OMA WARNING: took too long (>1200 sec) to find clusters

Question

[tauanajc]

Hi all,

I am running OMA standalone in a large set of transcriptomes. It finished the all-all stage and is now computing orthologs for a couple of days. I noticed it started writing a warning in the error file:

WARNING: took too long (>1200 sec) to find clusters for |G|=(1670,35696) on LUCA level. Going on on lower levels

There are several entries of this same line or variations with a long string of my species names instead of LUCA. Does anyone know what is going on?

Thank you. Best, Tauana

[GenoMax]

I am not familiar with OMA but since message is labeled a "warning" hopefully nothing bad but something to make a note of?

Answer 1

[Adrian Altenhoff]

Hi Tauana,

these warnings indicate that you are analysing big gene families. The top-down algorithm to infer HOGs gives up after a certain time (you can specify in the parameters file) and continues with a lower level. The effect is that for these gene families you won't be able to go back to very deep nodes. From OMA 2.0 onwards, you also have the choice to use the bottom-up algorithm, that will be much faster and thus will not suffer from this limitation.

Over all, the warning is nothing to be worried about ;-)

Cheers Adrian

Answer 2

[tauanajc]

Thank you, Adrian! I am using version 2.0, so next time I will check how to change the settings to use the bottom-up algorithm. My job just finished and I am so excited to see the results =)

Best, Tauana