Is the usearch --otutab and vsearch --usearch_global command is same

[Mushahid Shamim]

Hi there,

Recently I was using Parallel-Meta3 to process my 16s data. But for few samples PM was failing. PM uses vsearch in the backend and GreenGene18 database by default, after changing it to usearch it can pick otus. 

I have changed the following vsearch command 

vsearch --usearch_global non_chimeras.fa  -id 0.97 --db gg_database.fa --otutabout map_output.txt --threads 12

to the following 

usearch --otutab non_chimeras.fa --id 0.97 --otus  gg_database.fa   --otutabout map_output.txt --threads 12

Am I doing it right? Why the vsearch can't pick otus whereas usearch can? 

Thanks a lot. Your help will be much appreciated. 

 

[Colin J Brislawn]

Can you give us any more details? What error did you get while running vsearch?

Given that this error was found while running a pipeline, you could also ask the authors of this pipeline. Is Parallel-Meta3 open source on GitHub? If so, you could open an issue.

https://github.com/qibebt-bioinfo/parallel-meta 

[Frédéric Mahé]

Thanks Colin,

looking at Parallel-Meta3's repository (https://github.com/qibebt-bioinfo/parallel-meta) it does not seem to be maintained anymore (no changes in the last 3 years).

The README was pointing to vSearch, a project distinct from vsearch. I've created a pull request to fix that: https://github.com/qibebt-bioinfo/parallel-meta/pull/7

[Mushahid Shamim]

Hi @Colin,

I am not getting any error. Its just produce empty file which means no OTUs can be matched with the reference database. Whereas usearch can pick many OTUs from the reference database. My question is are the above mentioned commands identical in terms of functionality? If so why vsearch can't find any matched OTUs. 

Thank you.