Error when running Lefse

I’m hoping someone can help me with an error I am getting when running Lefse.

I am running the command:

mothur > lefse(shared=stability.opti_mcc.0.015.subsample.shared,, class=treatment, sets=DMSO-IPMP_0.1, lda=2)

And I get this error and Mothur aborts:

[ERROR]: requesting groups not present in files, aborting.

Segmentation fault: 11

I have run the same command with a different sets prior to this and it works:

mothur > lefse(shared=stability.opti_mcc.0.015.subsample.shared,, class=treatment, sets=0.05_IPMP-0.15_optafresh, lda=2)


Number of significantly discriminative features: 71 ( 71 ) before internal wilcoxon.

Number of discriminative features with abs LDA score > 2 : 71.

Output File Names:


Please could someone help resolve this? Thanks in advance!

Hi there,

Can you post the contents of your design file?


Hi Pat, thanks for getting back to me.

This is my design file:

group treatment

HT 0.05_IPMP
HT_12_2 IPMP_0.1
HT_12_3 0.15_optafresh
HT_12_4 IPMP_0.1
HT_12_5 0.15_optafresh
HT_12_6 0.05_IPMP
HT_12_7 DMSO
HT_13 0.05_IPMP
HT_13_9 DMSO
HT_13_10 IPMP_0.1
HT_13_11 0.15_optafresh
HT_13_12 IPMP_0.1
HT_13_13 0.15_optafresh
HT_13_14 0.05_IPMP
HT_13_15 DMSO
HT_14 0.05_IPMP
HT_14_17 DMSO
HT_14_18 IPMP_0.1
HT_14_19 0.15_optafresh
HT_14_20 IPMP_0.1
HT_14_21 0.15_optafresh
HT_14_22 0.05_IPMP
HT_14_23 DMSO

Could you send your logfile, shared and design files to so I can take a closer look for you?

Thank you, I’ve emailed them over

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