Closed jguides closed 1 year ago
When generating an nwb file on breeze, I got the following error. This is a new error from the last time I generated nwb files a few months ago. Thanks in advance for any help with this.
--------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) ~/anaconda3/envs/rec_to_nwb/lib/python3.7/site-packages/rec_to_binaries/trodes_data.py in get_trodes_version_from_path() 1498 try: -> 1499 result = str(subprocess.run(['exportmda', '-v'], capture_output=True) 1500 .stdout) ~/anaconda3/envs/rec_to_nwb/lib/python3.7/subprocess.py in run(input, capture_output, timeout, check, *popenargs, **kwargs) 487 --> 488 with Popen(*popenargs, **kwargs) as process: 489 try: ~/anaconda3/envs/rec_to_nwb/lib/python3.7/subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors, text) 799 errread, errwrite, --> 800 restore_signals, start_new_session) 801 except: ~/anaconda3/envs/rec_to_nwb/lib/python3.7/subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, start_new_session) 1550 err_msg += ': ' + repr(err_filename) -> 1551 raise child_exception_type(errno_num, err_msg, err_filename) 1552 raise child_exception_type(err_msg) FileNotFoundError: [Errno 2] No such file or directory: 'exportmda': 'exportmda' During handling of the above exception, another exception occurred: FileNotFoundError Traceback (most recent call last) /tmp/ipykernel_3703344/3730022203.py in <module> 32 output_path=output_path, 33 video_path=video_path, ---> 34 trodes_rec_export_args=trodes_rec_export_args) 35 36 content = builder.build_nwb() ~/Src/rec_to_nwb/rec_to_nwb/processing/tools/beartype/beartype.py in func_beartyped(__beartype_func, *args, **kwargs) ~/Src/rec_to_nwb/rec_to_nwb/processing/builder/raw_to_nwb_builder.py in __init__(self, data_path, animal_name, dates, nwb_metadata, output_path, video_path, preprocessing_path, extract_analog, extract_spikes, extract_lfps, extract_dio, extract_mda, overwrite, lfp_export_args, mda_export_args, analog_export_args, dio_export_args, time_export_args, spikes_export_args, parallel_instances, trodes_rec_export_args) 92 validation_registrator.validate() 93 ---> 94 trodes_version = get_trodes_version_from_path()[0] 95 96 if lfp_export_args is None: ~/anaconda3/envs/rec_to_nwb/lib/python3.7/site-packages/rec_to_binaries/trodes_data.py in get_trodes_version_from_path() 1500 .stdout) 1501 except FileNotFoundError: -> 1502 result = str(subprocess.run(['trodesexport', '-v'], capture_output=True) 1503 .stdout) 1504 version = (result ~/anaconda3/envs/rec_to_nwb/lib/python3.7/subprocess.py in run(input, capture_output, timeout, check, *popenargs, **kwargs) 486 kwargs['stderr'] = PIPE 487 --> 488 with Popen(*popenargs, **kwargs) as process: 489 try: 490 stdout, stderr = process.communicate(input, timeout=timeout) ~/anaconda3/envs/rec_to_nwb/lib/python3.7/subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors, text) 798 c2pread, c2pwrite, 799 errread, errwrite, --> 800 restore_signals, start_new_session) 801 except: 802 # Cleanup if the child failed starting. ~/anaconda3/envs/rec_to_nwb/lib/python3.7/subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, start_new_session) 1549 if errno_num == errno.ENOENT: 1550 err_msg += ': ' + repr(err_filename) -> 1551 raise child_exception_type(errno_num, err_msg, err_filename) 1552 raise child_exception_type(err_msg) 1553 FileNotFoundError: [Errno 2] No such file or directory: 'trodesexport': 'trodesexport'
When generating an nwb file on breeze, I got the following error. This is a new error from the last time I generated nwb files a few months ago. Thanks in advance for any help with this.