MetaPhlAn-users

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Welcome!

This group is meant to serve as a mailing list for notifying users of MetaPhlAn about new features, software updates, and related publications.

the MetaPhlAn2 Google Group has been replaced by the bioBakery Discourse.

Please post all the new questions in the bioBakery Discourse forum ( https://forum.biobakery.org ). This Google Group will be set as read-only.

Thank you

Nicola Segata

0 selected

songeric

4/26/21

no read_faxtx.py found

I install the metaphlan3 using conda but when I run it, always get the error as: fatal error running

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no read_faxtx.py found

I install the metaphlan3 using conda but when I run it, always get the error as: fatal error running

4/26/21

Francesco Beghini

2/17/20

Announcement

Google Groups Deprecation

Dear MetaPhlAn2 users, the MetaPhlAn2 Google Group has been replaced by the bioBakery Discourse.

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Announcement

Google Groups Deprecation

Dear MetaPhlAn2 users, the MetaPhlAn2 Google Group has been replaced by the bioBakery Discourse.

2/17/20

KM Tsui, Francesco Beghini2

2/14/20

re taxonomic information in the metaphlan database

Hi Clement, Each marker has included in the id the NCBI taxonomy id of the species (eg

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re taxonomic information in the metaphlan database

Hi Clement, Each marker has included in the id the NCBI taxonomy id of the species (eg

2/14/20

Christophe Lemetre, Aitor Blanco-Miguez12

2/13/20

sample2markers.py crashes because of handling of the fastq piped as standard input

Hi Christophe, Metaphlan2.96 is already available through conda. Best, Aitor El miércoles, 18 de

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sample2markers.py crashes because of handling of the fastq piped as standard input

Hi Christophe, Metaphlan2.96 is already available through conda. Best, Aitor El miércoles, 18 de

2/13/20

DEEP CHANDA

2/12/20

Q&A

metaphlan profile not showing any relative abundance

I used prefetch tool of "SRA-TOOLKIT-2.9.6" was used to download SRR11048974 (.sra file).

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metaphlan profile not showing any relative abundance

I used prefetch tool of "SRA-TOOLKIT-2.9.6" was used to download SRR11048974 (.sra file).

2/12/20

Nahui Medina

2/11/20

Identity score

Hi, I´m using Metaphlan2 and doing some taxonomic assignments, so I wonder what is the percentage of

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Identity score

Hi, I´m using Metaphlan2 and doing some taxonomic assignments, so I wonder what is the percentage of

2/11/20

Michael McLaren, Katie Lennard3

2/4/20

Q&A

Viruses in clade_profiles missing in default output

Hi Katie, No, I didn't; I stopped looking into this as it ended up not mattering for the project

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Q&A

Viruses in clade_profiles missing in default output

Hi Katie, No, I didn't; I stopped looking into this as it ended up not mattering for the project

2/4/20

Hiren Ghosh, Aitor Blanco-Miguez2

2/3/20

Strainplan sample2markers.py error

Hi Hiren, I think your problem is the version of samtools you are using. Citing the tutorial: Pre-

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Strainplan sample2markers.py error

Hi Hiren, I think your problem is the version of samtools you are using. Citing the tutorial: Pre-

2/3/20

Feargal Ryan, Aitor Blanco-Miguez2

1/31/20

What does the maker in clade flag do?

Hi Feargal, The marker_in_clade parameter establish a threshold for filtering samples (and reference

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What does the maker in clade flag do?

Hi Feargal, The marker_in_clade parameter establish a threshold for filtering samples (and reference

1/31/20

Megan Folkerts

1/30/20

Fatal error running metaphlan

Hello, I am suddenly getting the following error when running metaphlan: Fatal error running

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Fatal error running metaphlan

Hello, I am suddenly getting the following error when running metaphlan: Fatal error running

1/30/20

Megan Folkerts, Aitor Blanco-Miguez4

1/23/20

Strainphlan.py won't run when additional arguments are passed

That fixed it. Thank you! On Thu, Jan 23, 2020 at 8:22 AM Megan Folkerts <mfol...@tgen.org>

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Strainphlan.py won't run when additional arguments are passed

That fixed it. Thank you! On Thu, Jan 23, 2020 at 8:22 AM Megan Folkerts <mfol...@tgen.org>

1/23/20

XG Yang

1/14/20

Modifying metaphlan2 options in biobakery workflows

Is there any way of modifying the metaphlan2 default options in biobakery workflows (something like “

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Modifying metaphlan2 options in biobakery workflows

Is there any way of modifying the metaphlan2 default options in biobakery workflows (something like “

1/14/20

Haley Hallowell

1/10/20

Mapping to an assembly?

Is it possible to use assembled contigs as your reference for bowtie2 within this program, and then

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Mapping to an assembly?

