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