ways, except without "/" (you are a

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Hey Mike, Thank you SO much. I tried it in several ways, except without "/" (you are a

8/17/21

8/11/21

Anvio7 Fresh install on Mac Catalina (10.15.7)

I successfully installed anvio7 and the dependencies with no error. When I go to the anvi-self-test

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Anvio7 Fresh install on Mac Catalina (10.15.7)

I successfully installed anvio7 and the dependencies with no error. When I go to the anvi-self-test

8/11/21

8/10/21

anvio-interactive's server address does not load in google chrome

Hello Anvi'o team, I installed anvi'o in my local user in a server successfully, because

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anvio-interactive's server address does not load in google chrome

Hello Anvi'o team, I installed anvi'o in my local user in a server successfully, because

8/10/21

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