Is it possible to use assembled contigs as your reference for bowtie2 within this program, and then

1/10/20

aman, Len3

1/10/20

metaphlan2.py error - TypeError: unsupported operand type(s) for +: 'int' and 'tuple'

I just saw another response in a different topic which indicates a version issue: from the error, it

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metaphlan2.py error - TypeError: unsupported operand type(s) for +: 'int' and 'tuple'

I just saw another response in a different topic which indicates a version issue: from the error, it

1/10/20

Megan Folkerts, Aitor Blanco-Miguez4

12/20/19

Error during strainphlan

Nevermind on this. It seems the issue was that when I downloaded the repository from bitbucket, the

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Error during strainphlan

Nevermind on this. It seems the issue was that when I downloaded the repository from bitbucket, the

12/20/19

XG Yang, Valentina Galata8

12/19/19

Changing the MetaPhlAn2's normalized output

Thanks so much, Valentina for the comments. I didn't know that count data are considered

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Changing the MetaPhlAn2's normalized output

Thanks so much, Valentina for the comments. I didn't know that count data are considered

12/19/19

Andrew Lang2

12/18/19

Q&A

unknown & unclassified clade

Does anyone have thoughts on this? On Thursday, December 12, 2019 at 11:16:11 AM UTC-5, Andrew Lang

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unknown & unclassified clade

Does anyone have thoughts on this? On Thursday, December 12, 2019 at 11:16:11 AM UTC-5, Andrew Lang

12/18/19

Megan Folkerts, Aitor Blanco-Miguez5

12/17/19

Cannot find bcftools

I will try that. Thanks! On Sat, Dec 14, 2019 at 12:15 PM Aitor Blanco-Miguez <aitor.blancomiguez@

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Cannot find bcftools

I will try that. Thanks! On Sat, Dec 14, 2019 at 12:15 PM Aitor Blanco-Miguez <aitor.blancomiguez@

12/17/19

XG Yang, Aitor Blanco-Miguez4

12/10/19

strainPhlAn2 vs. strainPhlAn and the large number of unclassified strains

Hi again, There is a possibility to integrate both results from StrainPhlAn and PanPhlAn in order to

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strainPhlAn2 vs. strainPhlAn and the large number of unclassified strains

Hi again, There is a possibility to integrate both results from StrainPhlAn and PanPhlAn in order to

12/10/19

aman, … Christophe Lemetre9

12/9/19

Strainplan sample2markers.py error - ooSubprocessException: Failed when executing the command: dump_file.py --input_file sams/sampleE.sam.bz2

I did, but it didn't matter, the exe was gone as I showed above. Looking for bcftools before and

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Strainplan sample2markers.py error - ooSubprocessException: Failed when executing the command: dump_file.py --input_file sams/sampleE.sam.bz2

I did, but it didn't matter, the exe was gone as I showed above. Looking for bcftools before and

12/9/19

Marc Hoeppner, Aitor Blanco-Miguez3

12/9/19

2.9.22: Strainphlan error - trying to download bcftools

Hi Marc, thaks for getting in touch. You can install the last conda version of MetaPhlAn2, in which

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2.9.22: Strainphlan error - trying to download bcftools

Hi Marc, thaks for getting in touch. You can install the last conda version of MetaPhlAn2, in which

12/9/19

David Villani

11/29/19

Q&A

Unable to install

Hi , i am trying to install metaphlan2 and getting the following error. DVillani$ conda install -c

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Q&A

Unable to install

Hi , i am trying to install metaphlan2 and getting the following error. DVillani$ conda install -c

11/29/19

Jessie HOU, … Nhung Doan6

11/28/19

format_input.py error when using LEfSe

Hi guys, I am using the following command (lefse) Nguyens-iMac:~ Bioinformatics$ /Users/

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format_input.py error when using LEfSe

Hi guys, I am using the following command (lefse) Nguyens-iMac:~ Bioinformatics$ /Users/

11/28/19

Andrew Lang, Francesco Beghini4

11/26/19

Q&A

MetaPhlAn2 Database location in docker container

Thanks Francesco, I really would like to have a "all in one" container that has both the

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database

docker

Q&A

MetaPhlAn2 Database location in docker container

Thanks Francesco, I really would like to have a "all in one" container that has both the

11/26/19

guojun wu, Francesco Asnicar4

11/24/19

How to normalize distance

Hi, yes, that's right. Each pairwise phylogenetic distance divided by the median of all pairwise

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How to normalize distance

Hi, yes, that's right. Each pairwise phylogenetic distance divided by the median of all pairwise

11/24/19

David Tzeng, jacky wu2

11/22/19

Marker gene generated source code

yes, I have the same idea 在 2019年1月2日星期三 UTC+8下午3:16:39，David Tzeng写道： Dear developers of Metaphlan2

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Marker gene generated source code

yes, I have the same idea 在 2019年1月2日星期三 UTC+8下午3:16:39，David Tzeng写道： Dear developers of Metaphlan2

11/22/19

Nick, … Francesco Beghini4

11/15/19

Which database should I download for metaphlan2?

Hi Monica, from the error, it seems that you are trying to use the latest database with MetaPhlAn 2.7

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Which database should I download for metaphlan2?

Hi Monica, from the error, it seems that you are trying to use the latest database with MetaPhlAn 2.7

11/15/19

Monica Ticlla, aitor.blancomiguez2

11/15/19

StrainPhlAn --print_clades_only lists clades not listed by MetaPhlAn2

Hi Monica, The differences that you are seeing here are due the different ways MetaPhlAn2 and

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StrainPhlAn --print_clades_only lists clades not listed by MetaPhlAn2

Hi Monica, The differences that you are seeing here are due the different ways MetaPhlAn2 and

11/15/19

Haluk Dogan, aitor.blancomiguez2

11/15/19

how to characterize SNPs

Hi Haluk, Regarding your question, the best option would be map the MetaPhlAn2 database markers,

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gene

snp

how to characterize SNPs

Hi Haluk, Regarding your question, the best option would be map the MetaPhlAn2 database markers,

11/15/19

adrian...@inia.es, … Francesco Beghini11

11/15/19

metaphlan2.py running error

When you use --tmp_dir you have to provide a folder in which the temporary files are then saved.

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metaphlan2.py running error

When you use --tmp_dir you have to provide a folder in which the temporary files are then saved.

11/15/19