subprocess.py error while running data_prepare_one

aleks-karolak commented 2 years ago

Hi, I have tried to run data_prepare_one but I get the following error and the program stops within ipdb.

MLC02GC4Z3Q05P:masif_site 4464689$ ./data_prepare_one.sh 1AKJ_AB_DE
:/Users/4464689/Downloads/masif/source/
Structure exists: '/var/folders/mn/7xx5f6314c1glph1lkt4k_9m002gyq/T/pdb1akj.ent' 
--Call--
>    /opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py(875)__del__()
   873             self.wait()
   874 
--> 875     def __del__(self, _maxsize=sys.maxsize, _warn=warnings.warn):
    876         if not self._child_created:
    877             # We didn't get to successfully create a child process.

ipdb>

I appreciate any input, Aleks

Max1461 commented 2 years ago

@aleks-karolak

Hey Aleks,

I was wondering if you had solved this problem, as I am running into the exact same error as you. Any help or insight you could provide would be greatly appreciated.

Thanks for your help in advance.

aleks-karolak commented 2 years ago

Hi @Max1461

I haven't unfortunately. My 'python-friend' recommended to install the 3.6 python to be in line with Masif but my Macs don't allow it. I was told that the proper python version would solve it but since the program gets to the ipdb - the issue might be related to the underlying programs. Not all of them are available from the websites as in the original paper and I had to install them from other sources...

I will have look at it soon and get back to you. Thank you

ozkilim commented 2 years ago

Hi!

I am also running into this issue when running on Linux. Also the docker version works for me but when I upload my own file there I also get the same issue you described. (all in python 3.6)

zhangxinuyan commented 9 months ago

Hi!

I counted the same problem? Do you solve it?

orange2350 commented 8 months ago

Hi!

I counted the same problem? Do you solve it?

zhangxinuyan commented 8 months ago

no I do not solve it

发件人：orange2350 @.> 发送日期：2023-10-29 21:01:26 收件人：LPDI-EPFL/masif @.> 抄送人：zhangxinyand @.>,Comment @.> 主题：Re: [LPDI-EPFL/masif] subprocess.py error while running data_prepare_one (Issue #41)

Hi! I counted the same problem? Do you solve it? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

orange2350 commented 8 months ago

no I do not solve it 发件人：orange2350 @.> 发送日期：2023-10-29 21:01:26 收件人：LPDI-EPFL/masif @.> 抄送人：zhangxinyand @.>,Comment @.> 主题：Re: [LPDI-EPFL/masif] subprocess.py error while running data_prepare_one (Issue #41) Hi! I counted the same problem? Do you solve it? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***> 你好，我是批量运行会报这个错，一个蛋白一个蛋白运行的时候就不会报错。请问你也是吗？

zhangxinuyan commented 8 months ago

我运行一个也会报错，能加个联系方式吗？想请教一下你这个问题，我的微信13663125407

发件人：orange2350 @.> 发送日期：2023-10-31 10:30:14 收件人：LPDI-EPFL/masif @.> 抄送人：zhangxinyand @.>,Comment @.> 主题：Re: [LPDI-EPFL/masif] subprocess.py error while running data_prepare_one (Issue #41)

no I do not solve it 发件人：orange2350 @.> 发送日期：2023-10-29 21:01:26 收件人：LPDI-EPFL/masif @.> 抄送人：zhangxinyand @.>,Comment @.> 主题：Re: [LPDI-EPFL/masif] subprocess.py error while running data_prepare_one (Issue #41) Hi! I counted the same problem? Do you solve it? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.> 你好，我是批量运行会报这个错，一个蛋白一个蛋白运行的时候就不会报错。请问你也是吗？ — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.>

LPDI-EPFL / masif

subprocess.py error while running data_prepare_one #41