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allind / EukDetect

MIT License
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ModuleNotFoundError: No module named 'datrie' #40

Open fuesseler opened 1 year ago

fuesseler commented 1 year ago

Hello,

Thanks for creating this pipeline! Unofrtunately, I have issues getting it to run on HPC environment (Slurm). Snakemake scripts are unable to find packages that were installed using conda:

Command:

source activate ~/miniconda3/envs/eukdetect
export PYTHONPATH=$PYTHONPATH:/home/miniconda3/envs/eukdetect/lib/python3.6/site-packages
eukdetect --mode runall --configfile my_configfile.yml --cores 20

Error:

Traceback (most recent call last): File "/home/miniconda3/envs/eukdetect/lib/python3.6/site-packages/snakemake/__init__.py", line 476, in snakemake success = workflow.execute( File "/home/miniconda3/envs/eukdetect/lib/python3.6/site-packages/snakemake/workflow.py", line 377, in execute dag = DAG( File "/home/miniconda3/envs/eukdetect/lib/python3.6/site-packages/snakemake/dag.py", line 116, in __init__ self.update_output_index() File "/home/miniconda3/envs/eukdetect/lib/python3.6/site-packages/snakemake/dag.py", line 209, in update_output_index self.output_index = OutputIndex(self.rules) File "/home/miniconda3/envs/eukdetect/lib/python3.6/site-packages/snakemake/output_index.py", line 16, in __init__ import datrie ModuleNotFoundError: No module named 'datrie' datrie is installed under site-packages of the environment, but under the name "datrie.cpython-36m-x86_64-linux-gnu.so"

Do you have an idea how to fix this issue?

allind commented 1 year ago

Thanks for reaching out. How did you install snakemake? Googling this error, I see some people have run into it when installing snakemake via pip instead of via conda. Can you try installing snakemake via conda?