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issue with running sumstat.py script #52

@rezarahman12

Description

@rezarahman12

Dear Developer,

Thank you for developing this fantastic tools and scripts to make GWAS analysis more friendly.

I'm new in GWAS field.
I want to run peliofdr, however, to make the file compatible with pleiofdr I am running sumstat.py.

  1. I cloned the git clone https://github.com/precimed/python_convert in my high-performance computing (HPC) directory.
  2. Then I run the below code-
  3. #!/bin/bash
    #PBS -A UQ-QBI
    #PBS -l select=1:ncpus=8:mem=32GB
    #PBS -l walltime=1:00:00
    #PBS -N sumstatconv

cd $PBS_O_WORKDIR
module load python

python /scratch/project_mnt/S0077/convert_sumstat_pleiofdr/python_convert/sumstats.py csv --auto --sumstats /scratch/project_mnt/S0077/convert_sumstat_pleiofdr/traitfolder/traitfolder/EduYears_Main.txt.gz --n-val 328917 --out traitfolder/ssgac.edu.csv --force
python /scratch/project_mnt/S0077/convert_sumstat_pleiofdr/python_convert/sumstats.py csv --auto --sumstats /scratch/project_mnt/S0077/convert_sumstat_pleiofdr/traitfolder/traitfolder/SWB_Full.txt.gz --n-val 298420 --out traitfolder/ssgac.swb.csv --force
python /scratch/project_mnt/S0077/convert_sumstat_pleiofdr/python_convert/sumstats.py mat --sumstats /scratch/project_mnt/S0077/convert_sumstat_pleiofdr/traitfolder/traitfolder/ssgac.edu.csv --ref 9545380.ref --out /scratch/project_mnt/S0077/convert_sumstat_pleiofdr/traitfolder/traitfolder/ssgac.edu.mat
python /scratch/project_mnt/S0077/convert_sumstat_pleiofdr/python_convert/sumstats.py mat --sumstats /scratch/project_mnt/S0077/convert_sumstat_pleiofdr/traitfolder/traitfolder/ssgac.swb.csv --ref 9545380.ref --out /scratch/project_mnt/S0077/convert_sumstat_pleiofdr/traitfolder/traitfolder/ssgac.swb.mat

  1. The error I'm getting below-

Lmod has detected the following error: The following module(s) are unknown:
"pandas"

Please check the spelling or version number. Also try "module spider ..."
It is also possible your cache file is out-of-date; it may help to try:
$ module --ignore-cache load "pandas"

Also make sure that all modulefiles written in TCL start with the string
#%Module

Traceback (most recent call last):
File "/scratch/project_mnt/S0077/convert_sumstat_pleiofdr/python_convert/sumstats.py", line 8, in
import pandas as pd
ModuleNotFoundError: No module named 'pandas'
Traceback (most recent call last):
File "/scratch/project_mnt/S0077/convert_sumstat_pleiofdr/python_convert/sumstats.py", line 8, in
import pandas as pd
ImportError: No module named pandas
Traceback (most recent call last):
File "/scratch/project_mnt/S0077/convert_sumstat_pleiofdr/python_convert/sumstats.py", line 8, in
import pandas as pd
ImportError: No module named pandas
Traceback (most recent call last):
File "/scratch/project_mnt/S0077/convert_sumstat_pleiofdr/python_convert/sumstats.py", line 8, in
import pandas as pd
ImportError: No module named pandas

I will be very grateful if you kindly suggest how to solve this error.

I do highly appreciate your time and help.
Kind regards
Reza

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