Error when running Lefse

Commands in mothur
1

Hi,
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, design=mouse.time.design, 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, design=mouse.time.design, class=treatment, sets=0.05_IPMP-0.15_optafresh, lda=2)

0.015

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

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

Output File Names:

12_13_14/stability.opti_mcc.0.015.subsample.0.015.lefse_summary

Please could someone help resolve this? Thanks in advance!

2

Hi there,

Can you post the contents of your design file?

Pat

3

Hi Pat, thanks for getting back to me.

This is my design file:

group treatment

HT 0.05_IPMP
HT_12 DMSO
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

4

Could you send your logfile, shared and design files to mothur.bugs@gmail.com so I can take a closer look for you?

5

Thank you, I’ve emailed them over

6

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