Problem with Lefse

Hi Sir/Madam,

When I try Lefse analysis, I often get this kind of error “Job ran longer than the maximum allowed execution time (runtime: 0:15:15, limit: 00:15:00), please try different inputs or parameters”.

Can you advise how to fix it?

lefse error


User opinion:
Is your input that big?
My lefse runs on hutlab are always done in ~5min. Using ~200 features.

Look at this: Job and Tool Error Help.
Also, remember that hutlab is a 3rd party server.

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My file size is about 6 Mb, I am not sure if it is considered as big or not.

When I use the smaller size-file, I can get the result.

I think you should look at the number of rows rather than the file size.
By the way, I just checked one of my inputs, which is 269-lines long and 70kb, far smaller than yours.
Actuality, the number of columns will influence too; mine has 17 columns.
I mean, how many columns/rows is your input?

It is about 3948 rows and 741 columns.
I want to attach the file here for your reference but I do not know how to do

Whoa…Big boy of a file you got there. I’ve never tried anything close to this.
Can you partition this based on your variables? Or even filter it based on abundance/etc before going to LEfSe?