# Lefse\_run.py error

**URL:** <https://forum.biobakery.org/t/lefse-run-py-error/4429>\
**Category:** LEfSe\
**Created:** [November 22, 2022, 8:39am UTC](https://forum.biobakery.org/t/lefse-run-py-error/4429 "2022-11-22T08:39:40Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![jawen01059](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jawen01059/32/1739_2.png) [@jawen01059](https://forum.biobakery.org/u/jawen01059)\
**Post date:** [November 22, 2022, 8:39am UTC](https://forum.biobakery.org/t/lefse-run-py-error/4429/1 "2022-11-22T08:39:40Z")

</div>

Hi Meg,

I have installed lefse using : conda install -c bioconda lefse  
Then I downloaded the sample data: hmp\_small\_aerobiosis.txt

I produced a new file using this code:  
lefse\_format\_input.py hmp\_small\_aerobiosis.txt hmp\_aerobiosis\_small.in -c 1 -s 2 -u 3 -o 1000000

However, when I tried the next code which is:  
lefse\_run.py hmp\_aerobiosis\_small.in hmp\_aerobiosis\_small.res

I get this error:  
$ lefse\_run.py hmp\_aerobiosis\_small.in hmp\_aerobiosis\_small.res  
Traceback (most recent call last):  
File “/home/ihopelab/miniconda3/lib/python3.9/site-packages/rpy2/rinterface\_lib/openrlib.py”, line 18, in   
import \_rinterface\_cffi\_api as \_rinterface\_cffi # type: ignore  
ImportError: libffi.so.7: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):  
File “/home/ihopelab/miniconda3/bin/lefse\_run.py”, line 7, in   
from lefse.lefse\_run import lefse\_run  
File “/home/ihopelab/miniconda3/lib/python3.9/site-packages/lefse/lefse\_run.py”, line 4, in   
from lefse.lefse import \*  
File “/home/ihopelab/miniconda3/lib/python3.9/site-packages/lefse/lefse.py”, line 3, in   
import rpy2.robjects as robjects  
File “/home/ihopelab/miniconda3/lib/python3.9/site-packages/rpy2/robjects/ **init**.py”, line 15, in   
import rpy2.rinterface as rinterface  
File “/home/ihopelab/miniconda3/lib/python3.9/site-packages/rpy2/rinterface.py”, line 16, in   
from rpy2.rinterface\_lib import openrlib  
File “/home/ihopelab/miniconda3/lib/python3.9/site-packages/rpy2/rinterface\_lib/openrlib.py”, line 20, in   
import \_rinterface\_cffi\_abi as \_rinterface\_cffi # type: ignore  
File “/home/ihopelab/miniconda3/lib/python3.9/site-packages/\_rinterface\_cffi\_abi.py”, line 2, in   
import \_cffi\_backend  
ImportError: libffi.so.7: cannot open shared object file: No such file or directory

May I ask your advise on how to proceed.

Thank you

James