tdoniger
commented
5 years ago I think I fixed this problem by updating the connection.py to a fixed connection.py
Closed tdoniger closed 5 years ago
tdoniger
commented
5 years ago I think I fixed this problem by updating the connection.py to a fixed connection.py
Finished library initialization in 0.0007174015045166016 seconds.
* Converting reads to bed format for 2 libraries... Process Process-1: Traceback (most recent call last): File "/private/software/packages/miniconda2/envs/peakachu/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/private/software/packages/miniconda2/envs/peakachu/lib/python3.6/multiprocessing/process.py", line 93, in run self._target(self._args, **self._kwargs) File "/private/software/packages/miniconda2/envs/peakachu/lib/python3.6/concurrent/futures/process.py", line 181, in _process_worker result=r)) File "/private/software/packages/miniconda2/envs/peakachu/lib/python3.6/multiprocessing/queues.py", line 347, in put self._writer.send_bytes(obj) File "/private/software/packages/miniconda2/envs/peakachu/lib/python3.6/multiprocessing/connection.py", line 200, in send_bytes self._send_bytes(m[offset:offset + size]) File "/private/software/packages/miniconda2/envs/peakachu/lib/python3.6/multiprocessing/connection.py", line 393, in _send_bytes header = struct.pack("!i", n) struct.error: 'i' format requires -2147483648 <= number <= 2147483647 HYJLVBGX5_AP169_18s002168-1-1_Ibberson_lane1E2F16i12_sequenceAligned.sortedByCoord.out generated an exception: A process in the process pool was terminated abruptly while the future was running or pending. HYJLVBGX5_AP169_18s002168-1-1_Ibberson_lane1E2F17i8_sequenceAligned.sortedByCoord.out generated an exception: A process in the process pool was terminated abruptly while the future was running or pending. Traceback (most recent call last): File "/private/software/packages/miniconda2/envs/peakachu/bin/peakachu", line 161, in
sys.exit(main())
File "/private/software/packages/miniconda2/envs/peakachu/bin/peakachu", line 140, in main
args.func(controller)
File "/private/software/packages/miniconda2/envs/peakachu/bin/peakachu", line 150, in adaptive_approach
controller.adaptive_approach()
File "/private/software/packages/miniconda2/envs/peakachu/lib/python3.6/site-packages/peakachulib/controller.py", line 131, in adaptive_approach
adaptive.generate_combined_bed_file()
File "/private/software/packages/miniconda2/envs/peakachu/lib/python3.6/site-packages/peakachulib/adaptive.py", line 85, in generate_combined_bed_file
"reads"], fill_value=0)
KeyError: 'reads'