# Lefse \[ERROR\]: requesting groups not present in files, aborting. Segmentation fault: 11 **URL:** \ **Category:** Uncategorized\ **Created:** [January 3, 2023, 8:38pm UTC](https://forum.mothur.org/t/lefse-error-requesting-groups-not-present-in-files-aborting-segmentation-fault-11/21679 "2023-01-03T20:38:15Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![sgeorge](https://avatars.discourse-cdn.com/v4/letter/s/e19adc/32.png) [@sgeorge](https://forum.mothur.org/u/sgeorge)\ **Post date:** [January 3, 2023, 8:38pm UTC](https://forum.mothur.org/t/lefse-error-requesting-groups-not-present-in-files-aborting-segmentation-fault-11/21679/1 "2023-01-03T20:38:15Z")
Hi! I’m trying to run lefse according to Riffomonas tutorials on youtube, but this error appears: [ERROR]: requesting groups not present in files, aborting. Segmentation fault: 11. what am I doing wrong? Thnks so much! SG ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [January 5, 2023, 7:14pm UTC](https://forum.mothur.org/t/lefse-error-requesting-groups-not-present-in-files-aborting-segmentation-fault-11/21679/2 "2023-01-05T19:14:21Z")
Can you post the syntax of the command you are running along with what your design file looks like? Pat ---
**Author:** ![sgeorge](https://avatars.discourse-cdn.com/v4/letter/s/e19adc/32.png) [@sgeorge](https://forum.mothur.org/u/sgeorge)\ **Post date:** [January 5, 2023, 7:57pm UTC](https://forum.mothur.org/t/lefse-error-requesting-groups-not-present-in-files-aborting-segmentation-fault-11/21679/3 "2023-01-05T19:57:56Z")
the syntax of the command i’m running is: mothur \> lefse(shared=sano\_diarrea.shared, design=sano\_diarrea.design, inputdir=processed\_data) this is what appears: [ERROR]: cannot access processed\_data/ Unable to open sano\_diarrea.shared. Trying MOTHUR\_FILES directory /Users/sergiogeorge 1/Desktop/code\_club/mothur/sano\_diarrea.shared. Unable to open sano\_diarrea.design. Trying MOTHUR\_FILES directory /Users/sergiogeorge 1/Desktop/code\_club/mothur/sano\_diarrea.design. You did not provide a class, using grupo. Comparing Sano-Diarrea: [ERROR]: requesting groups not present in files, aborting. Segmentation fault: 11 logout Saving session… …copying shared history… …saving history…truncating history files… …completed. [Proceso completado] The design file looks like this: A tibble: 83 × 2 Group grupo 1 sample1 Sano 2 sample10 Diarrea 3 sample11 Diarrea 4 sample12 Diarrea 5 sample13 Sano 6 sample14 Diarrea 7 sample15 Diarrea 8 sample16 Diarrea 9 sample17 Sano 10 sample18 Diarrea # … with 73 more rows ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [January 9, 2023, 9:27pm UTC](https://forum.mothur.org/t/lefse-error-requesting-groups-not-present-in-files-aborting-segmentation-fault-11/21679/4 "2023-01-09T21:27:49Z")
Can you post the output of running… ```auto system(ls) system(pwd) ``` Thanks, Pat ---
**Author:** ![sgeorge](https://avatars.discourse-cdn.com/v4/letter/s/e19adc/32.png) [@sgeorge](https://forum.mothur.org/u/sgeorge)\ **Post date:** [January 10, 2023, 5:58pm UTC](https://forum.mothur.org/t/lefse-error-requesting-groups-not-present-in-files-aborting-segmentation-fault-11/21679/5 "2023-01-10T17:58:30Z")
mothur \> system(ls) GENUS BARRCHART AND HEATMAP.R GENUS LOGSCALE.R GENUS STATISTICS GRAPHS.R GENUS STATISTICS.R GENUS box plot and range plot.R Genus grouped barchart 3 groups.R Grouped box plot and range plot.R Grouped plott of jittered data Phylum.R Grouped stacked barchart Phyllum.R HEATMAP MICROBIOTA SERGIO .R LDA Genus 3 grupos.R MICROBIOTA SERGIO DEC22.R MICROBIOTA SERGIO GRAFICO BARRA PHYLLUM 3 GRUPOS.R PHYLUM STATISTICS GRAPHS.R code\_club.Rproj mothur mothur.1672760890.logfile mothur.1672777717.logfile mothur.1672777838.logfile mothur.1672779425.logfile mothur.1673372894.logfile mothur.1673373008.logfile processed\_data raw\_data schubert.subsample.shared mothur \> system(pwd) /Users/sergiogeorge 1/Desktop/code\_club Thanks!! SG ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [January 12, 2023, 2:44pm UTC](https://forum.mothur.org/t/lefse-error-requesting-groups-not-present-in-files-aborting-segmentation-fault-11/21679/6 "2023-01-12T14:44:35Z")
Sorry one more - ```auto system(ls processed_data) ``` Pat ---
**Author:** ![sgeorge](https://avatars.discourse-cdn.com/v4/letter/s/e19adc/32.png) [@sgeorge](https://forum.mothur.org/u/sgeorge)\ **Post date:** [January 12, 2023, 4:26pm UTC](https://forum.mothur.org/t/lefse-error-requesting-groups-not-present-in-files-aborting-segmentation-fault-11/21679/7 "2023-01-12T16:26:59Z")
mothur \> system(ls processed\_data) sano\_diarrea.design sano\_diarrea.shared sano\_diarrea2.design sano\_diarrea2.shared thnks! SG ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [January 16, 2023, 4:55pm UTC](https://forum.mothur.org/t/lefse-error-requesting-groups-not-present-in-files-aborting-segmentation-fault-11/21679/8 "2023-01-16T16:55:14Z")
Sorry, but I’m really not sure what’s going on. I wonder if you were in a different directory when you first ran the command and go the error. Could you try running this? ```auto mothur > lefse(shared=processed_data/sano_diarrea.shared, design=processed_data/sano_diarrea.design) ``` ---
**Author:** ![elximo](https://avatars.discourse-cdn.com/v4/letter/e/a9a28c/32.png) [@elximo](https://forum.mothur.org/u/elximo)\ **Post date:** [August 25, 2023, 1:18pm UTC](https://forum.mothur.org/t/lefse-error-requesting-groups-not-present-in-files-aborting-segmentation-fault-11/21679/9 "2023-08-25T13:18:24Z")
I am having the same issue on Windows 10. I am using the most recent release version of Mothur. ![image](https://canada1.discourse-cdn.com/flex036/uploads/mothur/original/1X/f51fca9b9587392bb9da21a540f44b94191fde89.png) ---
**Author:** ![elximo](https://avatars.discourse-cdn.com/v4/letter/e/a9a28c/32.png) [@elximo](https://forum.mothur.org/u/elximo)\ **Post date:** [August 27, 2023, 10:19pm UTC](https://forum.mothur.org/t/lefse-error-requesting-groups-not-present-in-files-aborting-segmentation-fault-11/21679/10 "2023-08-27T22:19:58Z")
I followed the [Code Club tutorial on youtube](https://www.youtube.com/watch?v=ym9biWqrXIY) and adjusted the files accordingly. I just added the label and numOtus columns to the shared file and worked fine. Error was gone.