Which database should I download for metaphlan2?

[Nick]

On the metaphlan2 main page description: 

"...the marker information file mpa_v20_m200_marker_info.txt.bz2 can be found in the Download page here"

However, on the download page, the latest database is: 

mpa_v29_CHOCOPhlAn_201901_marker_info.txt.bz2

But then I see that "ChocoPhlAn is a proprietary database used with HUMAnN2." So why is this database being used with metaphlan2?

Which one should I use? What's the different between the two? 

[Francesco Beghini]

Hi Nick,

the mpa_v20 database is the only (for now) database compatible with HUMAnN2. We provided an updated but not final version of the database called mpa_v29 which currently is working only with MetaPhlAn2. mpa_v29 contains a new set of markers extracted from an expanded set of reference genomes. 

As I previously mentioned, the database is not final and we are currently working on it with refinements and further benchmarks.

Francesco

Francesco Beghini

PhD Student - Laboratory of Computational Metagenomics

Department of Cellular, Computational and Integrative Biology - CIBIO

University of Trento

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[Monica Ticlla]

Hi Francesco,

A related question, rather issue:

I run metaphlan2.py with mpa_v20 successfully but when I ask metaphlan2.py to use the mpa_v29 by passing this --index v294_CHOCOPhlAn_201901,

I got the following error:

Help message for read_fastx.py
Traceback (most recent call last):
  File "/scif/apps/MetaPhlAn2/metaphlan2/metaphlan2.py", line 1565, in <module>
    metaphlan2()
  File "/scif/apps/MetaPhlAn2/metaphlan2/metaphlan2.py", line 1457, in metaphlan2
    tree = TaxTree( mpa_pkl, ignore_markers )
  File "/scif/apps/MetaPhlAn2/metaphlan2/metaphlan2.py", line 1134, in __init__
    add_lens( self.root )
  File "/scif/apps/MetaPhlAn2/metaphlan2/metaphlan2.py", line 1131, in add_lens
    lens.append( add_lens( c ) )
  File "/scif/apps/MetaPhlAn2/metaphlan2/metaphlan2.py", line 1131, in add_lens
    lens.append( add_lens( c ) )
  File "/scif/apps/MetaPhlAn2/metaphlan2/metaphlan2.py", line 1131, in add_lens
    lens.append( add_lens( c ) )
  [Previous line repeated 4 more times]
  File "/scif/apps/MetaPhlAn2/metaphlan2/metaphlan2.py", line 1132, in add_lens
    node.glen = sum(lens) / len(lens)
TypeError: unsupported operand type(s) for +: 'int' and 'tuple'

I checked the bowtie2out and samout files and they were created, here the first five lines of each file:

D00535:105:CD1MBANXX:3:1102:15530:83073_1:N:0:AGGCAGAA+GAGCCTTA	329__B2UJE8__OR214_02957
D00535:105:CD1MBANXX:3:1307:11308:81771_1:N:0:AGGCAGAA+GAGCCTTA	329__B2UJE8__OR214_02957
D00535:105:CD1MBANXX:3:1101:3257:2186_1:N:0:AGGCAGAA+GAGCCTTA	329__A0A0B1ZCK1__BEK68_22290
D00535:105:CD1MBANXX:3:1101:9153:30973_1:N:0:AGGCAGAA+GAGCCTTA	305__F6G7E3__KR96_18365
D00535:105:CD1MBANXX:3:1205:13241:66934_1:N:0:AGGCAGAA+GAGCCTTA	305__F6G7E3__KR96_18365

@HD	VN:1.0	SO:unsorted
@SQ	SN:1774__A0A145SSN4__BKG84_01780	LN:549
@SQ	SN:1774__A0A1S1KP69__BKG84_29780	LN:371
@SQ	SN:1774__A0A0E3TQG9__BKG84_03055	LN:489
@SQ	SN:1774__A0A0E3XU86__BKG84_13495	LN:480

but the output with the relative abundances is empty.

Any clue of why is this happening?

Thanks,

Monica

On Monday, September 9, 2019 at 4:37:53 PM UTC-5, Francesco Beghini wrote:

Hi Nick,

the mpa_v20 database is the only (for now) database compatible with HUMAnN2. We provided an updated but not final version of the database called mpa_v29 which currently is working only with MetaPhlAn2. mpa_v29 contains a new set of markers extracted from an expanded set of reference genomes. 

As I previously mentioned, the database is not final and we are currently working on it with refinements and further benchmarks.

Francesco

Francesco Beghini

PhD Student - Laboratory of Computational Metagenomics

Department of Cellular, Computational and Integrative Biology - CIBIO

University of Trento

On Thu, Sep 5, 2019 at 5:07 AM Nick <nicochun...@gmail.com> wrote:

On the metaphlan2 main page description: 

"...the marker information file mpa_v20_m200_marker_info.txt.bz2 can be found in the Download page here"

However, on the download page, the latest database is: 

mpa_v29_CHOCOPhlAn_201901_marker_info.txt.bz2

But then I see that "ChocoPhlAn is a proprietary database used with HUMAnN2." So why is this database being used with metaphlan2?

Which one should I use? What's the different between the two? 

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[Francesco Beghini]

Hi Monica,

from the error, it seems that you are trying to use the latest database with MetaPhlAn 2.7 or older. mpa_v294_CHOCOPhlAn_201901 is only compatible with MetaPhlAn2 2.9. You can get this version from here https://bitbucket.org/biobakery/metaphlan2/src/2.9/

However, this version it is not final and it is still in testing.

Best,

Francesco Beghini

PhD Student - Laboratory of Computational Metagenomics

Department of Cellular, Computational and Integrative Biology - CIBIO

University of Trento

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