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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the MetaPhlAn2 Google Group has been replaced by the bioBakery Discourse.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
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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Dear MetaPhlAn2 users, the MetaPhlAn2 Google Group has been replaced by the bioBakery Discourse.
unread,locked,
Announcement
Google Groups Deprecation
Dear MetaPhlAn2 users, the MetaPhlAn2 Google Group has been replaced by the bioBakery Discourse.
2/17/20
KM Tsui
,
Francesco Beghini
2
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-Miguez
12
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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clade
diversity
metaphlan2
unknown
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).
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 Lennard
3
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-Miguez
2
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-Miguez
2
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-Miguez
4
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
,
Len
3
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-Miguez
4
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 Galata
8
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 Lang
2
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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clade
docker
singularity
unclassified
unknown
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
12/18/19
Megan Folkerts
,
Aitor Blanco-Miguez
5
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-Miguez
4
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 Lemetre
9
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-Miguez
3
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 Doan
6
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 Beghini
4
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 Asnicar
4
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 wu
2
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 Beghini
4
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.blancomiguez
2
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.blancomiguez
2
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 Beghini
11
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