doctor.py error message

[ghost]

After installing software and running doctor.py I am getting the following error message:

$ doctor.py

Doctor! Doctor! Give me the news.

Checking symptoms ...

bwa ... Traceback (most recent call last):

File "/Users/jeffkiefer/bin/doctor.py", line 125, in
health_check()
File "/Users/jeffkiefer/bin/doctor.py", line 105, in health_check
errors += tool_check(tools=TOOLS)
File "/Users/jeffkiefer/bin/doctor.py", line 69, in tool_check
res = subprocess.run(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
AttributeError: 'module' object has no attribute 'run'
(base)

Any thoughts on what may be the issue and possible fix?

Thanks in advance.

I am on M1 mac and running latest Mac OS 12.4

[ialbert]

it appears that you have installed an older version of Python (less than 3.5)

https://stackoverflow.com/a/40590445

I will add an additional error catching to capture this error as well.

Make sure to activate bioinfo environment when running the doctor.py If you follow the instructions Python 3.8 should be the version of python that is active in that environment.

[ghost]

Thanks for pointing out my error. Yep, it wasn't pointing to python 3.8. My fault. Got if fixed, but now I have the fastqdump error I see on this board. My next challenge... Thanks again.

[WiloVictor]

I am using in Ubuntu. I have a similar problem, but with "bio". I am running doctor.py and I am getting the following error message:

bio ... Traceback (most recent call last):

File "/home/wilo_victor/bin/doctor.py", line 125, in
health_check()
File "/home/wilo_victor/bin/doctor.py", line 105, in health_check
errors += tool_check(tools=TOOLS)
File "/home/wilo_victor/bin/doctor.py", line 69, in tool_check
res = subprocess.run(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
File "/home/wilo_victor/miniconda3/envs/bioinfo/lib/python3.6/subprocess.py", line 423, in run
with Popen(*popenargs, **kwargs) as process:
File "/home/wilo_victor/miniconda3/envs/bioinfo/lib/python3.6/subprocess.py", line 729, in init
restore_signals, start_new_session)
File "/home/wilo_victor/miniconda3/envs/bioinfo/lib/python3.6/subprocess.py", line 1364, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'bio': 'bio'
(bioinfo)

[ialbert]

looks like bio was not installed for some reason, you can rectify that by

pip install bio

[WiloVictor]

Thank you, it worked