incomplete completeness (Six-frame Pfam)

[Dimitri Meier]

Hi Marc,

came across this issue a while ago, but had no time to post it here.

With the 3.5 version the completeness values of my bins became extremely low, rarely ever surpassing 50%.
When I run CheckM with exactly the same marker file, I get 80 - > 90% completeness for the same bins.

I also noticed, that the longer the contigs get, the lower the completeness. Finally I realized, that there is always only one single-copy gene per contig listed in the contig table. So it seems, that it always only checks the first several (1000 ?) bases.

However, when I open the same project in Metawatt 3.3 and run the Six-Frame Pfam module, all is fine.

Have you encountered this issue or heard from anyone else having this?

Cheers,
Dimitri

[Marc Strous]

Hi Dimitry,
Thanks for investigating this problem! It should not occur if you use
the hmm profile database supplied with metawatt, at least I cannot
reproduce the problem with that database. The only possibility I can see
at the moment is that the problem is related to the hmm database you
use. Can you point me to a link for that database or send it to me by
email (mstrous@ucalgary.ca) so that I can investigate?

Best wishes,
Marc

On 11/13/15 01:19, Dimitri Meier wrote:

Hi Marc,

came across this issue a while ago, but had no time to post it here.

With the 3.5 version the completeness values of my bins became
extremely low, rarely ever surpassing 50%.
When I run CheckM with exactly the same marker file, I get 80 - > 90%
completeness for the same bins.

I also noticed, that the longer the contigs get, the lower the
completeness. Finally I realized, that there is always only one
single-copy gene per contig listed in the contig table. So it seems,
that it always only checks the first several (1000 ?) bases.

However, when I open the same project in Metawatt 3.3 and run the
Six-Frame Pfam module, all is fine.

Have you encountered this issue or heard from anyone else having this?

Cheers,
Dimitri

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incomplete completeness (Six-frame Pfam)
https://sourceforge.net/p/metawatt/discussion/general/thread/c97c55dd/?limit=25#cd37

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--
Marc Strous
CAIP Research Chair in Microbiology
Energy Bioengineering Group
Department of Geoscience
University of Calgary
www.ucalgary.ca/ebg
tel: (403) 220 6604
2500 University Drive NW
Calgary, AB, Canada T2N 1N4
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Room 509

[Dimitri Meier]

Hi Marc,

the database I use is just the one generated by Metawatt during the database update module.

As i said, the Metawatt 3.3 uses the very same database (I just have one databases folder) and performs fine. Also when I give the very same hmm-profile from MetaWatt to CheckM, it shows the correct values.
Could be related to the HMMer output and how metawatt is reading it out? I'm using Hmmer 3.1b1.

Anyhow, I sent you an e-mail with my hmm database.

Cheers,
Dimitri