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MetAnnotate / MetAnnotate

MetAnnotate is a tool and web application for taxonomic profiling of shotgun metagenomes.
http://metannotate.uwaterloo.ca
Apache License 2.0
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Only fraction of metagenomic sequence received taxonomic assignment. #66

Open rahulnccs opened 6 years ago

rahulnccs commented 6 years ago

Hello, We've performed Metannoatae on big metagenomic file(translated) against hmm of interest. Though we got the results, more than 99% remained to be assigned.

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please help in this issue.

microbod commented 6 years ago

Even I am facing the same problem.

Can anyone share script used during analysis?

LeeBergstrand commented 6 years ago

@microbod and @rahulnccs. Hi guys! which version are you running? The original bitbucket version or the version from this repo? When you downloaded and installed it would help us determine if these issues have been addressed yet.

LeeBergstrand commented 6 years ago

@jmtsuji Could it be related to them using the old version of RefSeq?

https://bitbucket.org/doxeylab/metannotate/issues/7/possible-error-with-taxonomy-assignment

LeeBergstrand commented 6 years ago

@rahulnccs Which version of RefSeq are you using?

rahulnccs commented 6 years ago

I am using original package provided on link https://bitbucket.org/doxeylab/metannotate . One think I should mention for taxonomic assignment we were not using --run_mode=both, as FastTree, pplacer were showing error, assignment was USEARCH based ONLY.

LeeBergstrand commented 6 years ago

@rahulnccs Using the installation on bitbucket, the installer pulls the latest version of RefSeq from NCBI. This RefSeq is not compatible with MetAnnotate since it no longer has GI numbers.

The last version of RefSeq with GI numbers can be found here:

https://zenodo.org/record/1098450#.WqLYAmYZPao

Swap out the DB and see if that fixes things.

LeeBergstrand commented 6 years ago

We have some work arounds to make MetAnnotate work with the latest RefSeq, but they are not yet complete. We are waiting to do a new release before we incorporate them.

rahulnccs commented 6 years ago

Thank you, we'll try and let you know.