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frankvogt / vcf2gwas

Python API for comprehensive GWAS analysis using GEMMA
GNU General Public License v3.0
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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? #19

Open zxljiqixuexi opened 1 year ago

zxljiqixuexi commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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):

But we have installed seaborn

frankvogt commented 1 year ago

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