Good morning,
We have tried to run TelemereCat on set of paired-end BAM files.
telomerecat telbam2length sample.bam
The software exists with the same error message included below.
Please could you advise?
Thank you for your help!
[Error] telomerecat stopped unexpectedly, sorry!
Traceback (most recent call last):
File "parabam/core.pyx", line 61, in parabam.core.CmdLineInterface.handle
File "/Users/m026645/opt/anaconda3/lib/python3.9/site-packages/telomerecat/telbam2length.py", line 862, in run_cmd
self.run(
File "/Users/m026645/opt/anaconda3/lib/python3.9/site-packages/telomerecat/telbam2length.py", line 911, in run
vital_stats = vital_stats_finder.get_vital_stats(sample_path)
File "/Users/m026645/opt/anaconda3/lib/python3.9/site-packages/telomerecat/telbam2length.py", line 446, in get_vital_stats
vital_stats_csv = self.run_vital_rule(sample_path)
File "/Users/m026645/opt/anaconda3/lib/python3.9/site-packages/telomerecat/telbam2length.py", line 503, in run_vital_rule
out_paths = stat_interface.run(
File "parabam/command/stat.pyx", line 368, in parabam.command.stat.Stat.run
File "parabam/command/core.pyx", line 558, in parabam.command.core.Interface.run
File "parabam/core.pyx", line 610, in parabam.core.Leviathan.run
File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/context.py", line 284, in _Popen
return Popen(process_obj)
File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 32, in init
super().init(process_obj)
File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/popen_fork.py", line 19, in init
self._launch(process_obj)
File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 47, in _launch
reduction.dump(process_obj, fp)
File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/reduction.py", line 60, in dump
ForkingPickler(file, protocol).dump(obj)
AttributeError: Can't pickle local object 'VitalStatsFinder.run_vital_rule..rule'
Good morning, We have tried to run TelemereCat on set of paired-end BAM files. telomerecat telbam2length sample.bam The software exists with the same error message included below. Please could you advise? Thank you for your help!
[Error] telomerecat stopped unexpectedly, sorry! Traceback (most recent call last): File "parabam/core.pyx", line 61, in parabam.core.CmdLineInterface.handle File "/Users/m026645/opt/anaconda3/lib/python3.9/site-packages/telomerecat/telbam2length.py", line 862, in run_cmd self.run( File "/Users/m026645/opt/anaconda3/lib/python3.9/site-packages/telomerecat/telbam2length.py", line 911, in run vital_stats = vital_stats_finder.get_vital_stats(sample_path) File "/Users/m026645/opt/anaconda3/lib/python3.9/site-packages/telomerecat/telbam2length.py", line 446, in get_vital_stats vital_stats_csv = self.run_vital_rule(sample_path) File "/Users/m026645/opt/anaconda3/lib/python3.9/site-packages/telomerecat/telbam2length.py", line 503, in run_vital_rule out_paths = stat_interface.run( File "parabam/command/stat.pyx", line 368, in parabam.command.stat.Stat.run File "parabam/command/core.pyx", line 558, in parabam.command.core.Interface.run File "parabam/core.pyx", line 610, in parabam.core.Leviathan.run File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/process.py", line 121, in start self._popen = self._Popen(self) File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/context.py", line 224, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/context.py", line 284, in _Popen return Popen(process_obj) File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 32, in init super().init(process_obj) File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/popen_fork.py", line 19, in init self._launch(process_obj) File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 47, in _launch reduction.dump(process_obj, fp) File "/Users/m026645/opt/anaconda3/lib/python3.9/multiprocessing/reduction.py", line 60, in dump ForkingPickler(file, protocol).dump(obj) AttributeError: Can't pickle local object 'VitalStatsFinder.run_vital_rule..rule'