Question: OMA WARNING: took too long (>1200 sec) to find clusters
0
gravatar for tauanajc
21 months ago by
tauanajc0
tauanajc0 wrote:

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

oma • 581 views
ADD COMMENTlink modified 21 months ago • written 21 months ago by tauanajc0

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

ADD REPLYlink written 21 months ago by genomax60k
1
gravatar for adrian.altenhoff
21 months ago by
Switzerland
adrian.altenhoff440 wrote:

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

ADD COMMENTlink written 21 months ago by adrian.altenhoff440
0
gravatar for tauanajc
21 months ago by
tauanajc0
tauanajc0 wrote:

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

ADD COMMENTlink written 21 months ago by tauanajc0
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