metaphlan2: its output for Qiime? count human reads?

[Ming Liao]

Hello, there

I am currently using Metaphlan2 for metagenomics and MacQiime for 16s data.

1. There was a metaphlan2biom.by for Metaphlan, but not for Metaphlan2. As I used it to convert my merged output from Metaphalan2, it gave me the biom file that did not work in qiime.

TypeError: merge.biom does not appear to be a BIOM file!

Does anyone try to use metaphlan2 output in Qiime?

2. I read some papers in which they count the human reads from the short gun sequencing of gut micro biome. Can metaphlan2 do that? If not, what kind of tool can make it?

Thanks in advance.

Ming

[George Weingart]

Hi Ming,

In metaphlan2 you can use the --biom biom_output  

parameters,  where biom_output is the name of your output file.

You also can invoke that option in Galaxy...

Give it a try and let me know..

Best regards,

George Weingart, PhD

Huttenhower Lab

Ming

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[Ming Liao]

Thanks George
I am still confused about the conversion to biom file.

I got the merged file as below:
$ python utils/merge_metaphlan_tables.py metaphlan_output1.txt metaphlan_output2.txt metaphlan_output3.txt > output/merged_abundance_table.txt

I thought the "merged_abundance_table.txt" can be converted to biom format so that it can be used in the Qiime.

but the "--input_type" of metaphalan2 did not have "txt". Did I do something wrong?


Ming

On Wednesday, December 2, 2015 at 9:48:24 PM UTC-5, george.weingart wrote:
> Hi Ming,
>
>
> In metaphlan2 you can use the --biom biom_output  
>
>
> parameters,  where biom_output is the name of your output file.
> You also can invoke that option in Galaxy...
>
>
> Give it a try and let me know..
> Best regards,
>
>
> George Weingart, PhD
> Huttenhower Lab
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>

[George Weingart]

Use the biom conversion program to convert your abundance file to biom

[Ming Liao]

Can you help me to figure out where is the problem? The "merge.txt" is "merged_abundance_table.txt" resulted from "merge_metaphlan_tables.py"


MacQIIME blk073:breast $ python ~/Downloads/_metaphlan2/metaphlan2.py ./1_Data/merge.txt --biom merge.biom --nproc 6 --mpa_pkl ~/Downloads/_metaphla2/db_v20/mpa_v20_m200.pkl
....
metaphlan2.py: error: argument --input_type is required


MacQIIME blk073:breast $ python ~/Downloads/_metaphlan2/metaphlan2.py ./1_Data/merge.txt --biom merge.biom --nproc 6 --mpa_pkl ~/Downloads/_metaphla2/db_v20/mpa_v20_m200.pkl --input_type txt
...
metaphlan2.py: error: argument --input_type: invalid choice: 'txt' (choose from 'fastq', 'fasta', 'multifasta', 'multifastq', 'bowtie2out', 'sam')

Thanks!

Ming

[Ming Liao]

the first try is actually like this:

MacQIIME blk073:breast $ python ~/Downloads/_metaphlan2/metaphlan2.py ./1_Data/merge.txt --biom merge.biom

...
metaphlan2.py: error: argument --mpa_pkl is required