How to install HUMAnN, How to use metaphlan2 results in HUMAnN?

[liaom...@gmail.com]

Hello, there

I am totally new to humman. Currently I have completed the MetaPhlAn analysis. Next, I am going to use HUMAnN to make gene annotation and pathway analysis (By the way, am I on the right way to do metagenomic analysis?)

Q1: how to install and use HUMAnN?

is there an easy way like hg, pipe,or make install **?
As I used MetaPhlAn before, it can be easily installed in this way:
hg clone https://bitbucket.org/biobakery/metaphlan2
can HUMAnN be installed in similar ways?

When I referred to the humann tutorial, it is only about the PREREQUISITES. Do I need to install each PREREQUISITE one by one? Even after that, I can not find how to install humann or how to use it, because I cannot find any scripts like "humann --input --ouput ".

Q2: what is the input for HUMAnN?

I just got the taxa abundance following the MetaPhlAn tutorial
(https://bitbucket.org/biobakery/metaphlan2). As shown in the tutorial:
"metagenome.fastq" is the input of MetaPhlAn,
"profiled_metagenome.txt" is the taxa abundance as the output,
"metagenome.bowtie2.bz2" is another output, which seems to be the proxzy of raw data.

Anyway, I am going to use HUMAnN, but what is the input for HUMAnN?
When I referred to the HUMAnN tutorial, it says like this:

INPUTS
One or more of the following:

Tabular translated BLAST (blastx) output files files matching sequence read IDs to gene IDs.

Q 2.1: Is it the raw data like metagenome.fastq, as shown in tutorial of metaphlan2?

Mapping (bowtie, bwa, etc.) output in BAM format.

Q 2.2: : s it the data like metagenome.bowtie2.bz2, which I got from metaphlan2?

Tab-delimited text containing one or more pre-quantified gene abundances.

Q 2.3: s it the taxa abundance like profiled_metagenome.txt, which I got from metaphlan2?

Any comments or answers are welcome? I am looking forward to your help. Thanks a lot.

Sincerely,

Ming

[Lauren McIver]

Hello Ming,

You can use the taxonomic abundance output file from MetaPhlAn2 as input to HUMAnN2. To do this add the option "--taxonomic-profile metaphlan2_abundance.tsv" (replacing metaphlan2_abundance.tsv with the name of your file) when running humann2. This parameter is optional and if it is not set, by default, humann2 will run MetaPhlAn2 to create this profile. Please see the following link for steps on how to install humann2. The section on how to run humann2 describes the basic run mode and lists all input file types. For more details, see the humann2 user manual.

Please let me know if you have any additional questions.

Thank you,

Lauren

[liaom...@gmail.com]

Hello, Lauren,

Thank you so much. I think I previously went to wrong place (https://bitbucket.org/biobakery/humann), where there were no so many details about HUMAnN. I really appreciate your help.

By the way, I came up with another two questions:

1. I am going to install HUMAnN on my MacBook Pro (Retina, 13-inch, Early 2015), but its memory was only 8 GB 1867 MHz DDR3. It do not meet the HUMAnN requirement as Memory (>= 16 GB). However, I remembered there was someone in this group who can successfully run HUMAnN on Mac. Is that really possible? I just wanna to be sure about that before I tried to install it on my Mac.

2. About the KEGG database issue, it is now in commercial use. Is there any ways we can get access to the old free version? or is it possible that we can still keep our pathway analysis moving on without purchasing the KEGG database?

I am looking forward to your reply or someone else. Thanks.

Sincerely,


Ming

[Lauren McIver]

Hello Ming,

Yes, I believe you might be able to run with 8GB of memory if you add the option "--bypass-translated-search". Please note applying this option will result in the "unclassified" (ie non-species specific) gene families and pathways not being computed. If you choose to run with this option you do not need to download the UniRef database.

You are correct in that if you run with the default HUMAnN2 mode you do not need the KEGG database. The default run mode uses ChocoPhlAn, UniRef, and MetaCyc. However, if you are interested in using KEGG instead, here is the section in the user manual on how to run with the legacy database: http://huttenhower.sph.harvard.edu/humann2/manual#markdown-header-legacy-databases 

Thank you,

Lauren

[liaom...@gmail.com]

Thanks Lauren, I really appreciated it. I have followed your instructions and successfully installed the HUMAnN 2.0! I am so glad than I make it. Thanks again.

Sincerely,

Ming

On Monday, February 8, 2016 at 7:07:57 PM UTC-5, lauren.j.mciver wrote: