Hello,
As shown below, I got some error messages when running Step 3 for neoantigen prediction. I run "predict_binding.py" separately and the example commands in the README file. Everything is working well.

I'm running ScanNeo under conda environment. I wondered the multi-threading (subprocess.py ...) was not working well. Can I set the parameter to turn the "muti-threading" off, or do you have other suggestions? Noted that I'm not good at Python programming.

Thank you very much,
Paul (Hsih-Te)

==============================
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Exception in thread Thread-1:
Traceback (most recent call last):
File "/data/anaconda3/envs/NeoAg/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File "/data/anaconda3/envs/NeoAg/lib/python2.7/threading.py", line 754, in run
self.__target(*self.__args, **self.__kwargs)
File "/data/anaconda3/envs/NeoAg/lib/python2.7/site-packages/concurrent/futures/process.py", line 208, in _que
ue_management_worker
result_item = result_queue.get(block=True)
File "/data/anaconda3/envs/NeoAg/lib/python2.7/multiprocessing/queues.py", line 117, in get
res = self._recv()
TypeError: init() takes at least 3 arguments (1 given)

Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()
IOError: [Errno 9] Bad file descriptor
Traceback (most recent call last):
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 484, in
Prediction().main()
File "/data/tools/mhc_i/mhc_i/src/predict_binding.py", line 463, in main
stdin = sys.stdin.readline().strip()