hello, I have recently been trying to use vcf2gwas, but I have encountered the following issues. Can you please advise me on how to solve them?

[zxljiqixuexi]

hello, I have recently been trying to use vcf2gwas, but I have encountered the following issues. Can you please advise me on how to solve them?

vcf2gwas v0.8.8

Initialising..

Traceback (most recent call last):
File "/home/zxl/miniconda3/bin/vcf2gwas", line 10, in
sys.exit(run_main())
File "/home/zxl/miniconda3/lib/python3.9/site-packages/vcf2gwas/main.py", line 73, in run_main
sys.exit(main(timestamp))
File "/home/zxl/miniconda3/lib/python3.9/site-packages/vcf2gwas/main.py", line 39, in main
P = Parser(argvals)
File "/home/zxl/miniconda3/lib/python3.9/site-packages/vcf2gwas/parsing.py", line 225, in init
self.args = getArgs(args)
File "/home/zxl/miniconda3/lib/python3.9/site-packages/vcf2gwas/parsing.py", line 99, in getArgs
"-M", "--memory", metavar="", type=int, default=int(((virtual_memory().total/1e9)//2)*1e3),
File "/home/zxl/miniconda3/lib/python3.9/site-packages/psutil/init.py", line 1963, in virtual_memory
ret = _psplatform.virtual_memory()
File "/home/zxl/miniconda3/lib/python3.9/site-packages/psutil/_pslinux.py", line 435, in virtual_memory
mems[fields[0]] = int(fields[1]) * 1024
IndexError: list index out of range

[frankvogt]

Hi, seems like there is a problem with psutil.
On what OS are you running vcf2gwas or are you running it in a container, respectively?
Could you also send me your command line input?

[zxljiqixuexi]

Everything is normal when we run vcf2gwas on the personal computer, but there is a problem on the server.
(base) zxl@shpc-407-instance-TOCY9lcr:~$ vcf2gwas

vcf2gwas v0.8.8
Initialising..
Traceback (most recent call last):
File "/home/zxl/miniconda3/bin/vcf2gwas", line 10, in
sys.exit(run_main())
File "/home/zxl/miniconda3/lib/python3.9/site-packages/vcf2gwas/main.py", line 73, in run_main
sys.exit(main(timestamp))
File "/home/zxl/miniconda3/lib/python3.9/site-packages/vcf2gwas/main.py", line 39, in main
P = Parser(argvals)
File "/home/zxl/miniconda3/lib/python3.9/site-packages/vcf2gwas/parsing.py", line 225, in init
self.args = getArgs(args)
File "/home/zxl/miniconda3/lib/python3.9/site-packages/vcf2gwas/parsing.py", line 99, in getArgs
"-M", "--memory", metavar="", type=int, default=int(((virtual_memory().total/1e9)//2)*1e3),
File "/home/zxl/miniconda3/lib/python3.9/site-packages/psutil/init.py", line 1963, in virtual_memory
ret = _psplatform.virtual_memory()
File "/home/zxl/miniconda3/lib/python3.9/site-packages/psutil/_pslinux.py", line 435, in virtual_memory
mems[fields[0]] = int(fields[1]) * 1024
IndexError: list index out of range

(base) zxl@shpc-407-instance-TOCY9lcr:~$ vcf2gwas -v test
vcf2gwas v0.8.8
Initialising..
Copying example input files to current working directory..
Copying README and LICENSE files..
Collecting package metadata (current_repodata.json): done
Solving environment: |
Warning: >10 possible package resolutions (only showing differing packages):

• https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::libiconv-1.17-h166bdaf_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::libnsl-2.0.0-h7f98852_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-14.2.4-h0b41bf4_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-cpp-14.2.4-hcb278e6_0
• https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::libiconv-1.17-h166bdaf_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::libnsl-2.0.0-h7f98852_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-14.2.4-h0b41bf4_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-cpp-14.2.4-hcb278e6_0
• https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::libnsl-2.0.0-h7f98852_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::libiconv-1.17-h166bdaf_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-14.2.4-h0b41bf4_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-cpp-14.2.4-hcb278e6_0
• https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::libiconv-1.17-h166bdaf_0, https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::libnsl-2.0.0-h7f98852_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-14.2.4-h0b41bf4_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-cpp-14.2.4-hcb278e6_0
• https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::libnsl-2.0.0-h7f98852_0, https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-14.2.4-h0b41bf4_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::libiconv-1.17-h166bdaf_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-cpp-14.2.4-hcb278e6_0
• https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::libiconv-1.17-h166bdaf_0, https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::libnsl-2.0.0-h7f98852_0, https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-14.2.4-h0b41bf4_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-cpp-14.2.4-hcb278e6_0
• https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-14.2.4-h0b41bf4_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::libiconv-1.17-h166bdaf_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::libnsl-2.0.0-h7f98852_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-cpp-14.2.4-hcb278e6_0
• https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::libiconv-1.17-h166bdaf_0, https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-14.2.4-h0b41bf4_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::libnsl-2.0.0-h7f98852_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-cpp-14.2.4-hcb278e6_0
• https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-14.2.4-h0b41bf4_0, https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-cpp-14.2.4-hcb278e6_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::libiconv-1.17-h166bdaf_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
• https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-cpp-14.2.4-hcb278e6_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::libiconv-1.17-h166bdaf_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::libnsl-2.0.0-h7f98852_0, https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64::reproc-14.2.4-h0b41bf4_0
  ... and othedone

All requested packages already installed.

Traceback (most recent call last):
File "/home/zxl/miniconda3/lib/python3.9/site-packages/vcf2gwas/utils.py", line 54, in
import seaborn as sns
ModuleNotFoundError: No module named 'seaborn'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/zxl/miniconda3/lib/python3.9/site-packages/vcf2gwas/starter.py", line 23, in
from vcf2gwas.utils import *
File "/home/zxl/miniconda3/lib/python3.9/site-packages/vcf2gwas/utils.py", line 57, in
import seaborn as sns
ModuleNotFoundError: No module named 'seaborn'

But we have installed seaborn

[frankvogt]

Did you set up a new environment and run vcf2gwas in this environment as detailed under Installation via conda?