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Hello HUMAnN users! 
Please direct all future questions about HUMAnN to our new Discourse forum:
https://forum.biobakery.org/
This forum can be viewed by anyone, but you will need to ***create an account to post a new question***. 
This Google Group is now set as "read only": You may continue to browse existing message threads within the Group, but new messages sent to the Group will bounce back as "undeliverable".

By migrating all questions and answers to a centralized forum, we aim to both increase their visibility across the bioBakery user community in addition to improving response times.
Sincerely,
The bioBakery Support Team

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1/21/20

New HUMAnN Forum !

Hello HUMAnN users! Please direct all future questions about HUMAnN to our new Discourse forum: https

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New HUMAnN Forum !

Hello HUMAnN users! Please direct all future questions about HUMAnN to our new Discourse forum: https

1/21/20

adamber1187, Eric Franzosa3

1/16/20

Low Community Composition

Hi Eric, Thanks for the reply. Is this considered a normal thing? In the past when I've used

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Low Community Composition

Hi Eric, Thanks for the reply. Is this considered a normal thing? In the past when I've used

1/16/20

1/16/20

Are only filtered reads in $DIR/$SAMPLENAME_$TRANSLATEDALIGN_aligned.tsv file?

Hello! I am wondering if the alignments reported in the temp file $DIR/$SAMPLENAME_$

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Are only filtered reads in $DIR/$SAMPLENAME_$TRANSLATEDALIGN_aligned.tsv file?

Hello! I am wondering if the alignments reported in the temp file $DIR/$SAMPLENAME_$

1/16/20

Angel Dai, Eric Franzosa3

1/16/20

How is the relab in humann2_renorm_table calculated

Hi Eric, How are you doing? Just wanna confirm that, the CPM is calculated as the count in RPK that

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How is the relab in humann2_renorm_table calculated

Hi Eric, How are you doing? Just wanna confirm that, the CPM is calculated as the count in RPK that

1/16/20

Marie P, Lauren McIver3

1/7/20

ValueError when trying to run humann2

Hello Lauren, thank you very much for your reply! I solved the problem today by removing and re-

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ValueError when trying to run humann2

Hello Lauren, thank you very much for your reply! I solved the problem today by removing and re-

1/7/20

12/26/19

Detecting high abundance of mammalian MetaCyc pathways

Hi, I've run Humann2 (using default settings and the chocophlan database) on human gut shotgun

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Detecting high abundance of mammalian MetaCyc pathways

Hi, I've run Humann2 (using default settings and the chocophlan database) on human gut shotgun

12/26/19

Minjae Kim, Eric Franzosa5

12/20/19

Is it okay to apply statistical methods (e.g., kruskal wallis and others) with humann2 output (RPK value)?

Thanks for the reply I will try to do it On Friday, December 20, 2019 at 11:01:07 AM UTC-6, Eric

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Is it okay to apply statistical methods (e.g., kruskal wallis and others) with humann2 output (RPK value)?

Thanks for the reply I will try to do it On Friday, December 20, 2019 at 11:01:07 AM UTC-6, Eric

12/20/19

Angel Dai, Eric Franzosa2

12/11/19

Humann2 unpack pathways result table format

This script won't change the units of the input genes. Rather it's showing you how different

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Humann2 unpack pathways result table format

This script won't change the units of the input genes. Rather it's showing you how different

12/11/19

cecilia silvestri, Eric Franzosa4

12/11/19

pathways abundances

You can look up individual pathways in MetaCyc's own database, which includes information about

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pathways abundances

You can look up individual pathways in MetaCyc's own database, which includes information about

12/11/19

Levesque, Nicole M., Eric Franzosa2

12/11/19

FW: about humann2 database licenses

Hi Guangxi, We don't bundle any of the commercial elements of MetaCyc or KEGG with HUMAnN2. The

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FW: about humann2 database licenses

Hi Guangxi, We don't bundle any of the commercial elements of MetaCyc or KEGG with HUMAnN2. The

12/11/19

12/4/19

Google Groups Deprecation

The Google group list serve will be replaced by our bioBakery Discourse site on [23rd Dec, 2019]. The

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Google Groups Deprecation

The Google group list serve will be replaced by our bioBakery Discourse site on [23rd Dec, 2019]. The

12/4/19

nmg...@163.com, Lauren McIver2

11/21/19

Using the temporary files from uniref90 search mode as the temporary files for uniref50 search mode

Hello Mort, With that setting most of the options that are changed are filters applied after running

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Using the temporary files from uniref90 search mode as the temporary files for uniref50 search mode

Hello Mort, With that setting most of the options that are changed are filters applied after running

11/21/19

jiakang yin, Eric Franzosa2

11/18/19

how to display all the KOs that were significant between control and treat

You could in principle write a loop at the command-line to do this. However, I would recommend using

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how to display all the KOs that were significant between control and treat

You could in principle write a loop at the command-line to do this. However, I would recommend using

11/18/19

Marco Severgnini, Eric Franzosa2

11/18/19

beta-diversity analysis on pathways/functions

Hi Marco, Definitely fair to do this sort of analysis on function totals OR function stratifications

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beta-diversity analysis on pathways/functions

Hi Marco, Definitely fair to do this sort of analysis on function totals OR function stratifications

11/18/19

Nick, Lauren McIver2

11/14/19

thread.error: can't start new thread

Hello Nick - It is possible another process is also running on the machine? If you reduce the number

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thread.error: can't start new thread

Hello Nick - It is possible another process is also running on the machine? If you reduce the number

11/14/19

Eric Franzosa, Seraph Zhang2

11/7/19

Re: About version v2.9 of HUMAnN2

Hi Eric, I am wondering how is the new database going? I look forward to using the latest version.

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Re: About version v2.9 of HUMAnN2

Hi Eric, I am wondering how is the new database going? I look forward to using the latest version.

11/7/19

Billy Taj, Eric Franzosa4

11/5/19

humann2 thread efficiency

Correct - HUMAnN2 will not launch multiple instances of the alignment binaries. Thanks, Eric On Tue,

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humann2 thread efficiency

Correct - HUMAnN2 will not launch multiple instances of the alignment binaries. Thanks, Eric On Tue,

11/5/19

Jessie HOU, Eric Franzosa2

10/30/19

Functional analysis with newer version of KEGG database

Dolosigranulum pigrum exists in the HUMAnN2's pangenome database, though that specific isolate

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Functional analysis with newer version of KEGG database

Dolosigranulum pigrum exists in the HUMAnN2's pangenome database, though that specific isolate

10/30/19

Billy Taj, Eric Franzosa2

10/25/19

differences between the various metacyc pathway files

Hi Billy, "mp" is a legacy file intended to maintain compatibility with certain aspects of

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differences between the various metacyc pathway files

Hi Billy, "mp" is a legacy file intended to maintain compatibility with certain aspects of

10/25/19

10/22/19

The way to do different gene abundance analyses using genefamilies.tsv files.

Hello, after getting the genefamilies.tsv files from metagenomics data. I want to do different gene

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The way to do different gene abundance analyses using genefamilies.tsv files.

Hello, after getting the genefamilies.tsv files from metagenomics data. I want to do different gene

10/22/19

adamber1187, Eric Franzosa4

10/21/19

Specific Gene Abundance

Hi Adam, That starts to get beyond the scope of the profiling HUMAnN2 does and into statistical

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Specific Gene Abundance

Hi Adam, That starts to get beyond the scope of the profiling HUMAnN2 does and into statistical

10/21/19

Angel Dai, Eric Franzosa5

10/17/19

ValueError: need more than 1 value to unpack when running humann2_barplot on stratified pathway abundance table

Oh so the sample id is in the first row, I put it in the row after the phenotype like lefse asked.

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ValueError: need more than 1 value to unpack when running humann2_barplot on stratified pathway abundance table

Oh so the sample id is in the first row, I put it in the row after the phenotype like lefse asked.

10/17/19

Changan Liu, Eric Franzosa5

10/16/19

Humann2 stucks at bowtie2 alignment step

I didn't plug Kraken2 into HUMAnN2. The two processes are independent for me. For getting OTU

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Humann2 stucks at bowtie2 alignment step

I didn't plug Kraken2 into HUMAnN2. The two processes are independent for me. For getting OTU

10/16/19

Nick, Eric Franzosa4

10/16/19

MetaCyc pathways from unclassified species

Thanks, just wanted to make sure I wasn't misunderstanding. So if we want to be more conservative

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MetaCyc pathways from unclassified species

Thanks, just wanted to make sure I wasn't misunderstanding. So if we want to be more conservative

10/16/19

Billy Taj, Eric Franzosa6

10/16/19

humann2's pathway abundance calculations

It's a standard HUMAnN2 abundance file: 2 columns, headers, first column = (stratified) feature

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humann2's pathway abundance calculations

It's a standard HUMAnN2 abundance file: 2 columns, headers, first column = (stratified) feature

10/16/19

utritala, … John G6

10/14/19

humann2_barplot sample labels not displayed

Hi Eric, I was able to get this approach to work, but I have 12 samples and it appears the color map

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humann2_barplot sample labels not displayed

Hi Eric, I was able to get this approach to work, but I have 12 samples and it appears the color map

10/14/19

10/9/19

path coverage confidence score calculations

How are the path coverage scores determined? I understand that 1 signifies that the path is likely

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path coverage confidence score calculations

How are the path coverage scores determined? I understand that 1 signifies that the path is likely

10/9/19

Paul Naphtali, Eric Franzosa2

10/9/19

bugs_list.tsv question

Hi Paul, Those sequencing depths are pretty low relative to where our methods usually operate.

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bugs_list.tsv question

Hi Paul, Those sequencing depths are pretty low relative to where our methods usually operate.

10/9/19

Nick, Eric Franzosa5

10/8/19

Unaligned reads rate for nucleotide vs translated search?

The ground truth was based on the gene content of the genomes in the community augmented by their

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Unaligned reads rate for nucleotide vs translated search?

The ground truth was based on the gene content of the genomes in the community augmented by their

10/8/19

Armin Anocic, … Eric Franzosa4

10/8/19

Constructing custom nucleotide database from Prodigal output.

I recommend checking out the sections starting with "Custom..." in the HUMAnN2 manual:

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Constructing custom nucleotide database from Prodigal output.

I recommend checking out the sections starting with "Custom..." in the HUMAnN2 manual:

10/8/19

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