OSError: AF_UNIX path too long if environment $TMPDIR is too long

[janoppelt]

Dear @dawnmy ,

Thank you for such an incredible tool! I have experienced some issues that I could circumvent but might deserve a fix in the future.

I like to set the environment $TMPDIR variable to a local directory. However, RiboDetector (version 0.3.1) does not seem to like it and fails with OSError: AF_UNIX path too long (see the log below). I can run the tool if I change $TMPDIR to the system default tmp director (for example, /tmp/ribodetector). The local $TMPDIR was 89 characters long. I tried python 3.8 and python 3.9 and the error was the same.

I believe the error is related to this python/cpython#93852 (or psf/black#2105). Their fixes are mentioned in python/cpython#93852 (comment) (or psf/black#2105 (comment)). Their solution is not to use environment $TMPDIR if it's too long and to create a new, shorter one.

The length of the input or output files doesn't matter and doesn't trigger the error.

Process SyncManager-1:                                                                                                                                                                                              
Traceback (most recent call last):                                                                                                                                                                                  
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap                                                     
    self.run()                                                                                                                                                                                                      
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/multiprocessing/process.py", line 108, in run                                                            
    self._target(*self._args, **self._kwargs)                                                                                                                                                                       
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/multiprocessing/managers.py", line 583, in _run_server                                                   
    server = cls._Server(registry, address, authkey, serializer)                                                                                                                                                    
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/multiprocessing/managers.py", line 156, in __init__                                                      
    self.listener = Listener(address=address, backlog=16)                                                                                                                                                           
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/multiprocessing/connection.py", line 448, in __init__                                                    
    self._listener = SocketListener(address, family, backlog)                                                                                                                                                       
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/multiprocessing/connection.py", line 591, in __init__                                                    
    self._socket.bind(address)                                                                                                                                                                                      
OSError: AF_UNIX path too long                                                                                                                                                                                      
Traceback (most recent call last):                                                                                                                                                                                  
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/bin/ribodetector_cpu", line 10, in <module>                                                                            
    sys.exit(main())                                                                                                                                                                                                
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/site-packages/ribodetector/detect_cpu.py", line 825, in main                                             
    seq_pred.detect()                                                                                                                                                                                               
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/site-packages/ribodetector/detect_cpu.py", line 602, in detect                                           
    self.run_with_chunks()                                                                                                                                                                                          
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/site-packages/ribodetector/detect_cpu.py", line 392, in run_with_chunks                                  
    manager = mp.Manager()                                                                                                                                                                                          
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/multiprocessing/context.py", line 57, in Manager                                                         
    m.start()                                                                                                                                                                                                       
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/multiprocessing/managers.py", line 558, in start                                                         
    self._address = reader.recv()                                                                                                                                                                                   
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/multiprocessing/connection.py", line 250, in recv                                                        
    buf = self._recv_bytes()                                                                                                                                                                                        
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/multiprocessing/connection.py", line 414, in _recv_bytes                                                 
    buf = self._recv(4)                                                                                                                                                                                             
  File "/tools/miniforge3-24.3.0-0/envs/ribodetector/lib/python3.9/multiprocessing/connection.py", line 383, in _recv                                                       
    raise EOFError                                                                                                                                                                                                  
EOFError

[dawnmy]

Great catch! Thank you for brining this issue to our attention.