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.
- I cloned the git clone https://github.com/precimed/python_convert in my high-performance computing (HPC) directory.
- Then I run the below code-
- #!/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
- 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It is also possible your cache file is out-of-date; it may help to try: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
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.
#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
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